bluuebunny/crossref_metadata_2025_split huggingface dataset:
Pandora, a PAthway and Network DiscOveRy Approach based on common biological evidence
Authors: Zhang Kelvin Xi , Ouellette B. F. Francis 
Published: December 2009

Abstract
Motivation: Many biological phenomena involve extensive interactions between many of the biological pathways present in cells. However, extraction of all the inherent biological pathways remains a major challenge in systems biology. With the advent of high-throughput functional genomic techniques, it is now possible to infer biological pathways and pathway organization in a systematic way by integrating disparate biological information.
Results: Here, we propose a novel integrated approach that uses network topology to predict biological pathways. We integrated four types of biological evidence (protein–protein interaction, genetic interaction, domain–domain interaction and semantic similarity of Gene Ontology terms) to generate a functionally associated network. This network was then used to develop a new pathway finding algorithm to predict biological pathways in yeast. Our approach discovered 195 biological pathways and 31 functionally redundant pathway pairs in yeast. By comparing our identified pathways to three public pathway databases (KEGG, BioCyc and Reactome), we observed that our approach achieves a maximum positive predictive value of 12.8% and improves on other predictive approaches. This study allows us to reconstruct biological pathways and delineates cellular machinery in a systematic view.
Availability: The method has been implemented in Perl and is available for downloading from http://www.oicr.on.ca/research/ouellette/pandora. It is distributed under the terms of GPL (http://opensource.org/licenses/gpl-2.0.php)
Contact: francis@oicr.on.ca
Supplementary information: Supplementary data are available at Bioinformatics online.
Over‐expression of CCL3  MIP‐1α in a blastoid mantle cell lymphoma with hypercalcemia
Authors: Hattori Norimichi , Nakamaki Tsuyoshi , Ariizumi Hirotsugu , Homma Mayumi , Yamochi‐Onizuka Toshiko , Ota Hidekazu , Tomoyasu Shigeru 
Published: December 2009

AbstractWe analyzed a case with the blastoid variant of mantle cell lymphoma (MCL‐BV), a rare subtype of B‐cell lymphoma, presenting with marked hypercalcemia at diagnosis. Enzyme‐linked immunosorbent assay (ELISA) showed elevated serum levels of interleukin‐6 (IL‐6), tumor necrosis factor‐α (TNF‐α), macrophage inflammatory protein‐1α (MIP‐1α), and type I collagen telopeptide, but not parathyroid hormone, calcitriol or parathyroid hormone‐related peptide at diagnosis, suggesting local osteoclastic hypercalcemia in this case. By reverse transcription polymerase chain reaction (RT‐PCR) analysis, we found predominant expression of mRNA for MIP‐1α in addition to those for receptor‐activator of nuclear‐factor kappa B ligand (RANKL), TNF‐α, and IL‐6 in lymphoma cells obtained from the patient. Furthermore, recombinant MIP‐1α significantly stimulated 3H‐thymidine uptake by isolated MCL cells in vitro. Treatment with intravenous fluids, bisphosphonate, and methylprednisolone followed by combination chemotherapy promptly corrects the hypercalcemia and successfully induced complete remission, which was accompanied by a decrease of these cytokines in the serum, including MIP‐1α. In the present case, MIP‐1α, an osteoclast‐activating factor produced by mantle lymphoma cells, may contribute to the development of hypercalcemia. It likely acts through RANKL expression in tumor cells and/or stroma cells, as indicated in multiple myeloma (MM) and adult T‐cell leukemia/lymphoma (ATLL). Furthermore, MIP‐1α is also involved in the development of an aggressive phenotype on MCL by stimulating proliferation of these lymphoma cells. In summary, the present study demonstrated that MIP‐1α is an important factor in the development of both hypercalcemia and an aggressive phenotype in some types of B‐cell lymphoma.
Dialogue and the Imagination: Reflections by an Indian Christian Artist
Authors: Sahi Jyoti 
Published: December 2009

AbstractAs an Indian Christian artist, I have reflected on Jesus’s dialogue with the Woman at the Well . Here we see the relation of Jesus to cultures beyond the Jewish one. The Biblical text has many layers of meaning. In Indian aesthetics, we learn of the ‘Dhvani’ or ‘implied meaning’ of a text. This implied meaning is discovered by the imagination, and is the basis for a re-interpretation of the text in our modern context of religious diversity, and ecological challenges. Attempts to relate Biblical narratives to images found in other religious traditions such as Hinduism and Buddhism, have sometimes been questioned as being syncretistic. However, a story like that of the woman at the well, has echoes in a similar story to be found in the Buddhist tradition, and in the universal theme of water, and its importance for life.
Odontogenic keratocysts in Nevoid basal cell carcinoma syndrome: a case report
Authors: Mohtasham Nooshin , Nemati Somayyeh , Jamshidi Shokoofeh , Habibi Ataollah , Johari Masume 
Published: December 2009

Abstract
Nevoid basal cell carcinoma syndrome, a rare autosomal dominant disorder, comprises a number of abnormalities such as multiple nevoid basal cell carcinomas, skeletal abnormalities and multiple odontogenic keratocysts. Considering the rarity of this syndrome, we present a 12-year-old boy affected by this syndrome. He had multiple okcs, calcification of falx cerebri, bifid ribs, frontal bossing and hypertelorism. Characteristic cutaneous manifestation (nevoid basal cell carcinoma) was not present in this patient. The jaw cysts were treated with marsupialization then enucleation. The dental clinician may be the first to encounter and identify this syndrome, when the multiple cystlike radiolucencies are discovered on panoramic view.
The Community Approach to Participation: Outcomes Following Acquired Brain Injury Intervention
Authors: Sloan Sue , Callaway Libby , Winkler Dianne , McKinley Kirsten , Ziino Carlo , Anson Katie 
Published: December 2009

AbstractObjective: To investigate the participation outcomes of individuals with severe acquired brain injury (ABI) who were provided with up to 12 months of intervention based on the Community Approach to Participation (CAP). Method: A case series study design was undertaken with a total of 85 participants from two private practices specialising in community-based, CAP rehabilitation for people with severe ABI. Inclusion criteria were the person had sustained an acquired brain injury, was aged over 18 years and had received up to 12 consecutive months of CAP input from one of the two practices within a three-year period between January 2004 and January 2007. Twenty-six of the 85 participants were an average of 343 days post injury (Early group) and 59 of the participants were an average of 10.2 years post injury (Late group). They were living in a range of community environments and residential facilities. Initial participants were identified for the study in January 2005. Data were gathered using the Functional Independence Measure (FIM™), Community Integration Questionnaire (CIQ), and Role Checklist (RC Part 1) at two time points: prior to intervention (baseline), and after a 12-month period or at discharge (TI). Within the intervention period, all participants received a customised community occupational therapy (OT) rehabilitation program based on the key principles of the CAP. Intervention focused on participation goals of the individual, and development of the associated skills that underpinned valued role performance. Results: Participants each received an average of 51.01 hours of CAP OT during the 12-month period of intervention. Considerable improvement was seen in functional independence, community integration, and role participation after intervention in both the Early and Late groups. A statistically significant increase in FIM™ and CIQ total scores was found for all participants from Baseline to T1. The number of roles in which participants engaged increased on average by almost one role per participant following intervention, from a mean of 3.06 to 3.99. Increased participation in volunteer, home maintainer, participant in organisations and hobbyist roles were most common. Conclusion: Increased functional independence, community integration, and participation in both the Early and Late groups over a 12 month period demonstrates the potential for improved participation outcomes for people with complex needs following ABI, even many years post injury.
Planning Ability Following Moderate to Severe Traumatic Brain Injury: Performance on a 4-Disk Version of the Tower of London
Authors: Shum David , Gill Hannah , Banks Miranda , Maujean Annick , Griffin Janelle , Ward Heather 
Published: December 2009

AbstractThis study aimed to assess planning ability in adults with traumatic brain injury (TBI) using a 4-disk version of the Tower of London (TOL). Thirty three individuals with TBI were compared with equivalent numbers of matched controls. Overall, the TOL4 was shown to be sensitive to the effects of brain injury, with the TBI group performing significantly more poorly on this version of the planning test than the matched controls. More specifically, group differences were found to be related to the complexity of the planning problems, particularly among a TBI subgroup with localised prefrontal damage. Results of the study provide support for the adverse effects of TBI on planning ability, and the important role of the prefrontal cortex in planning.
Demand Elasticity, Risk Classification and Loss Coverage: When Can Community Rating Work?
Authors: Thomas R. Guy 
Published: December 2009

AbstractThis paper investigates the effects of high or low fair-premium demand elasticity in an insurance market where risk classification is restricted. The effects are represented by the equilibrium premium, and the risk-weighted insurance demand or “loss coverage”. High fair-premium demand elasticity leads to a collapse in loss coverage, with an equilibrium premium close to the risk of the higher-risk population. Low fair-premium demand elasticity leads to an equilibrium premium close to the risk of the lower-risk population, and high loss coverage – possibly higher than under more complete risk classification. The demand elasticity parameters which are required to generate a collapse in coverage in the model in this paper appear higher than the values for demand elasticity which have been estimated in several empirical studies of various insurance markets. This offers a possible explanation of why some insurance markets appear to operate reasonably well under community rating, without the collapse in coverage which insurance folklore suggests.
Option Pricing in a Jump-Diffusion Model with Regime Switching
Authors: Yuen Fei Lung , Yang Hailiang 
Published: December 2009

AbstractNowadays, the regime switching model has become a popular model in mathematical finance and actuarial science. The market is not complete when the model has regime switching. Thus, pricing the regime switching risk is an important issue. In Naik (1993), a jump diffusion model with two regimes is studied. In this paper, we extend the model of Naik (1993) to a multi-regime case. We present a trinomial tree method to price options in the extended model. Our results show that the trinomial tree method in this paper is an effective method; it is very fast and easy to implement. Compared with the existing methodologies, the proposed method has an obvious advantage when one needs to price exotic options and the number of regime states is large. Various numerical examples are presented to illustrate the ideas and methodologies.
A Bootstrap Estimate of the Predictive Distribution of Outstanding Claims for the Schnieper Model
Authors: Liu Huijuan , Verrall Richard 
Published: December 2009

AbstractThis paper considers the bootstrapping approach for measuring reserve uncertainty when applying the model of Schnieper for reserves which separate Incurred But Not Reported (IBNR) and Incurred But Not Enough Reserved (IBNER) claims. The Schnieper method has been explored in Liu and Verrall (2009), and the Mean Square Errors of Prediction (MSEP) derived. This paper takes this further by deriving the full predictive distribution, using bootstrapping. Numerical examples are provided and the MSEP from the bootstrapping approach are compared with those obtained analytically.
Independent changes in female body shape with parity and age: A life‐history approach to female adiposity
Authors: Wells Jonathan C.K. , Griffin Lewis , Treleaven Philip 
Published: December 2009

AbstractBoth aging and reproduction have been shown to influence female body shape in industrialized populations, involving redistribution of fat from lower to upper body regions. However, the extent to which effects of parity vary by age and the extent to which age affects shape independent of parity remain unclear. We studied shape variability in relation to age and parity in a cross‐sectional survey of 4,130 white British women, using three‐dimensional photonic scanning. In women ≤40 years, bearing children was associated with increased abdominal and reduced thigh girths, independent of age and BMI. Very few such differences were statistically significant in women >40 years, suggesting the effects of parity on shape wash out over time. In nulliparous women, aging was associated with shape variability, independent of BMI, with a similar pattern of associations evident in women both ≤40 and >40 years. Our data support previous findings of “covert maternal depletion” in relation to parity, but show that this is merely a more pronounced component of a general strategic shift of fat from lower to upper body with age. These findings are consistent with a life‐history model of female energy stores being allocated to competing “reproduction” and “maintenance” depots, with the optimal trade‐off strategy changing with age and with that strategic shift accelerated by bearing children. This model is relevant to the “grandmother hypothesis.” The dual effects of age and parity on fat distribution substantially resolve by old age the profound sexual dimorphism in adiposity present at the start of adult life. Am. J. Hum. Biol. 2010. © 2009 Wiley‐Liss, Inc.
Deleterious effects of plant cystatins against the banana weevil Cosmopolites sordidus
Authors: Kiggundu Andrew , Muchwezi Josephine , Van der Vyver Christell , Viljoen Altus , Vorster Juan , Schlüter Urte , Kunert Karl , Michaud Dominique 
Published: December 2009

AbstractThe general potential of plant cystatins for the development of insect‐resistant transgenic plants still remains to be established given the natural ability of several insects to compensate for the loss of digestive cysteine protease activities. Here we assessed the potential of cystatins for the development of banana lines resistant to the banana weevil Cosmopolites sordidus, a major pest of banana and plantain in Africa. Protease inhibitory assays were conducted with protein and methylcoumarin (MCA) peptide substrates to measure the inhibitory efficiency of different cystatins in vitro, followed by a diet assay with cystatin‐infiltrated banana stem disks to monitor the impact of two plant cystatins, oryzacystatin I (OC‐I, or OsCYS1) and papaya cystatin (CpCYS1), on the overall growth rate of weevil larvae. As observed earlier for other Coleoptera, banana weevils produce a variety of proteases for dietary protein digestion, including in particular Z‐Phe‐Arg‐MCA‐hydrolyzing (cathepsin L–like) and Z‐Arg‐Arg‐MCA‐hydrolyzing (cathepsin B–like) proteases active in mildly acidic conditions. Both enzyme populations were sensitive to the cysteine protease inhibitor E‐64 and to different plant cystatins including OsCYS1. In line with the broad inhibitory effects of cystatins, OsCYS1 and CpCYS1 caused an important growth delay in young larvae developing for 10 days in cystatin‐infiltrated banana stem disks. These promising results, which illustrate the susceptibility of C. sordidus to plant cystatins, are discussed in the light of recent hypotheses suggesting a key role for cathepsin B–like enzymes as a determinant for resistance or susceptibility to plant cystatins in Coleoptera. © 2009 Wiley Periodicals, Inc.
Randomized clinical trial of symptom control after stapled anopexy or diathermy excision for haemorrhoid prolapse
Authors: Nyström P-O , Qvist N , Raahave D , Lindsey I , Mortensen N 
Published: December 2009

Abstract

Background
This multicentre randomized clinical trial studied how symptoms improved after either stapled anopexy or diathermy excision of haemorrhoids.

Methods
The study involved 18 hospitals in Sweden, Denmark and the UK. Some 207 patients were randomized to either anopexy or Milligan–Morgan haemorrhoidectomy, of whom 90 in each group were operated on. Patients reported symptoms before surgery and after 1 year. Daily postoperative pain scores were recorded in a patient diary. Surgeons evaluated the anal anatomy before surgery and after 1 year.

Results
Correction of prolapse in the anopexy and haemorrhoidectomy groups was similar at 1 year (88 and 90 per cent respectively; P = 0·80). Freedom from symptoms was obtained in 44 and 69 per cent respectively (P = 0·002). Stapled anopexy was associated with less postoperative pain, which resolved more quickly (P = 0·004). Significant improvements were noted in anal continence and well-being 1 year after both operations (P &lt; 0·001). Excessive pain was the most common complication after diathermy excision and disturbed bowel function after stapled anopexy.

Conclusion
Haemorrhoidal prolapse was corrected equally by either operation. Diathermy haemorrhoidectomy gave better symptom relief but was more painful. Neither operation provided complete cure but well-being was greatly improved. Registration number: ISRCTN68315343 (http://www.controlled-trials.com).
Quality of life after transperineal rectosigmoidectomy
Authors: Kim M , Reibetanz J , Boenicke L , Germer C-T , Jayne D , Isbert C 
Published: December 2009

Abstract

Background
This study evaluated continence, constipation and quality of life before and after perineal rectosigmoidectomy for full-thickness rectal prolapse.

Methods
Consecutive patients with full-thickness rectal prolapse undergoing perineal rectosigmoid- ectomy (Altemeier's procedure) between May 2004 and June 2008 were studied. A standardized questionnaire, including the Cleveland Clinic Constipation Score (CCCS), Cleveland Clinic Incontinence Score (CCIS) and quality of life scores (EuroQol—Five Dimensions, EuroQol—Visual Analogue Scale and Patient Assessment of Constipation—Quality of Life (PAC-QOL)), was administered before and after operation.

Results
Thirty-eight patients (32 women) of mean(s.d.) age 75(13) years underwent rectosigmoid- ectomy. Seven patients developed postoperative complications and one died. There was one recurrence 5 months after surgery. Twenty-nine patients completed the follow-up questionnaire and were reviewed after a median of 24 (range 6–48) months. Constipation and incontinence were significantly improved after surgery (mean CCCS from 10·21 to 3·58 and CCIS from 14·17 to 11·42; P &lt; 0·001). Quality of life, in terms of mobility, usual activities, pain/discomfort and anxiety/depression, were significantly better at follow-up (P &lt; 0·001), as was subjective health status (P &lt; 0·001). The PAC-QOL score improved significantly in all dimensions (P &lt; 0·001).

Conclusion
Transperineal rectosigmoidectomy improves general and constipation-related quality of life with good functional results.
Mid-term outcome of endovascular revascularization for chronic mesenteric ischaemia
Authors: Dias N V , Acosta S , Resch T , Sonesson B , Alhadad A , Malina M , Ivancev K 
Published: December 2009

Abstract

Background
This study aimed to assess mid-term outcome after endovascular revascularization of chronic occlusive mesenteric ischaemia (CMI) and to identify possible predictors of mortality.

Methods
Consecutive patients undergoing primary elective stenting for CMI between 1995 and 2007 were registered prospectively in a database. Patients with acute ischaemia were excluded. Retrospective case-note review and data analysis were performed.

Results
Forty-three patients (10 men) were treated for stable (n = 30) or exacerbated (n = 13) CMI. Their median (interquartile range (i.q.r.)) age was 70 (60–79) years. Revascularization was successful in 47 of 49 vessels. The superior mesenteric artery (SMA), either alone (n = 34) or in combination with the coeliac trunk (n = 6), was the predominant target vessel. No patient died within 30 days. Median follow-up was 43 (i.q.r. 25–63) months and the estimated (s.e.) 3-year overall survival rate was 76(7) per cent. Two patients died from distal SMA occlusive disease and intestinal infarction after 6 and 18 months respectively. Previous stroke (P = 0·016), male sex (P = 0·057) and age (P = 0·066) were associated with mid-term mortality on univariable, but not multivariable analysis. Reintervention was needed in 14 patients, achieving a 3-year cumulative rate of freedom from recurrent symptoms of 88(5) per cent.

Conclusion
Endovascular treatment provided high early and mid-term survival rates in this series of patients with CMI, with low complication rates.
Skeletal muscle contractile properties and proinflammatory cytokine gene expression in human endotoxaemia
Authors: McNicol F J , Hoyland J A , Cooper R G , Carlson G L 
Published: December 2009

Abstract

Background
Muscle dysfunction associated with sepsis contributes to morbidity and mortality but the underlying mechanisms are unclear. This study examined whether muscle weakness relates to an intrinsic defect in contraction, or to central mechanisms associated with acute illness, and whether systemic endotoxaemia induces changes in gene expression for proinflammatory cytokines within human muscle in vivo.

Methods
In this experimental study, 12 healthy men received intravenous Escherichia coli lipopolysaccharide (LPS, 4 ng/kg) or saline (control). Voluntary and electrically stimulated quadriceps contraction, and tumour necrosis factor (TNF) α mRNA expression in quadriceps muscle biopsies were studied before and after the infusion.

Results
Endotoxaemia induced transient weakness of voluntary quadriceps contraction, equivalent to a 7·8 (95 per cent confidence interval 2·1 to 13·5) per cent reduction in contractile force at 180 min (P = 0·027) and a 9·0 (5·2 to 12·8) per cent reduction at 300 min (P = 0·008). Electrically stimulated contraction was unaffected. LPS administration resulted in an apparent fibre-specific induction of TNF-α mRNA.

Conclusion
Endotoxaemia results in a reduction in voluntary muscle contractile force without an apparent defect in stimulated muscle contraction. Loss of volition may be a more important factor than intrinsic dysfunction in acute sepsis-associated human muscle weakness.