bluuebunny/crossref_metadata_2025 huggingface dataset:
AllerTool: a web server for predicting allergenicity and allergic cross-reactivity in proteins
Authors: Zhang Zong Hong , Koh Judice L. Y. , Zhang Guang Lan , Choo Khar Heng , Tammi Martti T. , Tong Joo Chuan
Published: December 2006

Summary: Assessment of potential allergenicity and patterns of cross-reactivity is necessary whenever novel proteins are introduced into human food chain. Current bioinformatic methods in allergology focus mainly on the prediction of allergenic proteins, with no information on cross-reactivity patterns among known allergens. In this study, we present AllerTool, a web server with essential tools for the assessment of predicted as well as published cross-reactivity patterns of allergens. The analysis tools include graphical representation of allergen cross-reactivity information; a local sequence comparison tool that displays information of known cross-reactive allergens; a sequence similarity search tool for assessment of cross-reactivity in accordance to FAO/WHO Codex alimentarius guidelines; and a method based on support vector machine (SVM). A 10-fold cross-validation results showed that the area under the receiver operating curve (AROC) of SVM models is 0.90 with 86.00% sensitivity (SE) at specificity (SP) of 86.00%.

Availability: AllerTool is freely available at

Contact:  zhzhang@i2r.a-star.edu.sg
Protein solubility: sequence based prediction and experimental verification
Authors: Smialowski Pawel , Martin-Galiano Antonio J. , Mikolajka Aleksandra , Girschick Tobias , Holak Tad A. , Frishman Dmitrij
Published: December 2006

Motivation: Obtaining soluble proteins in sufficient concentrations is a recurring limiting factor in various experimental studies. Solubility is an individual trait of proteins which, under a given set of experimental conditions, is determined by their amino acid sequence. Accurate theoretical prediction of solubility from sequence is instrumental for setting priorities on targets in large-scale proteomics projects.

Results: We present a machine-learning approach called PROSO to assess the chance of a protein to be soluble upon heterologous expression in Escherichia coli based on its amino acid composition. The classification algorithm is organized as a two-layered structure in which the output of primary support vector machine (SVM) classifiers serves as input for a secondary Naive Bayes classifier. Experimental progress information from the TargetDB database as well as previously published datasets were used as the source of training data. In comparison with previously published methods our classification algorithm possesses improved discriminatory capacity characterized by the Matthews Correlation Coefficient (MCC) of 0.434 between predicted and known solubility states and the overall prediction accuracy of 72% (75 and 68% for positive and negative class, respectively). We also provide experimental verification of our predictions using solubility measurements for 31 mutational variants of two different proteins.

Availability: A web server for protein solubility prediction is available at http://webclu.bio.wzw.tum.de:8080/proso

Contact:  d.frishman@wzw.tum.de

Supplementary information: Supplementary data are available at Bioinformatics online
Vascular Pharmacology of Mokuboito (Mu‐Fang‐Yi‐Tang) and Its Constituents on the Smooth Muscle and the Endothelium in Rat Aorta
Authors: Nishida Seiichiro , Satoh Hiroyasu
Published: December 2006

Pharmacological actions of Mokuboito and its constituents (Sinomenium acutum and sinomenine) on rat aorta were examined. Mokuboito and S. acutum at lower concentrations (0.03–1 mg ml−1) contracted the non‐loaded aorta, but at higher concentrations (1–3 mg ml−1), reversed to dilate it. The vasoconstriction was blocked by phentolamine (10 μM). Sinomenine failed to exhibit the vasoconstriction. On the other hand, Mokuboito and S. acutum dilated the NE (5 μM)‐induced vasoconstriction: at 3 mg ml−1, by 98.9 ± 2.5% (n = 6, P < 0.01) and 97.0 ± 4.8% (n = 6, P < 0.01). Vasorelaxation induced by Mokuboito and S. acutum was attenuated by indomethacin, L‐NMMA and nicardipine. Propranolol decreased the vasorelaxation induced by Mokuboito, but not by S. acutum. Sinomenine also relaxed the constriction and at 100 μM, by 68.8 ± 5.1% (n = 7, P < 0.01). This vasorelaxation was attenuated by indomethacin, L‐NMMA and nicardipine, and also by propranolol. Therefore, these results indicate that Mokuboito and its constituents exert both vasodilating actions mediated by endothelium‐dependent mechanisms (PGI2 and NO from endothelium) and by endothelium‐independent mechanisms (Ca2+ influx control on smooth muscle cells). Simultaneously, Mokuboito and S. acutum cause the vasoconstrictions mediated through α‐adrenoceptor stimulation, but not sinomenine. Also, Mokuboito and sinomenine possess β‐adrenoreceptor stimulating action, but not S. acutum.
Genome characteristics of facultatively symbiotic Frankia sp. strains reflect host range and host plant biogeography
Authors: Normand Philippe , Lapierre Pascal , Tisa Louis S. , Gogarten Johann Peter , Alloisio Nicole , Bagnarol Emilie , Bassi Carla A. , Berry Alison M. , Bickhart Derek M. , Choisne Nathalie , Couloux Arnaud , Cournoyer Benoit , Cruveiller Stephane , Daubin Vincent , Demange Nadia , Francino Maria Pilar , Goltsman Eugene , Huang Ying , Kopp Olga R. , Labarre Laurent , Lapidus Alla , Lavire Celine , Marechal Joelle , Martinez Michele , Mastronunzio Juliana E. , Mullin Beth C. , Niemann James , Pujic Pierre , Rawnsley Tania , Rouy Zoe , Schenowitz Chantal , Sellstedt Anita , Tavares Fernando , Tomkins Jeffrey P. , Vallenet David , Valverde Claudio , Wall Luis G. , Wang Ying , Medigue Claudine , Benson David R.
Published: December 2006

Soil bacteria that also form mutualistic symbioses in plants encounter two major levels of selection. One occurs during adaptation to and survival in soil, and the other occurs in concert with host plant speciation and adaptation. Actinobacteria from the genus Frankia are facultative symbionts that form N2-fixing root nodules on diverse and globally distributed angiosperms in the “actinorhizal” symbioses. Three closely related clades of Frankia sp. strains are recognized; members of each clade infect a subset of plants from among eight angiosperm families. We sequenced the genomes from three strains; their sizes varied from 5.43 Mbp for a narrow host range strain (Frankia sp. strain HFPCcI3) to 7.50 Mbp for a medium host range strain (Frankia alni strain ACN14a) to 9.04 Mbp for a broad host range strain (Frankia sp. strain EAN1pec.) This size divergence is the largest yet reported for such closely related soil bacteria (97.8%–98.9% identity of 16S rRNA genes). The extent of gene deletion, duplication, and acquisition is in concert with the biogeographic history of the symbioses and host plant speciation. Host plant isolation favored genome contraction, whereas host plant diversification favored genome expansion. The results support the idea that major genome expansions as well as reductions can occur in facultative symbiotic soil bacteria as they respond to new environments in the context of their symbioses.
Exploring genomic dark matter: A critical assessment of the performance of homology search methods on noncoding RNA
Authors: Freyhult Eva K. , Bollback Jonathan P. , Gardner Paul P.
Published: December 2006

Homology search is one of the most ubiquitous bioinformatic tasks, yet it is unknown how effective the currently available tools are for identifying noncoding RNAs (ncRNAs). In this work, we use reliable ncRNA data sets to assess the effectiveness of methods such as BLAST, FASTA, HMMer, and Infernal. Surprisingly, the most popular homology search methods are often the least accurate. As a result, many studies have used inappropriate tools for their analyses. On the basis of our results, we suggest homology search strategies using the currently available tools and some directions for future development.
Viewing videotape of themselves while experiencing delirium tremens could reduce the relapse rate in alcohol‐dependent patients
Authors: Mihai Adriana , Damsa Cristian , Allen Michael , Baleydier Bertrand , Lazignac Coralie , Heinz Andreas
Published: December 2006

Aims  The aim of this prospective randomized controlled study was to determine whether viewing videotape of themselves while experiencing delirium tremens (DT) reduces the relapse rate in alcohol‐dependent patients. Our hypothesis about the efficacy of videotapes exposure to DT is consistent with a cognitive behavior model.

Design  Sixty patients with DT and a minimum of 3 years of severe alcohol dependence [Diagnostic and Statistical Manual version IV (DSM‐IV criteria] were included in this study. Patients were videotaped during the acute phase of DT and randomized into two groups: group A patients received individual exposure to their videotape and an explanation of the symptoms by a psychiatrist; and control group B patients, who were without videotape experience. Both groups received the same treatment during the acute and the maintenance phases, without aversive therapy or psychotherapy. The two groups did not differ significantly in number of drinks per day prior to admission, age, marital status, social environment, education, professional and financial status or family psychiatric history.

Setting  An in‐patient crisis unit for patients with alcohol dependence.

Measurements  All patients were observed for 6 months during monthly visits. Outcomes included relapse, drinking days per week and number of drinks per drinking day. All patients and their families signed informed consent.

Findings  The patients with videotape experience had a significantly lower relapse rate after the first month (0% versus 20%), 2 months (13.33% versus 46.67%) and 3 months (26.67% versus 53.33%). Patients with videotape experience had less severe relapses and consumed fewer units of alcohol than controls.

Conclusions  Videotape exposure in delirium tremens is an original therapeutic method which seems to be effective in reducing relapse risk in patients with alcohol dependence.
Smoking in the absence of nicotine: behavioral, subjective and physiological effects over 11 days
Authors: Donny Eric C. , Houtsmuller Elizabeth , Stitzer Maxine L.
Published: December 2006

Aims  Sensorimotor stimuli associated with tobacco smoking influence smoking behavior; however, current research has focused almost exclusively on the effects of brief, laboratory‐based exposure to smoking‐related stimuli. The purpose of this experiment was to characterize the effects of smoking stimuli delivered in the absence of nicotine over an extended (11‐day) exposure.

Design, setting and participants  Thirty adult regular smokers participated in an in‐patient study. After assessing preferred brand smoking, participants were assigned randomly to one of three groups corresponding to subsequent smoking conditions: nicotine‐containing cigarettes, de‐nicotinized cigarettes or no smoking.

Measurements  Measures of smoking reinforcement, subjective effects, physiological effects, withdrawal/craving and puff topography were taken repeatedly during both periods of free access and controlled assessments during abstinence.

Findings  Daily de‐nicotinized cigarette use declined immediately by 1.7 cigarettes/day compared to the preferred brand baseline and declined by another 3.5 cigarettes over time; participants smoking de‐nicotinized cigarettes also demonstrated a 31% decline in the number of puffs earned on a progressive ratio, a measure of the motivation to smoke, during the study. Subjective ratings of smoking were largely negative throughout the study in the de‐nicotinized group, while the nicotine‐containing condition reported increasingly positive subjective effects with repeated exposure. Acute craving suppression following smoking remained evident throughout the study regardless of nicotine content.

Conclusions  These effects highlight the importance of non‐nicotine sensorimotor stimuli as determinants of the maintenance of smoking behavior and suggests that extinction of conditioned reinforcement in the absence of nicotine progresses slowly.
Tracheal tube tip displacement during laparoscopy in children*
Authors: Böttcher‐Haberzeth S. , Dullenkopf A. , Gitzelmann C. A. , Weiss M.
Published: December 2006

The risk of endobronchial intubation during laparoscopy because of displacement of the tip of the tracheal tube is a well known problem in adults. Laparoscopy in children is increasingly performed, but there are no data available regarding the above problem. We prospectively studied 46 children aged 2 months to 15.7 years (median 4.2 years) undergoing laparoscopy. After tracheal intubation with the Microcuff Pediatric Endotracheal Tube, with the ‘intubation depth marking’ of the tube at the vocal cords, the distance from the tracheal tube tip to the carina was endoscopically measured with the patient in the neutral position and with 20° head‐down tilt, both with and without capnoperitoneum. Maximal displacement of the tip of the tracheal tube tip in cm was 0.5 + (0.05 × age (years)) for 20° head‐down tilt, 0.6 + (0.09 × age (years)) for capnoperitoneum alone, and 1.2 + (0.11 × age (years)) for 20° head‐down tilt with capnoperitoneum. In no patients did endobronchial intubation occur with the tracheal tube placed according to the intubation depth marking.
A comparison of intubating conditions in children following induction of anaesthesia with propofol and suxamethonium or propofol and remifentanil
Authors: Morgan J. M. , Barker I. , Peacock J. E. , Eissa A.
Published: December 2006

Sixty ASA 1 and 2 children aged between 2 and 16 years who required tracheal intubation as part of anaesthesia for elective surgery were studied. We evaluated intubating conditions, haemodynamic responses and duration of apnoea following propofol 4 mg.kg−1 combined with either remifentanil 1.25 μg.kg−1 (group R), or suxamethonium 1 mg.kg−1 (group S). Tracheal intubation was graded as excellent, good or poor according to ease of laryngoscopy, vocal cord position, coughing, and jaw relaxation and limb movement. Thirty of group S and 28 of group R children were successfully intubated on the first attempt. Overall, intubation conditions were excellent or good in 26/30 (87%) patients in group S and 20/30 (67%) in group R (p < 0.05). Mean apnoea time was 190 s in group S, and 362 s in group R (p < 0.001). Heart rate increased in response to suxamethonium (p < 0.01) and both systolic and diastolic blood pressure decreased in the remifentanil group (p < 0.01).
Inflation with air via a facepiece for facilitating insertion of a nasogastric tube: a prospective, randomised, double‐blind study
Authors: Gupta D. , Agarwal A. , Nath S. S. , Goswami D. , Saraswat V. , Singh P. K.
Published: December 2006

Insertion of a nasogastric tube is a routine procedure but during anaesthesia it is often difficult and time consuming. One hundred and sixty adults undergoing elective surgery under general anaesthesia were randomly divided into two groups. After induction of anaesthesia, neuromuscular blockade and tracheal intubation, a nasogastric tube was inserted through the nose with the head of the patient in the neutral position, either with or without prior inflation with air via a facepiece attached to a self‐inflating bag applied firmly with the face. Insertion of the nasogastric tube was successful in 75/78 (96%) following inflation compared with 54/80 (68%) without inflation (p < 0.001). In four patients receiving inflation, a fibreoptic endoscope was passed as far as the upper oesophageal sphincter; this revealed opening of the upper oesophageal sphincter during inflation.
Assessment of renal function in clinical practice at the bedside of burn patients
Authors: Conil J. M. , Georges B. , Fourcade O. , Seguin T. , Lavit M. , Samii K. , Houin G. , Tack I. , Saivin S.
Published: December 2006

What is already known about this subject

• In burn patients it has been shown ([2]), that there is a correlation between the creatinine clearance (CLCR) and the clearance of inulin.

• The CLCR has never been studied in burn patients who have normal serum creatinine.

• The Robert, Kirkpatrick and sMDRD formulae have never been evaluated in burn patients.

What this study adds

• Despite burn patients having normal serum creatinine concentrations, the study showed that there are large variations in CLCR which cannot be detected by single serum creatinine measurements, and which have important implications for drug therapy.

• It showed that the formulae currently used to calculate creatinine clearance on the basis of serum creatinine are inadequate for use in burn patients, and they should be abandoned in favour of direct measurement from a 24 h urine collection.

Aims

The aim of this study was to evaluate whether the renal function of burn patients could be correctly assessed using a single serum creatinine measurement, within normal limits, and three prediction equations of glomerular filtration taking into account, serum creatinine, age, weight and sex.

Methods

This was a prospective study comprising 36 adult burn patients with a serum creatinine <120 µmol l−1, within the second or third week following the burn injury. Renal function was assessed using serum creatinine, 24 h urinary CLCR, and the Cockcroft–Gault, Robert, Kirkpatrick and simplified MDRD equations.

Results

Despite normal serum creatinine concentrations in all patients, a significant number had a decreased CLCR. The urinary CLCR was <80 ml−1 min‐1 1.73 m−2 in nine patients (25%), and <60 ml−1 min−1 1.73 m−2 in five patients (14%). Between the groups having a CLCR lower or greater than 80 ml−1 min−1 1.73 m−2 there were no differences in gender, burn indices, percentage of mechanically ventilated patients or length of hospital stay, but a difference in age. The highest CLCR (>140 ml−1 min−1 1.73 m−2) was found in 13 patients younger than 40 years. Regression analysis, residual and Bland–Altman plots revealed that neither the Cockcroft–Gault, Robert, Kirkpatrick nor sMDRD equations were specific enough for the assessment of renal function.

Conclusions

In burn patients with normal serum creatinine during the hypermetabolic phase, serum creatinine and creatine based predictive equations are imprecise in assessing renal function.
Comparative assessment of four drug interaction compendia
Authors: Vitry Agnes I.
Published: December 2006

Aims

To assess the consistency of inclusion and grading of major drug interactions for 50 drugs in four leading international drug interaction compendia.

Methods

Four international drug interaction compendia were compared: the drug interactions appendix of the British National Formulary, the interaction supplement in the French drug compendium Vidal, and two US drug interaction compendia, Drug Interaction Facts and the Micromedex (Drug‐Reax) program. Major interactions were defined as potentially hazardous in BNF or with the warning ‘contraindication’ or ‘avoid’ in Vidal or with the significance grading 1 or 2 in DIF. Major interactions for a list of 50 drugs were searched in all four compendia.

Results

A total of 1264 interactions meeting the inclusion criteria were identified for these 50 drugs. After deletion of 169 duplicates, 1095 interactions were included in the analysis. Of the drug interactions classified as major in any one compendium between 14% and 44% were not listed in the other compendia. The grading systems used for the severity and the quality of the supporting evidence in Micromedex and DIF were inconsistent.

Conclusions

There is a lack of consistency in the inclusion and grading of drug interactions of major significance for 50 drugs across the four drug compendia examined. This may reflect the lack of standardization of the terminology used to classify drug interactions and the lack of good epidemiological evidence on which to base the assessment of the clinical relevance of drug interactions.
Acute and chronic neuroendocrine effects of interferon‐β 1a in multiple sclerosis
Authors: Then Bergh Florian , Kümpfel Tania , Yassouridis Alexander , Lechner Christian , Holsboer Florian , Trenkwalder Claudia
Published: December 2006

Objective  Treatment of multiple sclerosis with interferon‐β (IFN‐β) results in variable responses interindividually. Cytokine–hormone interactions may modulate the therapeutic effects of IFN‐β. Since hyperactivity of the hypothalamo‐pituitary‐adrenal (HPA) axis and other neuroendorine disturbances occur in multiple sclerosis, we determined the detailed neuroendocrine response of patients with multiple sclerosis to IFN‐β.

Design  Longitudinal open‐label study.

Patients  Eight patients with relapsing‐remitting multiple sclerosis (four women, age 31·9 ± 1·5 years, EDSS 1·5–2·5).

Measurements  Plasma ACTH, cortisol, prolactin, GH, TSH, LH and FSH were determined in 30‐min intervals during 8 h on four occasions: after intramuscular injection of saline; after the first dose of IFN‐β 1a; after the second IFN‐β dose with oral indomethacin pretreatment; and after 3 months of IFN‐β therapy. Dexamethasone–corticotropin‐releasing hormone test was performed before and at 3 months on IFN‐β.

Results  Compared to saline, IFN injection resulted in marked rise in plasma ACTH (mean, 370% of baseline), cortisol (214%), prolactin (253%) and GH (756%), between 2 and 6 h after injection. With indomethacin, hormone secretion occurred with reduced peak values. Endocrine response adapted partially after 3 months of treatment. HPA axis activity decreased in most patients, but increased in one patient with frequent relapses.

Conclusions  Marked neuroendocrine effects occur in response to IFN‐β in multiple sclerosis. Upon prolonged treatment, these effects partially adapt, and HPA axis hyperactivity is reduced. Prospective studies to determine the relation to individual treatment response can be based on these findings.
Should ‘low‐risk’ thyroid cancer patients with residual thyroglobulin be re‐treated with iodine 131?
Authors: Hindié Elif , Zanotti‐Fregonara Paolo , Duron Françoise , Keller Isabelle , Bouchard Philippe , Devaux Jean‐Yves
Published: December 2006

Objective  The American consensus statement on patients with low‐risk thyroid cancer, published in 2003, suggests repeat 131I therapy if the thyroglobulin value is elevated at first follow‐up. We evaluated this strategy in our practice.

Methods  Among 407 patients with thyroid cancer who had total thyroidectomy and 131I ablation between January 2000 and December 2003, 12 patients with stage I thyroid cancer (any tumour (T), any node (N), metastasis (M)0 if < 45 years or T1, N0, M0 if > 45 years), were re‐treated on the basis of their thyroglobulin level at first follow‐up. Mean patient age was 32·8 years. None of them had a T4 tumour. Thyroglobulin levels after thyroid hormone withdrawal ‘off‐T4’ ranged between 4·5 and 251 ng/ml (median 8). One to four courses of 3·7 GBq 131I were given.

Results  Three patients had a negative 131I therapy scan and an uneventful course. Two patients had slight residual uptake only in the thyroid bed and negative ultrasound examination. Four patients had isolated 131I uptake in the mediastinal region. No abnormalities were found on complementary mediastinal imaging. This finding was interpreted as benign 131I thymic uptake. The last three patients also had mediastinal thymic uptake associated with a slight thyroid bed uptake. One patient had a gradual increase in the thyroglobulin level, and underwent resection of nonfunctioning neck lymph nodes. Thyroglobulin levels declined in all other patients.

Conclusions  No distant lesions were found in a group of young ‘low‐risk’ thyroid cancer patients given empirical 131I therapy for residual thyroglobulin. When blind 131I therapy shows no uptake, or uptake limited to the thymus, 131I therapy should not be repeated. The authors also briefly discuss the hypothesis that enhanced thymus might be a source of benign thyroglobulin secretion.
DNA fragmentation assessment by flow cytometry and Sperm–Bos–Halomax (bright‐field microscopy and fluorescence microscopy) in bull sperm
Authors: García‐Macías Vanesa , De Paz Paulino , Martinez‐Pastor Felipe , Álvarez Mercedes , Gomes‐Alves Susana , Bernardo Jana , Anel Enrique , Anel Luis
Published: December 2006

The aim of this study was to find the relationship between fertility (as 90‐day non‐return rates) and DNA fragmentation assessed by two techniques [sperm chromatin structure assay (SCSA) and Sperm–Bos–Halomax (SBH)]. Furthermore, other quality parameters were achieved (motility, morphological abnormalities, cytoplasmic droplets, viability, capacitation and acrosomal and mitochondrial status) and their correlations with fertility were analysed. Bulls were divided into three fertility groups: high [non‐return rate (NRR) ≥ 80], medium (80 < NRR ≥ 70) and low (70 < NRR > 40). The results of this study indicate that there is a good correlation between fertility and different parameters of sperm quality (SBH and SCSA parameters, % of spermatozoa with head, neck and total abnormalities, and % of spermatozoa with proximal cytoplasmic droplets) and differences between fertility groups were observed in some of them (SBH and SCSA parameters and % of spermatozoa with head, neck and total abnormalities). In this sense, SBH parameters rendered good correlations with fertility (r = −0.42 using bright light microscope and r = −0.47 with fluorescence). Also, standard deviation of DNA fragmentation index (SD‐DFI) and DFIh (cells with High DNA fragmentation index) showed good correlations with fertility (r = −0.41 and r = −0.29). No correlations were observed between SCSA and SBH parameters. A multiple regression shows that four parameters (% of proximal cytoplasmic droplets, % of intact acrosomes in total population, SD‐DFI and percentage of fragmented DNA detected by bright light microscope) present a good predictive value of the fertility of sperm samples (r2 = 0.34, p < 0.001).
Verbal working memory in children with mild intellectual disabilities
Authors: Van der Molen M. J. , Van Luit J. E. H. , Jongmans M. J. , Van der Molen M. W.
Published: December 2006

Background  Previous research into working memory of individuals with intellectual disabilities (ID) has established clear deficits. The current study examined working memory in children with mild ID (IQ 55–85) within the framework of the Baddeley model, fractionating working memory into a central executive and two slave systems, the phonological loop and visuo‐spatial sketchpad.

Method  Working memory was investigated in three groups: 50 children with mild ID (mean age 15 years 3 months), 25 chronological age‐matched control children (mean age 15 years 3 months) and 25 mental age‐matched control children (mean age 10 years 10 months). The groups were given multiple assessments of the phonological‐loop and central‐executive components.

Results  The results showed that the children with mild ID had an intact automatic rehearsal, but performed poorly on phonological‐loop capacity and central‐executive tests when compared with children matched for chronological age, while there were only minimal differences relative to the performance of the children matched for mental age.

Conclusions  This overall pattern of results is consistent with a developmental delay account of mild ID. The finding of a phonological‐loop capacity deficit has important implications for the remedial training of children with mild ID.
Experiences and problems pre‐operative anti‐CD20 monoclonal antibody infusion therapy with splenectomy and plasma exchange for ABO‐incompatible living‐donor liver transplantation
Authors: Usui Masanobu , Isaji Shuji , Mizuno Shugo , Sakurai Hiroyuki , Uemoto Shinji
Published: December 2006

Abstract:  Background:  ABO‐incompatible living‐donor liver transplantation (LDLT) requires a reduction of the anti‐ABO antibody titer to <16 before transplantation, which is usually achieved by pre‐operative plasma exchange (PE) or double‐filtration plasmapheresis. ABO‐incompatible transplantations have been performed after a splenectomy with heavy drug immunosupression plus B‐cell‐specific drugs. Here, we evaluated a pre‐transplantation infusion protocol with an anti‐CD20 monoclonal antibody (rituximab) for ABO‐incompatible LDLT.

Methods:  Between March 2002 and December 2005, 73 adult patients underwent LDLT without retransplantation in our institution. Among these cases, 57 were ABO‐identical, 11 were ABO‐compatible and five were ABO‐incompatible. The rituximab infusion protocol consisted of a weekly infusion of rituximab (375 mg/m2) for three wk, which was administered to three of the five ABO‐incompatible LDLT patients. All three patients underwent a pre‐operative PE, as well as a splenectomy during the operation. A triple immunosuppression protocol of tacrolimus, low‐dose steroids and mycophenolate mofetil (1500 mg/d) was administered post‐operatively. In addition, the patients received a continuous intra‐arterial infusion of prostaglandin E1 and methylprednisolone, and a continuous intra‐portal infusion of a protease inhibitor for three and two wk after transplantation, respectively.

Results:  After the first rituximab infusion, the peripheral blood CD19+ B cell count rapidly decreased to <1%. All three patients treated with rituximab subsequently received an ABO‐incompatible LDLT, with donor/recipient blood groups of B/O, A1/B and A1/O. In two cases, the ABO‐antibody level transiently increased post‐operatively, then decreased and remained low. Rituximab infusion therapy did not develop any direct side effect except for mild allergic reaction to the first infusion, but post‐operatively all three patients suffered a cytomegalovirus and were successfully treated with ganciclovir, and one patient had a MRSA‐positive intra‐abdominal abscess. Two patients are currently alive at 20 and 18 months respectively, and show normal graft‐liver function. But one patient died of sepsis because of intra‐abdominal abscess.

Conclusions:  Although the protocol of rituximab administration is a conventional and safe regimen with no major side effects, the development of a new protocol is needed for prevention of the infection with bone suppression.
Pregnancy after renal transplantation – a five‐yr single‐center experience
Authors: Oliveira Leandro G. , Sass Nelson , Sato Jussara L. , Ozaki Kikumi S. , Medina Pestana Jose O.
Published: December 2006

Abstract:  Background:  There has been an increase in the number of pregnancies in renal transplant recipients. Our aim was to report our experience with a significant casuistic.

Methods:  Fifty‐two pregnancies in 52 patients (January 2001 to December 2005), with two patients having a multiple pregnancy, were evaluated and patients were characterized and evaluated as clinical and obstetrical and perinatal outcomes.

Results:  Mean patient age was 26.5 yr (range 17–38) with live donors in 34 (65.4%) and cadaver donors in 18 (34.6%). The mean transplantation‐pregnancy interval was 3.1 yr. Calcineurin inhibitors (cyclosporine or tacrolimus) comprised the immunosuppressive therapy in 49 pregnancies (94.2%). Pregnancy complications were chronic hypertension in 33 patients (63.5%), anemia in 31 (59.6%), urinary tract infection in 22 (42.3%) and diabetes in four (7.7%). Nine patients (17.3%) received blood transfusion. Preeclampsia was diagnosed in 16 cases (30.7%) and renal dysfunction in 23 (44.2%) with preeclampsia assumed to be the main cause. One patient (1.9%) had graft loss, as a result of hemorrhagic shock after preterm delivery at home. Premature rupture of membranes occurred in four cases (7.7%), and preterm delivery in 20 (38.4%). Sixteen (29.6%) newborn were small for gestational age. One case of neonatal death was registered as a result of excessive prematurity. Cesarean section was performed in 32 patients (61.5%), the main indications being related to hypertension syndromes and fetal distress.

Conclusions:  This group of patients is characterized by a wide range of antenatal and perinatal problems and must be managed in specialized tertiary units to achieve the very best results.
Intravenous and oral sequential itraconazole antifungal prophylaxis in paediatric stem cell transplantation recipients: A pilot study for evaluation of safety and efficacy
Authors: Grigull L. , Kuehlke O. , Beilken A. , Sander A. , Linderkamp C. , Schmid H. , Seidemann K. , Sykora K. W. , Schuster F. R. , Welte K.
Published: December 2006

Abstract:  This single‐centre, retrospective, observational pilot study was performed to evaluate the safety and efficacy of intravenous and oral itraconazole prophylaxis in paediatric haematopoietic stem cell transplantation (HCT). Study end‐points were proven invasive fungal infection (IFI), survival, adverse reactions and graft‐vs.‐host disease (GVHD); 53 children and one young adult (median age 8.6 yr; range 0.4–18.3) transplanted between November 2001 and August 2004 were included in this study. Itraconazole was given intravenously from day +3 after HCT until oral medication became possible and continued until day +100 after HCT. Two proven new IFI in the itraconazole group (candidiasis, n = 1; aspergillosis, n = 1) were observed. After a median follow‐up of 1.6 yr (0.3–6.1), six deaths (8%) were seen; 24 patients (45%) developed GVHD degree I–II, three children (6%) had GVHD degree III–IV. In 11 of 53 patients (21%), itraconazole prophylaxis was discontinued prematurely, mostly because of fever of unknown origin (n = 7). In total, 21 of 53 (40%) of the children had abnormal results of laboratory investigations during the prophylaxis. The results of this pilot study indicate that itraconazole prophylaxis during HCT in children is feasible and safe, despite abnormal laboratory results. The efficacy in terms of prevention of IFI, however, has to be addressed in a prospective large‐scale study.
Anemia and growth status in pediatric patients receiving maintenance dialysis after a failed renal transplant course: An NAPRTCS report
Authors: Goldstein Stuart L. , Mattoo Tej K. , Morgenstern Bruce , Martz Karen , Stablein Donald , Talley Lynya
Published: December 2006

Abstract:  We conducted a retrospective review of the North American Renal Transplant Cooperative Study (NAPRTCS) Registry transplant and dialysis arms to assess anemia and growth patterns in children who returned to dialysis after a failed renal transplant from January 1, 1992 to February 3, 2004. Of the 1807 potential study subjects, 1451 had transplant removal data (TxIn vs. TxOut) available for analysis. Four hundred and twenty‐one of 1451 patients (29%) had a transplant nephrectomy at the time of entry into the NAPRTCS Registry Dialysis arm. Anemia rates steadily decreased from 72.2% at 30 days after dialysis initiation to 59.5% at 12 months after dialysis initiation. Factors associated with anemia at 30 days after dialysis initiation included hemodialysis, lack of Epo use, and patients who comprised earlier study era cohorts. At one yr after return to dialysis, earlier study cohort era was the only factor associated with anemia status. Patients did not demonstrate significant improvement in height SDS over the course of the study (−2.17 at day 30 to −2.32 at 24 months). The high anemia, poor growth, and low recombinant human growth hormone utilization rates in a group of patients followed longitudinally as they transition from renal transplant to dialysis should cause the pediatric nephrology community to reassess the processes in place to provide optimal care to pediatric end‐stage renal disease patients.
Towards a Unified Dynamical Solver for Computer Graphics
Authors: Stam Jos
Published: December 2006

In this talk I will present some research I have done over the past few years in developing a unified dynamical solver for computer graphics. Currently many solvers are specialized for a given phenomenon such as fluid flow, cloth, rigid bodies, hair, etc. Having these different solvers interact is sometimes problematic. We propose to model all matter as a linked particle system having the topology of a simplicial complex. The dynamical complex evolves due to external forces like gravity and constraints such as collisions and internal deformation energies. We use a solution scheme that iteratively updates the velocities to achieve all constraints. Key to the stability of our system is to interleave the solve for the different constraints. The talk will cover the main ideas and ingredients of our solver and will be accompanied with live demonstrations.
An Improved Physically‐Based Soft Shadow Volume Algorithm
Authors: Lehtinen Jaakko , Laine Samuli , Aila Timo
Published: December 2006

We identify and analyze several performance problems in a state‐of‐the‐art physically‐based soft shadow volume algorithm, and present an improved method that alleviates these problems by replacing an overly conservative spatial acceleration structure by a more efficient one. The new technique consistently outperforms both the previous method and a ray tracing‐based reference solution in several realistic situations while retaining the correctness of the solution and other desirable characteristics of the previous method. These include the unintrusiveness of the original algorithm, meaning that our method can be used as a black‐box shadow solver in any offline renderer without requiring multiple passes over the image or other special accommodation. We achieve speedup factors from 1.6 to 12.3 when compared to the previous method.

Categories and Subject Descriptors (according to ACM CCS): I.3.7 [Three‐Dimensional Graphics and Realism]: Shadowing
Volume‐Surface Trees
Authors: Boubekeur Tamy , Heidrich Wolfgang , Granier Xavier , Schlick Christophe
Published: December 2006

Many algorithms in computer graphics improve their efficiency by using Hierarchical Space Subdivision Schemes (HS3), such as octrees, kD‐trees or BSP trees. Such HS3 usually provide an axis‐aligned subdivision of the 3D space embedding a scene or an object. However, the purely volume‐based behavior of these schemes often leads to strongly imbalanced surface clustering. In this article, we introduce the VS‐Tree, an alternative HS3 providing efficient and accurate surface‐based hierarchical clustering via a combination of a global 3D decomposition at coarse subdivision levels, and a local 2D decomposition at fine levels near the surface. First, we show how to efficiently construct VS‐Trees over meshes and point‐based surfaces, and analyze the improvement it offers for cluster‐based surface simplification methods. Then we propose a new surface reconstruction algorithm based on the volume‐surface classification of the VS‐Tree. This new algorithm is faster than state‐of‐the‐art reconstruction methods and provides a final semi‐regular mesh comparable to the output of remeshing algorithms.
Semantic Photo Synthesis
Authors: Johnson M. , Brostow G. J. , Shotton J. , Arandjelovic O. , Kwatra V. , Cipolla R.
Published: December 2006

Composite images are synthesized from existing photographs by artists who make concept art, e.g., storyboards for movies or architectural planning. Current techniques allow an artist to fabricate such an image by digitally splicing parts of stock photographs. While these images serve mainly to “quickly”convey how a scene should look, their production is laborious. We propose a technique that allows a person to design a new photograph with substantially less effort. This paper presents a method that generates a composite image when a user types in nouns, such as “boat”and “sand.”The artist can optionally design an intended image by specifying other constraints. Our algorithm formulates the constraints as queries to search an automatically annotated image database. The desired photograph, not a collage, is then synthesized using graph‐cut optimization, optionally allowing for further user interaction to edit or choose among alternative generated photos. An implementation of our approach, shown in the associated video, demonstrates our contributions of (1) a method for creating specific images with minimal human effort, and (2) a combined algorithm for automatically building an image library with semantic annotations from any photo collection.
Real‐Time Weighted Pose‐Space Deformation on the GPU
Authors: Rhee Taehyun , Lewis J.P. , Neumann Ulrich
Published: December 2006

WPSD (Weighted Pose Space Deformation) is an example based skinning method for articulated body animation. The per‐vertex computation required in WPSD can be parallelized in a SIMD (Single Instruction Multiple Data) manner and implemented on a GPU. While such vertex‐parallel computation is often done on the GPU vertex processors, further parallelism can potentially be obtained by using the fragment processors. In this paper, we develop a parallel deformation method using the GPU fragment processors. Joint weights for each vertex are automatically calculated from sample poses, thereby reducing manual effort and enhancing the quality of WPSD as well as SSD (Skeletal Subspace Deformation). We show sufficient speed‐up of SSD, PSD (Pose Space Deformation) and WPSD to make them suitable for real‐time applications.

Categories and Subject Descriptors (according to ACM CCS): I.3.1 [Computer Graphics]: Hardware Architecture‐Parallel processing, I.3.5 [Computer Graphics]: Computational Geometry and Object Modeling‐Curve, surface, solid and object modeling, I.3.7 [Computer Graphics]: Three‐Dimensional Graphics and Realism‐Animation.
Dancing‐to‐Music Character Animation
Authors: Shiratori Takaaki , Nakazawa Atsushi , Ikeuchi Katsushi
Published: December 2006

In computer graphics, considerable research has been conducted on realistic human motion synthesis. However, most research does not consider human emotional aspects, which often strongly affect human motion. This paper presents a new approach for synthesizing dance performance matched to input music, based on the emotional aspects of dance performance. Our method consists of a motion analysis, a music analysis, and a motion synthesis based on the extracted features. In the analysis steps, motion and music feature vectors are acquired. Motion vectors are derived from motion rhythm and intensity, while music vectors are derived from musical rhythm, structure, and intensity. For synthesizing dance performance, we first find candidate motion segments whose rhythm features are matched to those of each music segment, and then we find the motion segment set whose intensity is similar to that of music segments. Additionally, our system supports having animators control the synthesis process by assigning desired motion segments to the specified music segments. The experimental results indicate that our method actually creates dance performance as if a character was listening and expressively dancing to the music.

Categories and Subject Descriptors (according to ACM CCS): I.3.7 [Computer Graphics]: Three‐Dimensional Graphics and Realism Animation; J.5 [Arts and Humanities]: Performing Arts Music
Wrinkling Coarse Meshes on the GPU
Authors: Loviscach J.
Published: December 2006

The simulation of complex layers of folds of cloth can be handled through algorithms which take the physical dynamics into account. In many cases, however, it is sufficient to generate wrinkles on a piece of garment which mostly appears spread out. This paper presents a corresponding fully GPU‐based, easy‐to‐control, and robust method to generate and render plausible and detailed folds. This simulation is generated from an animated mesh. A relaxation step ensures that the behavior remains globally consistent. The resulting wrinkle field controls the lighting and distorts the texture in a way which closely simulates an actually deformed surface. No highly tessellated mesh is required to compute the position of the folds or to render them. Furthermore, the solution provides a 3D paint interface through which the user may bias the computation in such a way that folds already appear in the rest pose.

Categories and Subject Descriptors (according to ACM CCS): I.3.7 [Computer Graphics]: Animation, I.3.7 [Computer Graphics]: Color, shading, shadowing, and texture
Sweep‐based Freeform Deformations
Authors: Yoon Seung‐Hyun , Kim Myung‐Soo
Published: December 2006

We propose a sweep‐based approach to the freeform deformation of three‐dimensional objects. Instead of using a volume enclosing the whole object, we approximate only its deformable parts using sweep surfaces. The vertices on the object boundary are bound to the sweep surfaces and follow their deformation. Several sweep surfaces can be organized into a hierarchy so that they interact with each other in a controlled manner. Thus we can support intuitively plausible shape deformation of objects of arbitrary topology with multiple control handles. A sweep‐based approach also provides important advantages such as volume preservation. We demonstrate the effectiveness of our technique in several examples.

Categories and Subject Descriptors (according to ACM CCS): I.3.5 [Computational Geometry and Object Modeling]: Curve, surface, solid, and object representations
Cache‐Efficient Layouts of Bounding Volume Hierarchies
Authors: Yoon Sung‐Eui , Manocha Dinesh
Published: December 2006

We present a novel algorithm to compute cache‐efficient layouts of bounding volume hierarchies (BVHs) of polygonal models. Our approach does not make any assumptions about the cache parameters or block sizes of the memory hierarchy. We introduce a new probabilistic model to predict the runtime access patterns of a BVH. Our layout computation algorithm utilizes parent‐child and spatial localities between the accessed nodes to reduce both the number of cache misses and the size of the working set. Our algorithm also works well for spatial partitioning hierarchies including kd‐trees. We use our algorithm to compute layouts of BVHs and spatial partitioning hierarchies of large models composed of millions of triangles. We compare our cache‐efficient layouts with other layouts in the context of collision detection and ray tracing. In our benchmarks, our layouts consistently show better performance over other layouts and improve the performance of these applications by 26%–300%without any modification of the underlying algorithms or runtime applications.

Categories and Subject Descriptors (according to ACM CCS): I.3.3 [Computer Graphics]: Hierarchy and Geometric Transformations
Ray Tracing Animated Scenes using Motion Decomposition
Authors: Günther Johannes , Friedrich Heiko , Wald Ingo , Seidel Hans‐Peter , Slusallek Philipp
Published: December 2006

Though ray tracing has recently become interactive, its high precomputation time for building spatial indices usually limits its applications to walkthroughs of static scenes. This is a major limitation, as most applications demand support for dynamically animated models. In this paper, we present a new approach to ray trace a special but important class of dynamic scenes, namely models whose connectivity does not change over time and for which all possible poses are known in advance.

We support these kinds of models by introducing two new concepts: motion decomposition, and fuzzy kd‐trees. We analyze the animation and break the model down into submeshes with similar motion. For each of these submeshes and for every time step, we calculate a best affine transformation through a least square approach. Any residual motion is then captured in a single "fuzzy kd‐tree" for the entire animation.

Together, these techniques allow for ray tracing animations without rebuilding the spatial index structures for the submeshes, resulting in interactive frame rates of 5 to 15 fps even on a single CPU.

Categories and Subject Descriptors (according to ACM CCS): I.3.7 [Computer Graphics]: Ray tracing I.3.6 [Methodology and Techniques]: Graphics data structures and data types