bluuebunny/crossref_metadata_2025 huggingface dataset:
Robot-assisted gait training in multiple sclerosis: a pilot randomized trial
Authors: Beer S. , Aschbacher B. , Manoglou D. , Gamper E. , Kool J. , Kesselring J.
Published: October 2007

Objective To evaluate feasibility and perform an explanatory analysis of the efficacy of robot-assisted gait training (RAGT) in MS patients with severe walking disabilities (Expanded Disability Status Scale [EDSS] 6.0—7.5) in a pilot trial.

Methods Prospective, randomized, controlled clinical trial comparing RAGT with conventional walking training (CWT) in a group of stable MS patients ( n = 35) during an inpatient rehabilitation stay, 15 sessions over three weeks. All patients participated additionally in a multimodal rehabilitation program. The primary outcome measure was walking velocity and secondary measures were 6-minwalking distance, stride length and knee-extensor strength. All tests were performed by an external blinded assessor at baseline after three weeks and at follow-up after six months. Additionally, Extended Barthel Index (EBI) at entry and discharge was assessed (not blinded), and acceptance/convenience of RAGT rated by patients (Visual Analogue Scale [VAS]) was recorded.

Results Nineteen patients were randomly allocated to RAGT and 16 patients to CWT. Groups were comparable at baseline. There were 5 drop-outs (2 related directly to treatment) in the RAGT group and 1 in the CWT group, leaving 14 RAGT patients and 15 CWT patients for final analysis. Acceptance and convenience of RAGT as rated by patients were high. Effect sizes were moderate to large, although not significant, for walking velocity (0.700, 95% CI -0.089 to 1.489), walking distance (0.401, 95% CI - 0.370 to 1.172) and knee-extensor strength (right: 1.105, 95% CI 0.278 to 1.932, left 0.650, 95% CI -0.135 to 1.436) favouring RAGT. Prepost within-group analysis revealed an increase of walking velocity, walking distance and knee-extensor strength in the RAGT group, whereas in CWT group only walking velocity was improved. In both groups outcome values returned to baseline at follow-up after six months ( n = 23).

Conclusions Robot-assisted gait training is feasible and may be an effective therapeutic option in MS patients with severe walking disabilities. Effect size calculation and prepost analysis suggest a higher benefit on walking velocity and knee-extensor strength by RAGT compared to CWT. Due to several limitations, however, our results should be regarded as preliminary. Post hoc power calculation showed that two groups of 106 patients are needed to demonstrate a significant moderate effect size of 0.4 after three weeks of RAGT. Thus, further studies with a larger number of patients are needed to investigate the impact of this new treatment option in MS patients. Multiple Sclerosis 2008; 14: 231—236. http://msj.sagepub.com
Autologous stem-cell transplantation in malignant multiple sclerosis: a case with a favorable long-term outcome
Authors: Kimiskidis VK , Sakellari I. , Tsimourtou V. , Kapina V. , Papagiannopoulos S. , Kazis D. , Vlaikidis N. , Anagnostopoulos A. , Fassas A.
Published: October 2007

Malignant multiple sclerosis (MS) is a rare but clinically important subtype of MS characterized by the rapid development of significant disability in the early stages of the disease process. These patients are refractory to conventional immunomodulatory agents and the mainstay of their treatment is plasmapheresis or immunosuppression with mitoxantrone, cyclophosphamide, cladribine or, lately, bone marrow transplantation. We report on the case of a 17-year old patient with malignant MS who was treated with high-dose chemotherapy plus anti-thymocyte globulin followed by autologous stem cell transplantation. This intervention resulted in an impressive and long-lasting clinical and radiological response. It is concluded that intensive immunosuppression followed by autologous stem cell transplantation is a viable therapeutic option in patients with malignant MS unresponsive to conventional forms of treatment. Multiple Sclerosis 2008; 17 : 278—283. http://msj.sagepub.com
Manometric correlations of anorectal dysfunction and biofeedback outcome in patients with multiple sclerosis
Authors: Munteis E. , Andreu M. , Martinez-Rodriguez JE , Ois A. , Bory F. , Roquer J.
Published: October 2007

Objective To evaluate clinical and manometric characteristics of multiple sclerosis (MS) patients with anorectal dysfunction (ARD) and their influence on biofeedback outcome.

Patients and methods Patients were clinically and manometrically studied and compared with controls. Patients were subsequently offered to initiate biofeedback manoeuvres to improve ARD.

Results Fifty-two patients with ARD, 39 women, mean age 44.96 ± 9.26 years, mean Expanded Disability Status Scale 4.13 ± 1.72, were evaluated. Thirty-one patients had relapsing-remitting (RR), 16 secondary progressive and five primary progressive MS. ARD complaints were constipation (67.3%), double ARD (23.1%) and isolated incontinence (9.6%). The manometric study showed significant differences in patients compared with controls in maximal contraction pressures (98.1 ± 44.2 mm Hg versus 152.05 ± 66.9 mm Hg, P < 0.001) and anal inhibitory reflex threshold (92.9 ± 63.4 mL versus 40.45 ± 11.3 mL, P < 0.001). Maximal pressure was lower in progressive forms compared with RR forms (83.1 ± 36.2 mm Hg versus 108.2 ± 46.7 mm Hg, P < 0.05) in relation to higher disability. Patients with paradoxical contraction (PC) (35 patients, 67.3%) showed more manometric disturbances. From a total of 18 patients performing biofeedback, those reporting some improvement (six complete, two partial) had milder manometric abnormalities.

Conclusions The most frequent manometric abnormalities in our MS patients with ARD were alterations of maximal pressures, anal inhibitory reflex and PC. Biofeedback could be more useful in patients with lower disability and manometric alterations. Multiple Sclerosis 2008; 14: 237—242. http://msj.sagepub.com
Evaluation of the six-minute walk in multiple sclerosis subjects and healthy controls
Authors: Goldman Myla D , Marrie Ruth Ann , Cohen Jeffrey A
Published: October 2007

Objective To assess the characteristics of the 6-min walk (6MW) in multiple sclerosis (MS) subjects of varied disability, and controls. To assess the correlation of 6MW to subjective measures of fatigue, health status and ambulation using the modified fatigue impact scale (MFIS), short form-36 Health Questionnaire physical component score and MS walking scale (MSWS).

Methods Forty MS expanded disability status scale [(EDSS) 0—6.5] and 20 control subjects were recruited from a MS outpatient clinic. Subjects completed survey material and three 6MWs with 1-h interval rest in a single study visit.

Results There was no practice effect or fatigability with repeat 6MW tests with a one-h rest period between test sessions. The 6MW had excellent intra-[intraclass correlation coefficient (ICC) = 0.95] and inter-rater (ICC = 0.91) reliability. MS subjects demonstrated reduced 6MW distance and speed compared with controls ( P < 0.0001). Within the MS population 6MW distance was significantly reduced with increasing disability ( P = 0.05). Compared with the EDSS, the 6MW had a stronger correlation to subjective measures of ambulation and physical fatigue: MSWS ( r = -0.81 versus 0.69) and MFISphy (0.66 versus 0.63).

Conclusions The 6MW is a feasible, reproducible, and reliable measure in MS. MS subjects demonstrate motor fatigue in both 6MW distance and speed compared with controls. In MS subjects there is an inverse relationship between motor fatigue and disability. 6MW has a strong correlation to subjective measures of ambulation and physical fatigue. Multiple Sclerosis 2008; 14: 383—390. http://msj.sagepub.com
Children with autism's response to novel stimuli while participating in interventions targeting joint attention or symbolic play skills
Authors: Gulsrud Amanda C. , Kasari Connie , Freeman Stephanny , Paparella Tanya
Published: October 2007

Thirty-five children diagnosed with autism were randomly assigned to either a joint attention or a symbolic play intervention. During the 5—8 week treatment, three novel probes were administered to determine mastery of joint attention skills. The probes consisted of auditory and visual stimuli, such as a loud spider crawling or a musical ball bouncing. The current study examined affect, gaze, joint attention behaviors, and verbalizations at three different time points of intervention. Results revealed that children randomized to the joint attention group were more likely to acknowledge the probe and engage in shared interactions between intervener and probe upon termination of intervention. Additionally, the joint attention group improved in the proportion of time spent sharing coordinated joint looks between intervener and probe. These results suggest that generalization of joint attention skills to a novel probe did occur for the group targeting joint attention and provides further evidence of the effectiveness of the joint attention intervention.
Diagnostic trends in autistic spectrum disorders in the South Wales valleys
Authors: Latif A.H.A. , Williams W.R.
Published: October 2007

This study provides an analysis of the diagnostic trends in autistic spectrum disorder (ASD) for children aged under 17 years in the Rhondda and Taff Ely districts of South Wales. In the period 1988—2004, 336 children received a diagnosis of ASD and represent the case registry data of one community paediatric team. For the period 1994—2003, the caseload of 267 comprised Asperger (58%), Kanner (20%) and `other forms' of autism (22%). In comparison to the previous 5 year period, diagnosis of ASD in 1999—2003 increased for Asperger (2.9 fold) and `other forms' (4.4) but decreased for Kanner autism (0.69). Male:female gender ratios and age at diagnosis fell for all subcategories of ASD. Prevalences per 10,000 children born in Rhondda Taff Ely are ASD 61.2, Asperger 35.4, Kanner autism 12.7, and `other forms' 13.0. Detected prevalences and trends for ASD are in line with national standards and do not show an increase for Kanner autism.
Temporal context memory in high-functioning autism
Authors: Gras-Vincendon Agnès , Mottron Laurent , Salame Pierre , Bursztejn Claude , Danion Jean-Marie
Published: October 2007

Episodic memory, i.e. memory for specific episodes situated in space and time, seems impaired in individuals with autism. According to weak central coherence theory, individuals with autism have general difficulty connecting contextual and item information which then impairs their capacity to memorize information in context. This study investigated temporal context memory for visual information in individuals with autism. Eighteen adolescents and adults with high-functioning autism (HFA) or Asperger syndrome (AS) and age- and IQmatched typically developing participants were tested using a recency judgement task. The performance of the autistic group did not differ from that of the control group, nor did the performance between the AS and HFA groups. We conclude that autism in high-functioning individuals does not impair temporal context memory as assessed on this task. We suggest that individuals with autism are as efficient on this task as typically developing subjects because contextual memory performance here involves more automatic than organizational processing.
Locus of control fails to mediate between stress and anxiety and depression in parents of children with a developmental disorder
Authors: Hamlyn-Wright Sarah , Draghi-Lorenz Riccardo , Ellis Jason
Published: October 2007

Stress, anxiety and depression are raised amongst parents of children with a developmental disorder. However, the processes by which stress leads to depression and anxiety are poorly understood. In a cross-sectional survey, levels of parental stress, depression and anxiety were compared between parents of children with an autistic disorder, children with Down's syndrome and children with no disorder ( N = 619) and the mediational role of locus of control was examined. Anxiety and depression were higher in parents of children with a disorder, and highest in parents of children with autism. Locus of control was more external in parents of children with autism. Locus of control failed to mediate the relationship between stress and both anxiety and depression in parents of children with a disorder. This suggests that help for parents of a child with a disorder may be effective if focused on the sources of stress rather than perceived control over events.
Mathematical ability of students with Asperger syndrome and high-functioning autism
Authors: Chiang Hsu-Min , Lin Yueh-Hsien
Published: October 2007

This article reviews studies investigating cognitive ability and academic achievement of students with Asperger syndrome (AS) and high-functioning autism (HFA). Particular emphasis is placed on the mathematical ability of people with AS/HFA. A preliminary analysis of empirical data is presented. Findings indicate that: (1) the majority of individuals with AS/HFA have average mathematical ability; (2) the majority of individuals with AS/HFA have a significant but clinically modest math weakness; (3) some individuals with AS/HFA have mathematical giftedness.
Comparative minicolumnar morphometry of three distinguished scientists
Authors: Casanova Manuel F. , Switala Andrew E. , Trippe Juan , Fitzgerald Michael
Published: October 2007

It has been suggested that the cell minicolumn is the smallest module capable of information processing within the brain. In this case series, photomicrographs of six regions of interests (Brodmann areas 4, 9, 17, 21, 22, and 40) were analyzed by computerized image analysis for minicolumnar morphometry in the brains of three distinguished scientists and six normative controls. Overall, there were significant differences ( p < 0.001) between the comparison groups in both minicolumnar width (CW) and mean cell spacing (MCS). Although our scientists did not exhibit deficits in communication or interpersonal skills, the resultant minicolumnar phenotype bears similarity to that described for both autism and Asperger's syndrome. Computer modeling has shown that smaller columns account for discrimination among signals during information processing. A minicolumnar phenotype that provides for discrimination and/or focused attention may help explain the savant abilities observed in some autistic people and the intellectually gifted.
On the defensive
Authors: Gadd David , Jefferson Tony
Published: October 2007

The copyright for this article is assigned to David Gadd and Tony Jefferson. ©2007 D. Gadd and T. Jefferson.

Who was `Stanley'? What can this single case contribute to criminological theory? These questions remain inadequately answered despite two books and numerous articles devoted to The Jack-Roller. This article shows that scholars have been too willing to accept Stanley's account as `told', over-eager to read him as a `social type' and too slow to interrogate critically the relationship between Stanley's psychological defensiveness and his socio-cultural background. Reconsidering Stanley's account of himself from a psychoanalytically informed psychosocial perspective, this article sheds new light on Stanley's family relationships, jack-rolling and somewhat precarious desistance from crime. The central argument of this article is that it is only through exploring what Stanley said through the prism of his unconscious defences against anxiety that both the particularities and typicality of his life can be properly grasped and the case's wider theoretical significance fully realized.
The Jack-Roller
Authors: Gelsthorpe Loraine
Published: October 2007

Clifford Shaw pursued his interest in the development of the delinquent pattern in the individual boy and its links with the geography of the city and community disorganization by making the `life history' a key element of the work of the Institute for Juvenile Research. The Jack-Roller is based on `Stanley'. But can we be really sure where Shaw's own story ends and Stanley's begins? I explore the origins of `Stanley's' story in Shaw's own life and suggest that Shaw perhaps misses out the influence of his own biography in his analysis. The broader aim is to suggest that personal reflexivity on the part of the researcher (or what elsewhere is described as a psychosocial approach) is critical to an understanding of research.
The changing face of meningococcal disease in Birmingham, 1999 to 2002
Authors: Robertson W. , Wood A. , May H.
Published: October 2007

In the UK, a vaccination schedule against meningococcal group C infection (Men C) was introduced in Autumn 1999. Also, vaccination against groups A, C, W135 and Y (ACWY Vax) was recommended from February 2001 for pilgrims to Hajj or Umrah, it becoming a visa requirement from May 2001. To assess the impact of these vaccination schedules, the notification for meningococcal infection for Birmingham residents (1.1 million) from 1999 to 2002 was reviewed.

Notifications received for meningococcal infection in Birmingham declined from 103 in 1999 to 58 in 2002. Additionally, the number of laboratory confirmed cases decreased from 52 in 1999 to 28 in 2002. Group C infection declined from 14 cases in 1999 to one case in 2002, attributed to the success of the `Meningitis C Vaccination' campaign. W135 infection showed a peak in Birmingham in 2000 and 2001, and a decline in 2002 once the ACWY became a visa requirement. The vaccination schedules have successfully reduced the incidence of meningococcal disease in Birmingham.
Delivering an infection control link nurse programme: implementation and evaluation of a flexible teaching approach
Authors: Cooper T.
Published: October 2007

Infection control nurses work to ensure practice is evidence-based, thereby minimising infection risks. There is, however, a gap between theory and practice in infection control at clinical level. Link nurse groups have been used in an attempt to ensure practice is evidence-based.

This article describes a research study that examined the efficacy of an infection control link nurse programme, which had an educational programme based upon adult learning theory, delivered using an action-research approach. Results of the study are described in subsequent articles.
Improving weldability of aged 25Cr–35Ni heat resistant steel/alloy 800 dissimilar welds
Authors: Dehmolaei R. , Shamanian M. , Kermanpur A.
Published: October 2007

Dissimilar welding between the aged 25Cr–35Ni (wt-%) heat resistant steel and alloy 800 is not successful due to liquation cracking in the heat affected zone of the aged steel. Microstructures, mechanical properties and weldability of the dissimilar weld were characterised using SEM and Varestraint test. The effects of a preweld solution annealing, heat input, interpass temperature and type of filler metal were investigated. It was found that the most important step to improve weldability and to reduce cracking susceptibility was solution annealing. A suitable annealing treatment was then proposed. It was concluded that dissimilar welding of alloy 800 to the aged 25Cr–35Ni steel can be successfully carried out under the conditions of solution annealing, low heat input and low interpass temperature using Inconel 82 or 617 filler metals.
Multiple signaling pathways promote B lymphocyte stimulator–dependent B-cell growth and survival
Authors: Woodland Robert T. , Fox Casey J. , Schmidt Madelyn R. , Hammerman Peter S. , Opferman Joseph T. , Korsmeyer Stanley J. , Hilbert David M. , Thompson Craig B.
Published: October 2007

We investigated the mechanism by which B lymphocyte stimulator (BLyS)/BAFF, a tumor necrosis factor superfamily ligand, promotes B-cell survival and resistance to atrophy. BLyS stimulation activates 2 independent signaling pathways, Akt/mTOR and Pim 2, associated with cell growth and survival. BLyS blocks the cell volume loss (atrophy) that freshly isolated B cells normally undergo when maintained in vitro while concurrently increasing glycolytic activity and overall metabolism. This atrophy resistance requires Akt/mTOR. We used a genetic approach to resolve the contributions of Akt/mTOR and Pim kinase pathways to BLyS-mediated survival. Pim 2–deficient B cells are readily protected from death by BLyS stimulation, but this protection is completely abrogated by treatment with the mTOR inhibitor rapamycin. Furthermore, rapamycin treatment in vivo significantly reduces both follicular and marginal zone B cells in Pim-deficient but not healthy hosts. BLyS-dependent survival requires the antiapoptotic protein Mcl-1. Mcl-1 protein levels rise and fall in response to BLyS addition and withdrawal, respectively, and conditional deletion of the Mcl-1 gene renders B cells refractory to BLyS-mediated protection. Because BlyS is required for the normal homeostasis of all B cells, these data suggest a therapeutic strategy simultaneously inhibiting mTOR and Pim 2 could target pathogenic B cells.
Retinoic acid inhibits Th17 polarization and enhances FoxP3 expression through a Stat-3/Stat-5 independent signaling pathway
Authors: Elias Kevin M. , Laurence Arian , Davidson Todd S. , Stephens Geoffrey , Kanno Yuka , Shevach Ethan M. , O'Shea John J.
Published: October 2007

CD4+ helper T (Th) cells play a crucial role in the delicate balance between host defense and autoimmune disease. Two important populations of helper T cells are the proinflammatory, interleukin-17 (IL-17)–producing (Th17) cells and the anti-inflammatory forkhead box P3–positive (FoxP3+) T regulatory (Treg) cells. Here we show that all-trans retinoic acid (ATRA) and other agonists of the retinoic acid receptor alpha (RARα) inhibit the formation of Th17 cells and promote FoxP3 expression. Conversely, inhibition of retinoic acid signaling constrains transforming growth factor beta (TGF-β1) induction of FoxP3. The effect of ATRA is mediated independently of IL-2, signal transducer and activator of transcription 5 (Stat5) and Stat3, representing a novel mechanism for the induction of FoxP3 in CD4 T cells. As previous studies have shown that vitamin A derivatives are protective in animal models of autoimmune disease, the current data suggest a previously unrecognized role for RARα in the regulation of CD4+ T-cell differentiation and provide a mechanism for the anti-inflammatory effects of retinoic acid.
Characterization of the deoxyhemoglobin binding site on human erythrocyte band 3: implications for O2 regulation of erythrocyte properties
Authors: Chu Haiyan , Breite Andrew , Ciraolo Peter , Franco Robert S. , Low Philip S.
Published: October 2007

Band 3, the major protein of the human erythrocyte membrane, associates with multiple metabolic, ion transport, and structural proteins. Functional studies demonstrate that the oxygenation state of the erythrocyte regulates cellular properties performed by these and/or related proteins. Because deoxyhemoglobin, but not oxyhemoglobin, binds band 3 reversibly with high affinity, these observations raise the hypothesis that hemoglobin might regulate erythrocyte properties through its reversible, oxygenation-dependent association with band 3. To explore this hypothesis, we have characterized the binding site of deoxyHb on human erythrocyte band 3. We report that (1) deoxyHb binds to residues 12-23 of band 3; (2) mutation of residues on either side of this sequence greatly enhances affinity of deoxyHb for band 3, suggesting that evolution of a higher affinity interaction would have been possible had it been beneficial for survival; (3) Hb does not bind to 2 other sequences in band 3 despite their high sequence homology to residues 12-23, and (4) the Hb binding site on band 3 lies proximal to binding sites for glycolytic enzymes, band 4.1 and ankyrin, suggesting possible mechanisms through which multifarious erythrocyte properties might be regulated by the oxygenation state of the cell.
Clonal expansion of immunoglobulin M+CD27+ B cells in HCV-associated mixed cryoglobulinemia
Authors: Charles Edgar D. , Green Rashidah M. , Marukian Svetlana , Talal Andrew H. , Lake-Bakaar Gerond V. , Jacobson Ira M. , Rice Charles M. , Dustin Lynn B.
Published: October 2007

Hepatitis C virus (HCV) is associated with B-cell lymphoproliferative disorders such as mixed cryoglobulinemia (MC) and B-cell non-Hodgkin lymphoma (B-NHL). The pathogenesis of these disorders remains unclear, and it has been proposed that HCV drives the pro-liferation of B cells. Here we demonstrate that certain HCV+MC+ subjects have clonal expansions of immunoglobulin M (IgM)+κ+IgDlow/−CD21lowCD27+ B cells. Using RT-PCR to amplify Ig from these singly sorted cells, we show that these predominantly rheumatoid factor-encoding VH1-69/JH4 and Vκ3-20 gene segment-restricted cells have low to moderate levels of somatic hypermutations. Ig sequence analysis suggests that antigen selection drives the generation of mutated clones. These findings lend further support to the notion that specific antigenic stimulation leads to B-cell proliferation in HCV MC and that chronic B-cell stimulation may set the stage for malignant transformation and the development of B-NHL. The finding that these hypermutated, marginal zone-like IgM+CD27+ B cells are clonally expanded in certain subjects with MC offers insight into mechanisms of HCV-associated MC and B-cell malignancy. This study was registered at www.clinicaltrials.gov as NCT00219999.
Immunoglobulin free light chain ratio is an independent risk factor for progression of smoldering (asymptomatic) multiple myeloma
Authors: Dispenzieri Angela , Kyle Robert A. , Katzmann Jerry A. , Therneau Terry M. , Larson Dirk , Benson Joanne , Clark Raynell J. , Melton L. Joseph , Gertz Morie A. , Kumar Shaji K. , Fonseca Rafael , Jelinek Diane F. , Rajkumar S. Vincent
Published: October 2007

We hypothesized that increased monoclonal free kappa or lambda immunoglobulin light chains in smoldering multiple myeloma (SMM), as detected by the serum free light chain (FLC) assay, indicates an increased risk of progression to active myeloma. Baseline serum samples obtained within 30 days of diagnosis were available in 273 patients with SMM seen from 1970 to 1995. At a median follow-up of surviving patients of 12.4 years, transformation to active disease has occurred in 59%. The best breakpoint for predicting risk of progression was an FLC ratio of 0.125 or less, or 8 or more (hazard ratio, 2.3; 95% CI, 1.6-3.2). The extent of abnormality of FLC ratio was independent of SMM risk categories defined by number of bone marrow plasma cells (BMPCs) and size of serum M proteins (BMPC ≥ 10% and serum M protein ≥ 3 g/dL; BMPC ≥ 10% but serum M protein < 3 g/dL; and serum M protein≥ 3 g/dL but BMPC < 10%). Incorporating the FLC ratio into the risk model, the 5-year progression rates in high-, intermediate-, and low-risk groups were 76%, 51%, and 25%, respectively. The serum immunoglobulin FLC ratio is an important additional determinant of clinical outcome in patients with SMM.
fREDUCE: Detection of degenerate regulatory elements using correlation with expression
Authors: Wu Randy Z , Chaivorapol Christina , Zheng Jiashun , Li Hao , Liang Shoudan
Published: October 2007

Background

The precision of transcriptional regulation is made possible by the specificity of physical interactions between transcription factors and their cognate binding sites on DNA. A major challenge is to decipher transcription factor binding sites from sequence and functional genomic data using computational means. While current methods can detect strong binding sites, they are less sensitive to degenerate motifs.

Results

We present fREDUCE, a computational method specialized for the detection of weak or degenerate binding motifs from gene expression or ChIP-chip data. fREDUCE is built upon the widely applied program REDUCE, which elicits motifs by global statistical correlation of motif counts with expression data. fREDUCE introduces several algorithmic refinements that allow efficient exhaustive searches of oligonucleotides with a specified number of degenerate IUPAC symbols. On yeast ChIP-chip benchmarks, fREDUCE correctly identified motifs and their degeneracies with accuracies greater than its predecessor REDUCE as well as other known motif-finding programs. We have also used fREDUCE to make novel motif predictions for transcription factors with poorly characterized binding sites.

Conclusion

We demonstrate that fREDUCE is a valuable tool for the prediction of degenerate transcription factor binding sites, especially from array datasets with weak signals that may elude other motif detection methods.
Localized rbp4expression in the yolk syncytial layer plays a role in yolk cell extension and early liver development
Authors: Li Zhen , Korzh Vladimir , Gong Zhiyuan
Published: October 2007

Background

The number of genes characterized in liver development is steadily increasing, but the origin of liver precursor cells and the molecular control of liver formation remain poorly understood. Existing theories about formation of zebrafish visceral organs emphasize either their budding from the endodermal rod or formation of independent anlage followed by their later fusion, but none of these is completely satisfactory in explaining liver organogenesis in zebrafish.

Results

Expression of a gene encoding the retinol binding protein 4 (Rbp4) was analyzed in zebrafish. rbp4, which is expressed mainly in the liver in adults, was shown to be expressed in the yolk syncytial layer (YSL) during early embryogenesis. At 12–16 hpf rbp4 expression was restricted to the ventro-lateral YSL and later expanded to cover the posterior YSL. We demonstrated that rbp4 expression was negatively regulated by Nodal and Hedgehog (Hh) signalling and positively controlled by retinoic acid (RA). Knockdown of Rbp4 in the YSL resulted in shortened yolk extension as well as the formation of two liver buds, which could be due to impaired migration of liver progenitor cells. rbp4 appears also to regulate the extracellular matrix protein Fibronectin1 (Fn1) specifically in the ventro-lateral yolk, indicating a role of Fn1 in liver progenitor migration. Since exocrine pancreas, endocrine pancreas, intestine and heart developed normally in Rbp4 morphants, we suggest that rbp4 expression in the YSL is required only for liver development.

Conclusion

The characteristic expression pattern of rbp4 suggests that the YSL is patterned despite its syncytial nature. YSL-expressed Rbp4 plays a role in formation of both yolk extension and liver bud, the latter may also require migration of liver progenitor cells.
Characterization of Campylobacter phages including analysis of host range by selected Campylobacter Penner serotypes
Authors: Hansen Vinni Mona , Rosenquist Hanne , Baggesen Dorte Lau , Brown Stanley , Christensen Bjarke Bak
Published: October 2007

Background

The predominant food borne pathogen in the western world today is Campylobacter. Campylobacter specific bacteriophages (phages) have been proposed as an alternative agent for reducing the burden of Campylobacter in broilers. One concern in relation to phage biocontrol is the narrow host range often displayed by phages. To identify the potential of phages as a Campylobacter reducing agent we needed to determine their infectivity on a panel of isolates representing the Campylobacter strains found in broilers as well as humans.

Results

In this study, Campylobacter phages were isolated from the intestines of broilers and ducks and from abattoir sewage. Twelve phages were investigated to determine their ability to infect the Campylobacter Penner serotypes commonly present in Danish poultry and patients with campylobacteriosis. A total of 89% of the Campylobacter jejuni strains and 14% of the Campylobacter coli strains could be infected by at least one of the bacteriophages. The majority of the phages infected the most common serotypes in Danish broilers (O:1,44; O:2; O:4-complex), but showed limited ability to infect 21 of the less frequent Campylobacter serotypes. Pulse field gel electrophoresis (PFGE) and restriction endonuclease analysis (REA) were used to characterize the phage genomes. Three categories of bacteriophages were observed. I: a genome size of ~194 kb and refractory to digestion with HhaI; II: a genome size of ~140 kb and digestible by HhaI; and III: a genome size undeterminable in PFGE. The categorization of the phages correlated with the host range patterns displayed by the phages. Six phages were subjected to transmission electron microscopy (TEM). They all belonged to the family of Myoviridae.

Conclusion

We have characterized and identified the host range of 12 Danish Campylobacter phages. Due to their ability to infect the majority of the common serotypes in Denmark we suggest the phages can become an effective agent in the effort to reduce the incidence of campylobacteriosis in Denmark. This study provides the basis for future experiments in Campylobacter phages and knowledge for the selection of Campylobacter phages for biocontrol in broilers.
IS1111 insertion sequences of Coxiella burnetii: characterization and use for repetitive element PCR-based differentiation of Coxiella burnetii isolates
Authors: Denison Amy M , Thompson Herbert A , Massung Robert F
Published: October 2007

Background

Coxiella burnetiicontains the IS1111transposase which is present 20 times in the Nine Mile phase I (9Mi/I) genome. A single PCR primer that binds to each IS element, and primers specific to a region ~500-bp upstream of each of the 20 IS1111elements were designed. The amplified products were characterized and used to develop a repetitive element PCR genotyping method.

Results

Isolates Nine Mile phase II, Nine Mile RSA 514, Nine Mile Baca, Scottish, Ohio, Australian QD, Henzerling phase I, Henzerling phase II, M44, KAV, PAV, Q238, Q195 and WAV were tested by PCR and compared to 9Mi/I. Sequencing was used to determine the exact differences in isolates which lacked specific IS elements or produced PCR products of differing size. From this data, an algorithm was created utilizing four primer pairs that allows for differentiation of unknown isolates into five genomic groups. Additional isolates (Priscilla Q177, Idaho Q, Qiyi, Poker Cat, Q229 and Q172) and nine veterinary samples were characterized using the algorithm which resulted in their placement into three distinct genomic groups.

Conclusion

Through this study significant differences, including missing elements and sequence alterations within and near IS element coding regions, were found between the isolates tested. Further, a method for differentiation ofC. burnetiiisolates into one of five genomic groups was created. This algorithm may ultimately help to determine the relatedness between known and unknown isolates ofC. burnetii.
A non-circadian role for clock-genes in sleep homeostasis:a strain comparison
Authors: Franken Paul , Thomason Ryan , Heller H Craig , O'Hara Bruce F
Published: October 2007

Background

We have previously reported that the expression of circadian clock-genes increases in the cerebral cortex after sleep deprivation (SD) and that the sleep rebound following SD is attenuated in mice deficient for one or more clock-genes. We hypothesized that besides generating circadian rhythms, clock-genes also play a role in the homeostatic regulation of sleep. Here we follow the time course of the forebrain changes in the expression of the clock-genesperiod(per)-1, per2, and of the clock-controlled genealbumin D-binding protein(dbp) during a 6 h SD and subsequent recovery sleep in three inbred strains of mice for which the homeostatic sleep rebound following SD differs. We reasoned that if clock genes are functionally implicated in sleep homeostasis then the SD-induced changes in gene expression should vary according to the genotypic differences in the sleep rebound.

Results

In all three strainsperexpression was increased when animals were kept awake but the rate of increase during the SD as well as the relative increase inperafter 6 h SD were highest in the strain for which the sleep rebound was smallest; i.e., DBA/2J (D2). Moreover, whereas in the other two strainsper1andper2reverted to control levels with recovery sleep,per2expression specifically, remained elevated in D2 mice.dbpexpression increased during the light period both during baseline and during SD although levels were reduced during the latter condition compared to baseline. In contrast toper2,dbpexpression reverted to control levels with recovery sleep in D2 only, whereas in the two other strains expression remained decreased.

Conclusion

These findings support and extend our previous findings that clock genes in the forebrain are implicated in the homeostatic regulation of sleep and suggest that sustained, high levels ofper2expression may negatively impact recovery sleep.
Changes in the distribution pattern of Claudin tight junction proteins during the progression of mouse skin tumorigenesis
Authors: Arabzadeh Azadeh , Troy Tammy-Claire , Turksen Kursad
Published: October 2007

Background

Despite the fact that morphological and physiological observations suggest that the tight junction (TJ)-based permeability barrier is modified/disrupted in tumorigenesis, the role of members of the Claudin (Cldn) family of TJ proteins is not well-understood. Using a well-established two-stage chemical carcinogenesis model, we investigated the temporal and spatial changes in expression of those Cldns that we have previously demonstrated to be important in epidermal differentiation and the formation of the epidermal permeability barrier, i.e., Cldn1, Cldn6, Cldn11, Cldn12 and Cldn18.

Methods

The lower dorsal backskin of mice was treated topically with 7,12-dimethylbenz(a)anthracene (DMBA; 0.25 mg/ml in acetone) and following a 10-day incubation period, 12-O-tetradecanoyl-phorbol-13-acetate (TPA; 25 μg/ml in acetone) was applied three times a week to the same area. Backskin samples were dissected 2, 4, 6, 8 and 12 weeks after the initiation of the experimental protocol and immunohistochemistry was performed on sections using antibodies against the following: Cldn1, Cldn6, Cldn11, Cldn12, Cldn18, Ki67 and CD3.

Results

Our data indicate that along with the changes in epidermal cell morphology and differentiation that occur during tumor formation, there is a dramatic change in Cldn distribution consistent with cell polarity and barrier selectivity changes. Specifically, in the early stages of DMBA/TPA treatment, the suprabasal-specific Cldns occupy an expanded zone of expression corresponding to an increased number of suprabasal epidermal cell layers. As tumorigenesis progressed, the number of suprabasal epidermal layers positive for Cldn6, Cldn11, Cldn12 and Cldn18 was reduced, especially in the lower strata of the expanded suprabasal zone. In addition, a variably reduced cell membrane association of those differentiation-specific Cldns was observed, especially within the infiltrating epidermal structures. In contrast, Cldn1 (which is normally expressed in all the living layers of the epidermis) remained restricted to the cell membrane throughout the tumorigenesis protocol. However commencing 2 weeks after treatment there was a marked decrease in the number of Cldn1-positive basal cells, and the zone of Cldn1-null epidermal cells was expanded up into the lower stratified epidermis throughout the progression of DMBA/TPA treatment. In addition, there was no Cldn1 localization in the infiltrating epidermal structures of the tumorigenic epidermis.

Conclusion

This is the first demonstration of the changes in Cldn expression in the progression of DMBA/TPA-induced skin tumors; however further investigation into the molecular mechanisms regulating the observed changes in barrier selectivity during tumorigenesis is required.
In situdetection of non-polyadenylated RNA molecules using Turtle Probes and target primed rolling circle PRINS
Authors: Stougaard Magnus , Lohmann Jakob S , Zajac Magdalena , Hamilton-Dutoit Stephen , Koch Jørn
Published: October 2007

Background

In situ detection is traditionally performed with long labeled probes often followed by a signal amplification step to enhance the labeling. Whilst short probes have several advantages over long probes (e.g. higher resolution and specificity) they carry fewer labels per molecule and therefore require higher amplification for detection. Furthermore, short probes relying only on hybridization for specificity can result in non-specific signals appearing anywhere the probe attaches to the target specimen. One way to obtain high amplification whilst minimizing the risk of false positivity is to use small circular probes (e.g. Padlock Probes) in combination with target primed rolling circle DNA synthesis. This has previously been used for DNA detection in situ, but not until now for RNA targets.

Results

We present here a proof of principle investigation of a novel rolling circle technology for the detection of non-polyadenylated RNA molecules in situ, including a new probe format (the Turtle Probe) and optimized procedures for its use on formalin fixed paraffin embedded tissue sections and in solid support format applications.

Conclusion

The method presented combines the high discriminatory power of short oligonucleotide probes with the impressive amplification power and selectivity of the rolling circle reaction, providing excellent signal to noise ratios in combination with exact target localization due to the target primed reaction. Furthermore, the procedure is easily multiplexed, allowing visualization of several different RNAs.
Tumor-infiltrating B lymphocytes as an efficient source of highly specific immunoglobulins recognizing tumor cells
Authors: Pavoni Emiliano , Monteriù Giorgia , Santapaola Daniela , Petronzelli Fiorella , Anastasi Anna Maria , Pelliccia Angela , D'Alessio Valeria , De Santis Rita , Minenkova Olga
Published: October 2007

Background

There is much evidence that tumor cells elicit a humoral immune response in patients. In most cases, the presence of antibodies in peripheral blood is detected only in small proportion of patients with tumors overexpressing the corresponding antigen. In the present study, we analyzed the significance of local humoral response provided by tumor-infiltrating lymphocytes in breast cancer patients.

Methods

The ability of a patient's immune system to produce specific antibodies inside tumor tissue, capable of recognizing tumor cells, was explored through analysis of the oligoclonality of antibodies derived from tumor-infiltrating lymphocytes and construction of a series of recombinant antibody libraries in scFv format, derived from breast tumor-infiltrating B lymphocytes. These libraries and one from peripheral blood lymphocytes of a single breast cancer patient were panned against three purified surface tumor antigens, such as CEA, MUC1 and ED-B domain, and against intact MCF7 breast carcinoma cells.

Results

Application of novel display vector, pKM19, allowed isolation of a large panel of breast cancer-specific antibodies against known tumor antigens, as well as against breast carcinoma cells. Reactivity of novel scFvs was confirmed by ELISA, immunohistochemistry, fluorescence staining and flow cytometry. We demonstrated that seven of ten primary breast tumor specimens, obtained using discarded surgical material, could be exploited as an appropriate source for generation of phage display libraries, giving highly specific antitumor antibodies which recognize heterologous tumor cells.

Conclusion

Local humoral immune response within tumor tissue in breast cancer patients frequently has an oligoclonal character. Efficient selection of specific antitumor antibodies from recombinant antibody libraries, derived from such oligoclonal tumor-infiltrated B lymphocytes, indicates the presence of natural immune response against tumor antigens in these patients. The described method is very promising for development of antitumor antibodies, potentially useful for diagnostic and therapeutic approaches.
Enhancement of cell proliferation in various mammalian cell lines by gene insertion of a cyclin-dependent kinase homolog
Authors: Jaluria Pratik , Betenbaugh Michael , Konstantopoulos Konstantinos , Shiloach Joseph
Published: October 2007

Background

Genomics tools, particularly DNA microarrays, have found application in a number of areas including gene discovery and disease characterization. Despite the vast utility of these tools, little work has been done to explore the basis of distinct cellular properties, especially those important to biotechnology such as growth. And so, with the intent of engineering cell lines by manipulating the expression of these genes, anchorage-independent and anchorage-dependent HeLa cells, displaying markedly different growth characteristics, were analyzed using DNA microarrays.

Results

Two genes, cyclin-dependent kinase like 3 (cdkl3) and cytochrome c oxidase subunit (cox15), were up-regulated in the faster growing, anchorage-independent (suspension) HeLa cells relative to the slower growing, anchorage-dependent (attached) HeLa cells. Enhanced expression of either gene in the attached HeLa cells resulted in elevated cell proliferation, though insertion ofcdkl3had a greater impact than that ofcox15. Moreover, flow cytometric analysis indicated that cells with an insert ofcdkl3were able to transition from the G0/G1 phases to the S phase faster than control cells. In turn, expression ofcox15was seen to increase the maximum viable cell numbers achieved relative to the control, and to a greater extent thancdkl3. Quantitatively similar results were obtained with two Human Embryonic Kidney-293 (HEK-293) cell lines and a Chinese Hamster Ovary (CHO) cell line. Additionally, HEK-293 cells secreting adipocyte complement-related protein of 30 kDa (acrp30) exhibited a slight increase in specific protein production and higher total protein production in response to the insertion of eithercdkl3orcox15.

Conclusion

These results are consistent with previous studies on the functionalities ofcdkl3andcox15. For instance, the effect ofcdkl3on cell growth is consistent with its homology to thecdk3gene which is involved in G1 to S phase transition. Likewise, the increase in cell viability due tocox15expression is consistent with its role in oxidative phosphorylation as an assembly factor for cytochrome c oxidase and its involvement removing apoptosis-inducing oxygen radicals. Collectively, the present study illustrates the potential of using microarray technology to identify genes influential to specific cellular processes with the possibility of engineering cell lines as desired to meet production needs.
Influence of an e-mail with a drug information attachment on sales of prescribed drugs: a randomized controlled study
Authors: Edward Christina , Himmelmann Anders , Wallerstedt Susanna M
Published: October 2007

Background

To provide doctors with producer-independent information to facilitate choice of treatment is an important task. The objective of the present study was to evaluate if an e-mail with a drug information attachment has effects on sales of prescribed drugs and if the design of the attachment is of importance.

Methods

The Swedish pharmaceutical benefit board found rizatriptan (Maxalt®) 10 mg to be the most cost-effective triptan. All 119 heads of primary care units in western Sweden were randomized to receive information concerning this conclusion via (i) e-mail with attachment I, (ii) e-mail with attachment II or (iii) no information (control). Attachment I was a short one (heading plus three lines text), whereas attachment II was a long one (heading plus one page text and one page with tables). The change in percentage rizatriptan of total triptans sold before and after the intervention (May – July 2004 and May – July 2005, respectively) was compared between the groups.

Results

Totally 48,229 (2004) and 50,674 (2005) defined daily doses of triptans were prescribed and sold during May – July in primary care units in the western part of Sweden. The absolute change in percentage rizatriptan was greater in the intervention groups compared with the control group 2 (25th– 75thpercentile: -3 – 7) vs 0 (-7 - 5), P = 0.031). The absolute change in percentage rizatriptan did not differ between the two attachment groups (P = 0.93).

Conclusion

An e-mail with a drug information attachment may influence sales of prescribed drugs. No difference between different designs of the attachment could be detected.