bluuebunny/crossref_metadata_2025_split huggingface dataset:
Integrated minimum-set primers and unique probe design algorithms for differential detection on symptom-related pathogens
Authors: Huang Yu-Cheng , Chang Chun-Fan , Chan Chen-hsiung , Yeh Tze-Jung , Chang Ya-Chun , Chen Chaur-Chin , Kao Cheng-Yan 
Published: October 2005

Abstract
Motivation: Differential detection on symptom-related pathogens (SRP) is critical for fast identification and accurate control against epidemic diseases. Conventional polymerase chain reaction (PCR) requires a large number of unique primers to amplify selected SRP target sequences. With multiple-use primers (mu-primers), multiple targets can be amplified and detected in one PCR experiment under standard reaction condition and reduced detection complexity. However, the time complexity of designing mu-primers with the best heuristic method available is too vast. We have formulated minimum-set mu-primer design problem as a set covering problem (SCP), and used modified compact genetic algorithm (MCGA) to solve this problem optimally and efficiently. We have also proposed new strategies of primer/probe design algorithm (PDA) on combining both minimum-set (MS) mu-primers and unique (UniQ) probes. Designed primer/probe set by PDA-MS/UniQ can amplify multiple genes simultaneously upon physical presence with minimum-set mu-primer amplification (MMA) before intended differential detection with probes-array hybridization (PAH) on the selected target set of SRP.
Results: The proposed PDA-MS/UniQ method pursues a much smaller number of primers set compared with conventional PCR. In the simulation experiment for amplifying 12 669 target sequences, the performance of our method with 68% reduction on required mu-primers number seems to be superior to the compared heuristic approaches in both computation efficiency and reduction percentage. Our integrated PDA-MS/UniQ method is applied to the differential detection on 9 plant viruses from 4 genera with MMA and PAH of 11 mu-primers instead of 18 unique ones in conventional PCR while amplifying overall 9 target sequences. The results of wet lab experiments with integrated MMA-PAH system have successfully validated the specificity and sensitivity of the primers/probes designed with our integrated PDA-MS/UniQ method.
Contact: cykao@csie.ntu.edu.tw
Supplementary information:
Haplotype-based linkage disequilibrium mapping via direct data mining
Authors: Li Jing , Jiang Tao 
Published: October 2005

Abstract
Motivation: With the availability of large-scale, high-density single-nucleotide polymorphism markers and information on haplotype structures and frequencies, a great challenge is how to take advantage of haplotype information in the association mapping of complex diseases in case–control studies.
Results: We present a novel approach for association mapping based on directly mining haplotypes (i.e. phased genotype pairs) produced from case–control data or case–parent data via a density-based clustering algorithm, which can be applied to whole-genome screens as well as candidate-gene studies in small genomic regions. The method directly explores the sharing of haplotype segments in affected individuals that are rarely present in normal individuals. The measure of sharing between two haplotypes is defined by a new similarity metric that combines the length of the shared segments and the number of common alleles around any marker position of the haplotypes, which is robust against recent mutations/genotype errors and recombination events. The effectiveness of the approach is demonstrated by using both simulated datasets and real datasets. The results show that the algorithm is accurate for different population models and for different disease models, even for genes with small effects, and it outperforms some recently developed methods.
Availability: The software, HapMiner, and Supplementary materials are available on the authors' website at
Contact: jingli@eecs.case.edu
Automatic term list generation for entity tagging
Authors: Sandler Ted , Schein Andrew I. , Ungar Lyle H. 
Published: October 2005

Abstract
Motivation: Many entity taggers and information extraction systems make use of lists of terms of entities such as people, places, genes or chemicals. These lists have traditionally been constructed manually. We show that distributional clustering methods which group words based on the contexts that they appear in, including neighboring words and syntactic relations extracted using a shallow parser, can be used to aid in the construction of term lists.
Results: Experiments on learning lists of terms and using them as part of a gene tagger on a corpus of abstracts from the scientific literature show that our automatically generated term lists significantly boost the precision of a state-of-the-art CRF-based gene tagger to a degree that is competitive with using hand curated lists and boosts recall to a degree that surpasses that of the hand-curated lists. Our results also show that these distributional clustering methods do not generate lists as helpful as those generated by supervised techniques, but that they can be used to complement supervised techniques so as to obtain better performance.
Availability: The code used in this paper is available from
Contact: tsandler@seas.upenn.edu
Gene selection using support vector machines with non-convex penalty
Authors: Zhang Hao Helen , Ahn Jeongyoun , Lin Xiaodong , Park Cheolwoo 
Published: October 2005

AbstractMotivation: With the development of DNA microarray technology, scientists can now measure the expression levels of thousands of genes simultaneously in one single experiment. One current difficulty in interpreting microarray data comes from their innate nature of ‘high-dimensional low sample size’. Therefore, robust and accurate gene selection methods are required to identify differentially expressed group of genes across different samples, e.g. between cancerous and normal cells. Successful gene selection will help to classify different cancer types, lead to a better understanding of genetic signatures in cancers and improve treatment strategies. Although gene selection and cancer classification are two closely related problems, most existing approaches handle them separately by selecting genes prior to classification. We provide a unified procedure for simultaneous gene selection and cancer classification, achieving high accuracy in both aspects.Results: In this paper we develop a novel type of regularization in support vector machines (SVMs) to identify important genes for cancer classification. A special nonconvex penalty, called the smoothly clipped absolute deviation penalty, is imposed on the hinge loss function in the SVM. By systematically thresholding small estimates to zeros, the new procedure eliminates redundant genes automatically and yields a compact and accurate classifier. A successive quadratic algorithm is proposed to convert the non-differentiable and non-convex optimization problem into easily solved linear equation systems. The method is applied to two real datasets and has produced very promising results.Availability: MATLAB codes are available upon request from the authors.Contact: hzhang@stat.ncsu.eduSupplementary information:
PilZ domain is part of the bacterial c-di-GMP binding protein
Authors: Amikam Dorit , Galperin Michael Y. 
Published: October 2005

Abstract
Recent studies identified c-di-GMP as a universal bacterial secondary messenger regulating biofilm formation, motility, production of extracellular polysaccharide and multicellular behavior in diverse bacteria. However, except for cellulose synthase, no protein has been shown to bind c-di-GMP and the targets for c-di-GMP action remain unknown. Here we report identification of the PilZ (‘pills’) domain (Pfam domain PF07238) in the sequences of bacterial cellulose synthases, alginate biosynthesis protein Alg44, proteins of enterobacterial YcgR and firmicute YpfA families, and other proteins encoded in bacterial genomes and present evidence indicating that this domain is (part of) the long-sought c-di-GMP-binding protein. Association of the PilZ domain with a variety of other domains, including likely components of bacterial multidrug secretion system, could provide clues to multiple functions of the c-di-GMP in bacterial pathogenesis and cell development.
Contact: galperin@ncbi.nlm.nih.gov
Supplementary information:
Short‐Chain Fatty Acid Induces Intestinal Mucosal Injury in Newborn Rats and Down‐Regulates Intestinal Trefoil Factor Gene Expression In Vivo and In Vitro
Authors: Lin Jing , Peng Luying , Itzkowitz Steven , Holzman Ian R , Babyatsky Mark W 
Published: October 2005

ABSTRACTBackground:Luminal administration of short‐chain fatty acids (SCFAs) induces dose‐dependent intestinal mucosal injury in newborn rats. However, the mechanism underlying the injurious effects of SCFAs on intestinal mucosa in neonates is unclear. Intestinal trefoil factor (ITF) is a factor important for the maintenance and repair of the intestinal mucosal barrier. Regulation of ITF gene expression by SCFAs may be involved as one of the mechanisms.Objectives:To examine the effect of butyrate‐induced colonic injury on ITF gene expression in vivo and to determine the molecular mechanisms underlying the butyrate regulation of ITF gene expression in vitro.Methods:Whole‐section colonic tissues from 9‐ to 10‐day‐old Sprague‐Dawley rats that have received butyric acid at two different concentrations (150 mmol/L and 300 mmol/L) and for different time periods were processed for total RNA extraction and Northern blot analysis. Littermates that received normal saline or lactic acid at 300 mmol/L served as controls. The effect of butyrate on ITF gene expression was also examined in vitro with human colonic epithelial LS 174T cells. To further define ITF gene regulation by butyrate, transient transfection assays were performed on a 930 bp human ITF promoter‐luciferase reporter gene plasmid in LS174T cells with or without the presence of butyrate.Results:Concurrent with mucosal injury, butyric acid inhibited ITF gene expression in colonic tissues of newborn rats as well as in intestinal epithelial cells in a dose‐ and time‐dependent manner. Furthermore, butyrate reduced ITF promoter report gene activity in transfected LS174T cell, suggesting that butyric acid regulation of ITF gene is by way of a specific ITF promoter.Conclusions:Butyric acid induced‐intestinal mucosal injury in newborn rats is associated with down‐regulation of ITF gene expression. The changes in ITF gene expression in vivo may play a role in the pathogenesis of SCFA‐induced intestinal mucosal injury.
Liver Histology and Alanine Aminotransferase Levels in Children and Adults with Chronic Hepatitis C Infection
Authors: Murray Karen F , Finn Laura S , Taylor Shari L , Seidel Kristy D , Larson Anne M 
Published: October 2005

ABSTRACTBackground:Chronic hepatitis C is often a mild disease in children, but whether this is related to younger age or shorter duration of infection is unclear. Histologic severity has been shown to correlate with duration of infection regardless of age.Objectives:We compared histologic findings in children and adults with chronic hepatitis C while controlling for sex, duration of infection, hepatitis C virus (HCV)‐RNA level, and genotype.Methods:Twenty‐one children and 52 adults whose infection was less than 20 years in duration and who had undergone a liver biopsy were included. Two blinded liver pathologists reviewed the liver biopsies and scored inflammatory activity and fibrosis using the modified Knodell scoring system.Results:The groups were the same with respect to HCV‐RNA level (P = 0.8), and genotype (P = 0.6) but differed in duration of disease (P = 0.01) and sex composition (P = 0.005). Covariate analysis showed no influence of genotype, duration of infection, or HCV‐RNA level on outcome. In controlling for sex, children had significantly milder liver disease and alanine aminotransferase (ALT) elevations.Conclusions:With equal duration of infection, HCV‐RNA level, and genotype, children have lower serum ALT levels and less severe liver disease than adults infected with HCV.
Double‐Blind Randomized Evaluation of Clinical and Biological Tolerance of Polyethylene Glycol 4000 Versus Lactulose in Constipated Children
Authors: Dupont Christophe , Leluyer Bernard , Maamri Nassira , Morali Alain , Joye Jean‐Pierre , Fiorini Jean‐Marc , Abdelatif A , Baranes C , Benoît S , Benssoussan A , Boussioux J L , Boyer P , Brunet E , Delorme J , François‐Cecchin S , Gottrand F , Grassart M , Hadji S , Kalidjian A , Languepin J , Leissler C , Lejay D , Livon D , Lopez J P , Mougenot J F , Risse J C , Rizk C , Roumaneix D , Schirrer J , Thoron B , Kalach N 
Published: October 2005

ABSTRACTObjectives:To assess the safety of a polyethylene glycol (PEG) 4000 laxative without additional salts in pediatric patients.Study Design:This was a 3‐month multicenter, randomized, double‐blind, double‐dummy, lactulose‐controlled, parallel study enrolling 96 ambulatory constipated children aged 6 months to 3 years, treated daily with 4‐8 g PEG or 3.33 g‐6.66 g lactulose. Total protein, albumin, iron, electrolytes, and vitamins B9 (folates), A and D (25OHD3) were measured in blood before and after treatment (day 84) in a central laboratory.Results:The percentage of children with at least one value out of normal range at day 84 with respect to baseline status (with or without at least one value out of normal range), i.e. the primary endpoint, was 87% and 90% in the PEG and lactulose groups, respectively, without any difference between groups. The whole blood parameters showed no qualitative or quantitative treatment‐related changes. Vitamin A values were above normal range in 56% and 41% of children at baseline versus 33% and 36% at day 84 in the PEG and lactulose groups, respectively. Iron values were similarly under normal range in 47% and 51% at baseline versus 42% and 51% at day 84. Clinical tolerance was similar for both treatments except for vomiting and flatulence, which were significantly higher with lactulose. Significantly higher improvements were evidenced with PEG regarding stool consistency, appetite, fecaloma and use of additional laxatives.Conclusion:This 3‐month study in 96 constipated children aged 6 months to 3 years confirms the long‐term tolerance of PEG 4000 in pediatrics and indicates a PEG efficacy similar to or greater than that of lactulose.
Prevalence of Celiac Disease in Brazilian Children and Adolescents with Type 1 Diabetes Mellitus
Authors: Baptista Márcia Luiza , Koda Yu Kar Ling , Mitsunori Renato , Nisihara  , Ioshii Sérgio Ossamu 
Published: October 2005

ABSTRACTObjective:A previously unrecognized high prevalence of celiac disease (CD) has been found by screening among European and North American patients with type 1 diabetes mellitus (DM 1). The prevalence of CD among Brazilian children with DM1 is not known. This study was conducted to determine the prevalence of CD in Brazilian children and adolescents with DM 1.Methods:One hundred and four children and adolescents with DM 1 (52 males and 52 females; age range 22 months ‐ 19 years) and 105 age and gender‐matched control participants were screened for CD using the IgA antiendomysial antibody test (IgA‐EmA) and total serum IgA. A small bowel biopsy was performed in all patients with positive IgA‐EmA.Results:Nine of 104 diabetic patients (8.7%) had a positive IgA‐EmA. Biopsies were normal in four patients, two had partial or subtotal villous atrophy with elevated intraepithelial lymphocyte (IEL) counts, and three showed partial villous atrophy but with IEL counts under the maximun limit adopted (40 IEL/100 enterocytes). EmA‐IgA positive patients had mild, non‐specific gastrointestinal complaints including dyspepsia, abdominal pain, flatulence and constipation. All control participants had negative results for IgA‐EmA.Conclusion:The prevalence of CD in a group of Brazilian pediatric DM 1 patients was at least 4.8%, a prevalence comparable to European and North American studies. The high prevalence of CD among DM 1 emphasizes the need for routine screening in all countries including Brazil.
A Pilot Test of the Addition of Zinc to the Current Case Management Package of Diarrhea in a Primary Healthcare Setting
Authors: Bhandari Nita , Mazumder Sarmila , Taneja Sunita , Dube Brinda , Black Robert E , Fontaine Olivier , Mahalanabis Dilip , Bhan Maharaj Kishan 
Published: October 2005

ABSTRACTZinc is recommended for the treatment of acute diarrhea in children but the effect of its introduction on drug and oral rehydration solution use is unclear. Government care providers, private practitioners and community workers were trained to distribute zinc and oral rehydration solution to children seeking care for diarrhea. Periodic surveys showed that village‐based workers became a common source of diarrhea treatment and private practitioners were used less. Zinc was used in approximately half of the episodes; the prescription and use rates of oral rehydration solution packets increased from 7% at baseline to 44.9% 6 months later. Reduction in use of drugs during diarrhea ranged from 34% for tablets to 64% for injections 6 months later. The cost of treatment to families declined significantly. These findings need confirmation in a randomized controlled trial.
Safety of Percutaneous Liver Biopsy in Infants Less than Three Months Old
Authors: Azzam R K , Alonso E M , Emerick K M , Whitington P F 
Published: October 2005

ABSTRACTObjectives:To evaluate the safety, outcomes, and complications of percutaneous liver biopsies (PLB) in infants aged 0 to 3 months.Methods:We retrospectively reviewed the hospital records of all infants less than 3 months old who underwent PLB at Children's Memorial Hospital between July 1, 1997 and June 30, 2004 for complications surrounding the procedure and risk factors that might lead to complications.Results:Sixty‐six PLBs were performed in 63 infants. Most patients tolerated the procedure without complications. Twelve complications were recorded, for an overall complication rate of 18%. Of these, five were directly related to the procedure, and seven were sedation related. Three patients experienced a drop in hemoglobin greater than 2 gm/dL, one patient developed a bile leak, and one developed a skin hematoma. Seven patients had respiratory difficulty related to sedation, which manifested as increased work of breathing or decreased respiratory rate with depression in pulse oximetry.Conclusion:We conclude that PLB in young infants is associated with a somewhat higher risk of complications than in older children, particularly complications related to sedation.
Gabapentin reduces rectal mechanosensitivity and increases rectal compliance in patients with diarrhoea‐predominant irritable bowel syndrome
Authors: LEE K. J. , KIM J. H. , CHO S. W. 
Published: October 2005

SummaryBackground: Gabapentin has been shown to reduce elements of central sensitization in human experimental hyperalgesia. It remains uninvestigated whether gabapentin has beneficial effects for irritable bowel syndrome associated with visceral hypersensitivity.Aims: To evaluate the effects of gabapentin on sensory and motor function of the rectum in patients with diarrhoea‐predominant irritable bowel syndrome.Methods: Forty patients with diarrhoea‐predominant irritable bowel syndrome completed this randomized, double‐blind, placebo‐controlled, parallel‐grouped study. All patients received a barostat study and were subsequently randomized for 5‐day treatment with gabapentin 300 mg/day and then 600 mg/day or placebo. On day 6, after subjects had their morning dose, the barostat experiment was repeated.Results: The threshold pressures for bloating, discomfort and pain significantly increased after gabapentin, but not after placebo. Significant increase in the pressure and corresponding wall tension inducing discomfort or pain were observed in the gabapentin group, but not in the placebo group. Rectal compliance significantly increased after gabapentin, but not after placebo. The postprandial increase of rectal tone was not affected by gabapentin.Conclusion: Our results show that gabapentin reduces rectal sensory thresholds through attenuating rectal sensitivity to distension and enhancing rectal compliance in diarrhoea‐predominant irritable bowel syndrome patients. The clinical efficacy of this drug in irritable bowel syndrome patients warrants investigation.
Anti‐cyclic citrullinated peptide antibodies in type 1 autoimmune hepatitis
Authors: FUSCONI M. , VANNINI A. , DALL'AGLIO A. C. , PAPPAS G. , CASSANI F. , BALLARDINI G. , FRISONI M. , GRASSI A. , BIANCHI F. B. , ZAULI D. 
Published: October 2005

SummaryBackground : Besides the autoantibodies included in the diagnostic criteria of type 1 autoimmune hepatitis, many other autoantibodies have been described in this condition. Recently, antibodies against cyclic citrullinated peptide have been validated as specific diagnostic and prognostic markers of rheumatoid arthritis.Aim : To assess whether these antibodies are part of the autoantibody repertoire of type 1 autoimmune hepatitis and correlate with rheumatological manifestations.Methods : Antibodies against cyclic citrullinated peptide were tested by a commercially available enzyme‐linked immunosorbent assay.Results : The antibodies were found in 12 of 133 (9%) type 1 autoimmune hepatitis, two of 49 (4%) with primary biliary cirrhosis, one of 80 (1%) with hepatitis C virus‐related chronic liver disease and 53 of 89 (60%) with rheumatoid arthritis serum samples. High titres were found only in rheumatoid arthritis and type 1 autoimmune hepatitis. No clinical (in particular rheumatological manifestations), biochemical or immunoserological differences were detectable between antibodies against cyclic citrullinated peptide positive and negative type 1 autoimmune hepatitis sera, with the exception of rheumatoid factor, always negative in the positive ones.Conclusions : Antibodies against cyclic citrullinated peptide can be detected in a subgroup of patients with type 1 autoimmune hepatitis. They might be part of the wide range of autoantibody production characteristic of this condition and/or, less probably, be predictive of future rheumatoid arthritis development.
Comparison of the effects of intrathecal morphine and pethidine on shivering after Caesarean delivery under combined‐spinal epidural anaesthesia*
Authors: Hong J.‐Y. , Lee I. H. 
Published: October 2005

SummaryWe performed a prospective, randomised, double blind study to compare the antishivering effect of morphine and pethidine when added to intrathecal hyperbaric bupivacaine during elective Caesarean delivery under combined‐spinal epidural anaesthesia. Spinal anaesthesia consisted of either 8–10 mg of 0.5% bupivacaine alone (group B; n = 30) with 0.1 mg morphine (group BM0.1; n = 29), with 0.2 mg morphine ( group BM0.2; n = 30), or with 10 mg pethidine (group BPeth10; n = 30). The incidences of shivering were 23.3% (7/30) in group B, 17% (5/29) in group BM0.1, 13.3% (4/30) in group BM0.2 and 3.3% (1/30) in group BPeth10 (p < 0.05). The shivering intensity for each patient was significantly higher in group B than the other groups. In conclusion, intrathecal pethidine added to hyperbaric bupivacaine reduces the incidence and intensity of shivering more than does morphine (0.1 or 0.2 mg).