bluuebunny/crossref_metadata_2025_split huggingface dataset:
Ending a decade of deception: a valiant failure, a not‐so‐valiant failure, and a success story
Authors: Brooks Daniel R. , Dowling Ashley P. G. , Van Veller Marco G. P. , Hoberg Eric P. 
Published: March 2004

AbstractPrior studies involving two methods, Brooks Parsimony Analysis (BPA) and TreeMap, have found BPA to be the more reliable method. Recent criticisms leveled at these studies argue that the tests were unfairly created and biased in favor of BPA. The authors of a recent critique offered new exemplars to demonstrate flaws in BPA, plus a simple fix to correct the flaws found in TreeMap. A re‐evaluation of their exemplars clearly shows that the authors' calculations are incorrect, their understanding of the methods is lacking, and that their simple fix does not work. Additional analyses using TreeMap 2.02 are run to show that TreeMap 2.02, like TreeMap 1.0, cannot adequately deal with widespread parasites, contrary to the claims of its supporters. Furthermore, the exemplars corroborate previous findings that BPA, when calculated correctly, is more reliable than TreeMap1.0 and TreeMap 2.02 and therefore the method of choice in coevolutionary and biogeographic studies.
Transformation Series as an Ideographic Character Concept
Authors: Grant Taran , Kluge Arnold G. 
Published: March 2004

AbstractAn ideographic concept of character is indispensable to phylogenetic inference. Hennig proposed that characters be conceptualized as “transformation series”, a proposal that is firmly grounded in evolutionary theory and consistent with the method of inferring transformation events as evidence of phylogenetic propinquity. Nevertheless, that concept is usually overlooked or rejected in favor of others based on similarity. Here we explicate Hennig's definition of character as an ideographic concept in the science of phylogenetic systematics. As transformation series, characters are historical individuals akin to species and clades. As such, the related concept of homology refers to a historical identity relation and is not equivalent to or synonymous with synapomorphy. The distinction between primary and secondary homology is dismissed on the grounds that it conflates the concept of homology with the discovery operations used to detect instances of that concept. Although concern for character dependence is generally valid, it is often misplaced, focusing on functional or developmental correlation (both of which are irrelevant in phylogenetic systematics but may be valid in other fields) instead of the historical/transformational independence relevant to phylogenetic inference. As an ideographic science concerned with concrete objects and events (i.e. individuals), intensionally and extensionally defined properties are inconsistent with the individuation of characters for phylogenetic analysis, the utility of properties being limited to communicating results and facilitating future rounds of testing.
Identification of a new mouse Cd1d2 allele
Authors: Gozalbo‐López B. , Pérez‐Rosado A. , Parra‐Cuadrado J. F. , Martínez‐Naves E. 
Published: March 2004

SummaryThe mouse CD1 system is formed by two closely related genes named Cd1d1 and Cd1d2. Cd1d1 encodes a molecule that presents antigens to NKT cells. The function of the Cd1d2 gene has not been elucidated. Here we described a method to analyse variations in mouse Cd1 genes. We found a new allele for Cd1d2 characterized by a point mutation, resulting in a replacement of alanine at position 176 by a valine.
High birth weight is associated with human leukocyte antigen (HLA) DRB1*13 in full‐term infants
Authors: Aroviita P. , Partanen J. , Sistonen P. , Teramo K. , Kekomäki R. 
Published: March 2004

SummaryIn cord blood banking, substantial amounts of data on infants and cord blood are gathered at high cost, including birth weights and human leukocyte antigen (HLA) genotypes. As certain HLA alleles have been associated with protective host responses, it is possible that an HLA allele, or another factor linked to it, might even affect normal intrauterine growth. We explored cord blood bank data (n = 1381 infants) to elucidate whether there is an association between birth weight and HLA class II (DRB1) alleles. HLA DRB1 data were available from 1263 infants. We observed an association between birth weight and HLA DRB1*13, which was over‐represented among full‐term infants with the highest birth weights. The association remained when the birth weight was corrected for varying gestational age (relative birth weight) according to gender (P = 0.015). After correction of the P‐value for multiple comparisons, the association was not statistically significant. However, when the birth weights of all infants were analysed for the effect of DRB1*13, infants positive for HLA DRB1*13 (n = 319) were found to have higher birth weights than infants negative for this allele (n = 944; median 3690 g vs. 3650 g, respectively; P = 0.044). Although the difference in median birth weight was only 40 g, it may be considered significant because it appeared after segregation of the infants into two groups according to the single HLA class II allele group earlier associated with protection against, for example, childhood type 1 diabetes and certain infectious diseases. The present finding may thus suggest identification of a new factor affecting normal intrauterine growth.
Cloning of rat lymphocyte activation gene‐3 (Lag3; CD223) cDNA and its mRNA expression in rat tissues*
Authors: Chun T. , Cho H.‐S. , Chung Y.‐H. 
Published: March 2004

SummaryRat lymphocyte activation gene‐3 (Lag3; CD223) cDNA contains an open reading frame (1575 bp) encoding 525 amino acids. Rat Lag3 mRNA transcript was detected as a single species of approximately 2 kb from phytohemagglutinin (PHA)‐stimulated lymphocytes. Further analysis revealed that rat Lag3 mRNA was mainly expressed in lymphoid tissues.
Genotyping BoLA‐DRB3 alleles in Brazilian Dairy Gir cattle (Bos indicus) by temperature‐gradient gel electrophoresis (TGGE) and direct sequencing
Authors: Da Mota A. F. , Martinez M. L. , Coutinho L. L. 
Published: March 2004

SummaryBoLA‐DRB3 is a gene of the major histocompatibility complex (MHC) in cattle. The product of the BoLA‐DRB3 gene is a beta chain of an MHC class II molecule, a glycoprotein expressed on the surface of antigen‐presenting cells (APCs). Responses of CD4+ T lymphocytes to peptides are dependent on the presentation of peptide ligands bound to class II molecules on APCs. Genotyping of the BoLA‐DRB3 gene is relatively complex due to the extensive polymorphism of this locus. Current techniques for assignment of genotypes are polymerase chain reaction–restriction fragment length polymorphism (PCR‐RFLP), direct sequencing of PCR products, cloning‐sequencing, polymerase chain reaction using sequence‐specific oligonucleotide probes (PCR‐SSOP), and denaturant‐gradient gel electrophoresis. These techniques are time‐consuming, do not discriminate all possible alleles, or are not readily reproducible. The objective of this study was to genotype BoLA‐DRB3 using temperature‐gradient gel electrophoresis (TGGE) to separate alleles before sequencing. PCRs using 28 DNA samples from Gir Dairy cattle (a Brazilian breed of Bos indicus) were submitted to TGGE. New PCR products were generated from separated alleles, purified, and sequenced. Allele separation was possible in 21 out of 26 heterozygote samples (81%). Results indicate that two sequence reads (forward and reverse) were sufficient for accurate genotyping of BoLA‐DRB3 alleles. Separation of alleles by TGGE provides high‐throughput, reliable typing of BoLA‐DRB3, which is critical in disease association studies in cattle.
Allele‐specific binding to the −308 single nucleotide polymorphism site in the tumour necrosis factor‐alpha promoter
Authors: Baseggio L. , Bartholin L. , Chantome A. , Charlot C. , Rimokh R. , Salles G. 
Published: March 2004

SummarySingle nucleotide polymorphisms in the tumour necrosis factor alpha (TNF‐α) promoter region may modulate TNF‐α gene transcriptional activity by modifying the binding of transcription factors. Here we confirm that a specific DNA complex binds preferentially the variant TNF2 allele in various cell types and demonstrate that activating protein (AP)‐2, myeloid zinc finger gene 1 (MZF‐1) and Sp1 are not involved in this complex.
Transforming growth factor‐β1 genotype in sporadic breast cancer patients from India: status of enhancer, promoter, 5′‐untranslated‐region and exon‐1 polymorphisms
Authors: Saha A. , Gupta V. , Bairwa N. K. , Malhotra D. , Bamezai R. 
Published: March 2004

SummaryTransforming growth factor beta (TGF‐β) is an example for a large and still‐growing family of growth factors. TGF‐β1 is known to act both as a tumour suppressor and as a stimulator of tumour progression. This study examines the relationship amongst putative enhancer, promoter, 5′‐untranslated‐region (UTR) and exon‐1 polymorphisms of the TGF‐β1 gene (region I from −1881 to −1613; region II from −1410 to −1123, and region III from −55 to +176, as per human genome organisation (HUGO) nomenclature) in 26 breast cancer patients and 97 healthy control subjects. The germline and somatic status of the four known polymorphisms was ascertained, and a significant difference was observed for the germline C/T and T/T genotype distribution between patients and controls in comparison to C/C genotypes at position −1349 (χ2 = 6.193; P = 0.009). In addition to the somatic variations observed for some of the regions studied, in 10/26 (38%) sporadic breast cancer cases, a novel somatic mutation in codon 47 of exon 1 (GenBank accession number AY059373) was also detected in tumour samples. The risk of cancer was found to be significant (OR = 4.525) for the −1349 C/T and T/T genotype background, suggesting that this genetic background may act as a risk factor for sporadic breast cancer.
Variation of HLA class II genes in the Nganasan and Ket, two aboriginal Siberian populations
Authors: Uinuk‐ool T. S. , Takezaki N. , Derbeneva O. A. , Volodko N. V. , Sukernik R. I. 
Published: March 2004

SummaryAllelic frequencies at the three most polymorphic loci of the HLA class II region (DRB1, DQA1 and DQB1) were determined in the Nganasan and Ket, the remnants of the two most ancient groups in the Lower Yenisey River/Taimyr Peninsula region in northern Siberia. By single‐stranded conformational polymorphism typing, verified by sequencing, 19 HLA‐DRB1‐DQA1‐DQB1 haplotypes and 15 HLA‐DRB1, seven DQA1 and 11 DQB1 alleles were found. The most frequent alleles were DRB1*1301 (23.5%), DQA1*0103 (29.4%), *0501/03/05 (29.4%), and DQB1*0301/09 (32.4%) in the Ket, and DRB1*0901 (25%), DQA1*0301 (39.6%), and DQB1*0301/09 (37.5%) in the Nganasan. The distribution patterns and comprehensive phylogenic analysis based on the haplotype frequencies of 17 Siberian populations suggest that the founders of both the Ket and the Nganasan came from Palaeolithic populations in the Altai‐Sayan Upland.
Analysis of the CC chemokine receptor 5 (CCR5) Δ32 polymorphism in Behçet's disease
Authors: Yang X. , Ahmad T. , Gogus F. , Wallace G. R. , Madanat W. , Kanawati C. A. , Stanford M. R. , Fortune F. , Jewell D. P. , Marshall S. E. 
Published: March 2004

SummaryChemokines are important determinants of the early inflammatory response. The CC chemokine receptor 5 (CCR5) Δ32 variant results in a non‐functional form of the chemokine receptor, and has been implicated in a variety of immune‐mediated diseases. To investigate its role in the pathogenesis of Behçet's disease, we studied 350 patients and 519 healthy controls from three ethnic groups. While significant inter‐ethnic variation in allele frequency was observed, no association was identified with disease, even when data were stratified by the known susceptibility gene HLA‐B*51.
A review of sacral nerve stimulation for the treatment of faecal incontinence
Authors: Kenefick N. J. , Christiansen J. 
Published: March 2004

AbstractSacral nerve stimulation is an emerging surgical technique that uses chronic low‐level electrical stimulation, applied to the nerves of the sacral plexus, to produce a clinically beneficial physiological effect on the lower bowel, pelvic floor and anal canal. Faecal incontinence is common, maximal conservative therapy may improve some patients but many require surgery. Results are variable and often unsatisfactory and further options are limited, the traditional end‐point being the formation of a colostomy. Sacral nerve stimulation appears to be an alternative treatment that is successful, has low morbidity, is maintained in the medium term and associated with an improved quality of life. The technique has the advantage of a minimally invasive test procedure with high predictive value and the surgery is minor. The underlying mechanism of action although predominately neurological in nature remains to be determined. Precise patient selection is currently unclear however, results are superior to other techniques.
The effects of high field strength MRI on electrodes and pulse generator in dynamic graciloplasty
Authors: Rongen M.‐J. G. M. , Beets‐Tan R. G. H. , Backes W. H. , Baeten C. G. M. I. 
Published: March 2004

AbstractObjective  Dynamic graciloplasty is a treatment for intractable faecal incontinence. A gracilis muscle is transposed around the anus and stimulated with an implanted pulse generator (IPG). This in vitro study was designed to determine the safety of MRI in patients with implanted electrodes and pulse generators for dynamic graciloplasty.Methods  Temperatures were measured with fiberoptic probes around the devices in a cadaver model. Current was measured with an oscilloscope connected to electrodes and IPG. Movement and IPG parameter setting were observed before, during and after testing.Results  Minor temperature increase under 1°C were observed around the electrodes. Amplitudes measured were within the range of –1 and +1 Volt. No movement or changing of IPG parameters was noted.Conclusion  Changes noted are well within physiological ranges. Dynamic graciloplasty is not a contraindication for high field strength MRI.
Anal function following third degree tears
Authors: Mackenzie N. , Parry L. , Tasker M. , Gowland M. R. , Michie H. R. , Hobbiss J. H. 
Published: March 2004

AbstractObjective  To assess the anal function of women who have suffered a third degree perineal tear during parturition.Patients  Fifty‐three consecutive women who sustained a third degree tear, between January 1998 and March 2000, at the Princess Anne Maternity Unit, Royal Bolton Hospital were assessed.Methods  Women were assessed at 3 months post partum using the Cleveland Clinic Incontinence Score, digital assessment of anal sphincter and endo‐anal ultrasound scan.Results  At 3 months post partum 75% of the participants had no symptoms of anal incontinence, 18% had mild symptoms and 7% had more severe symptoms. Anal endosonography demonstrated normal anal sphincters in 66% of participants, an abnormality in the external sphincter in 29% and a defect in both sphincters in 2%. There was poor correlation between symptoms and scan defects.Conclusion  The incidence of anal incontinence following repair of a third degree tear was not high and it is unlikely that we are missing a hidden pool of symptomatic women. No major change in management policy is required. The routine assessment of anal function in women who had sustained a third degree tear was appreciated by the women and enabled us to identify the small portion of women with significant symptoms.
Can anal manometry predict anal incontinence after fistulectomy in males?
Authors: Pescatori M. , Ayabaca S. , Caputo D. 
Published: March 2004

AbstractBackground  Disordered continence is frequently reported after operations for anal fistulae and pre‐operative anorectal physiology may be carried out prior to surgery to improve functional outcome. Elderly patients and multiparous females are at higher risk for incontinence, whereas males under 60 have stronger sphincters. The aim of this study was to investigate the predictive role of anal manometry and the causes of postoperative soiling and its effect on the quality of life in males with intact sphincters undergoing excision of either trans or supra sphincteric fistulae.Methods  Thirty‐eight patients (median age 47 years) were analysed retrospectively. None had previous anal surgery and all were fully continent. Five had Crohn's disease. Anal pressures and rectal sensation were evaluated prior to fistulectomy by means of anal manometry in all cases and after surgery in those who had postoperative incontinence. A cutting seton was used in 17 patients, a rectal advancement flap in 15 and a double rectal‐cutaneous flap in six. None had a lay–open. The intersphincteric plane was explored and drained in all cases. A previously described incontinence grading and score was used to assess postoperative soiling. The median follow‐up was 22 (range 5–89) months. The patients with postoperative anal incontinence were evaluated with the Gastrointestinal quality of Life Index Questionnaire (0:poor, 4:good) at a median follow‐up of 49 months.Results  Twenty‐nine (76%) patients were continent after surgery, whereas 9 (24%) complained of some degree of anal incontinence (minor in 4, severe in 1, the 1–6 incontinence score being 3.7 ± 1.3 (mean ± s.d.m.). Their Quality of life score was 3.8 ± 0.5 (mean ± sdm). None of them had Crohn's disease, five had frequent diarrhoea, four had a reintervention for either anal fissure or recurrent fistula (two), three had a postseton anal deformity. No difference was found between continent and incontinent patients as far as pre‐operative anal pressures were concerned, but the maximum rectal volume threshold was significantly higher in incontinent patients, 165 ± 67 vs. 123 ± 49 ml of air (P = 0.04).Conclusions  Sphincter division, diarrhoea and anal deformity may cause soiling after fistulectomy in males and it does not severely affect quality of life. Surgery rather than manometry may predict it and rectal sensation may play a role which needs further investigation.
The use of Ligasure™ haemorrhoidectomy in patients taking oral anticoagulation therapy
Authors: Lawes D. A. , Palazzo F. F. , Clifton M. A. 
Published: March 2004

AbstractObjectives  To assess the safety of Ligasure™ haemorrhoidectomy in treating patients on long‐term anticoagulation therapy.Method  Three patients taking warfarin underwent Ligasure™ haemorrhoidectomy for prolapsing haemorrhoids.Results  Each had a successful procedure without complications.Conclusion  Ligasure™ haemorrhoidectomy can be safely performed in anticoagulated patients and reduces in‐patient hospital stay.
Is routine pouchogram prior to ileostomy closure in colonic J‐pouch really necessary?
Authors: Da Silva G. M. , Wexner S. D. , Gurland B. , Gervaz P. , Moon Seong Do , Efron J. , Nogueras J. J. , Weiss E. G. , Vernava A. M. , Zmora O. 
Published: March 2004

AbstractIntroduction  Colonic J‐pouch with coloanal anastomosis has gained popularity in the surgical treatment of middle and lower rectal pathologies. If a diverting ileostomy is performed, a pouchogram is frequently performed prior to ileostomy closure. The aim of this study was to assess the routine use of pouchogram prior to ileostomy closure in patients with colonic J pouch‐anal anastomosis.Methods  All patients who underwent a colonic J pouch‐anal anastomosis between 1990 and 2000 were retrospectively reviewed. Patients with temporary loop ileostomy who had pouchogram prior to ileostomy closure were included. Pouchogram results were compared to the patient's post ileostomy closure clinical outcome. Sensitivity, specificity and predictive values of pouchogram were assessed.Results  Eighty‐four patients had a pouchogram prior to ileostomy closure. Radiological abnormalities were evident in 6 patients, including 4 strictures, 1 pouch‐vaginal fistula and 1 leak. Of these findings, 4 were false positives (3 strictures and 1 leak) and two were true positives (1 stricture and 1 pouch‐vaginal fistula). The actual rate of pouch complications was 9.5% (8 complications) including 3 anastomotic leaks, all with normal pouchogram, 3 strictures requiring dilatation under anaesthesia, only one detected by pouchogram, and 2 pouch‐vaginal fistulas, only one diagnosed by pouchogram. The sensitivity and specificity of pouchogram, respectively, was 0 and 98% for anastomotic leak, 33 and 96% for stricture, and 50 and 100% for pouch‐vaginal fistula. Overall, pouchogram changed the management in only 1 of 84 patients.Conclusion  Pouchogram has a low sensitivity in predicting complications following ileostomy closure in patients after colonic J‐pouch anal anastomosis and rarely changes the management of these patients. The use of pouchogram prior to ileostomy closure may be unnecessary and should be reserved in cases of clinical suspicion of complications.
The two week referral for colorectal cancer: a retrospective analysis
Authors: Barwick T. W. , Scott S. B. , Ambrose N. S. 
Published: March 2004

AbstractObjective  The two‐week referral (TWR) system was introduced in July 2000 to address the delays in referral, diagnosis and treatment of colorectal cancer (CRC) and lessen the associated psychological morbidity of prolonged waiting. General practitioners complete a proforma outlining ‘high‐risk’ criteria for CRC to ensure an urgent referral within 14 days. The aim of the study was to analyse the TWR process and the proforma criteria.Patients and methods  One hundred and forty‐nine two‐week referral proforma were retrospectively reviewed between January and August 2001. The waiting times and proforma data, together with investigations performed and diagnoses made were gathered for 144 patients. Three did not attend clinic and two sets of notes were missing.Results  Ninety‐six percent of patients (n = 144) were two week compliant and 14 CRC (10%) were diagnosed. The most common referral symptom was a recent change in bowel habit (36.6%) but specificity for all criteria was low. The highest diagnostic yield was a palpable abdominal or rectal mass where 16.7% had CRC and iron deficiency anaemia had high sensitivity (90%) for surgical pathology. Per rectum examination and haemoglobin analysis by general practitioners was infrequently performed.Discussion  Our study has shown that CRC is difficult to diagnose by history and examination alone with a 10% detection rate. CRC incidence in TWR may be improved by primary care through routine rectal examinations, increased detection of iron deficiency anaemia and public education to reduce presentation via other referral routes. Further studies are needed to address these issues.