Signal peptide cleavage site prediction

A series of reports - and extracts of reports - from the Freedom of Information Conference, 6-7 July, 2000, New York Academy of Medicine. The conference was sponsored by BioMed Central, to promote debate about the communication and validation of biomedical research published on the internet. Details of the meeting and all presentations are available in full online at http://biomedcentral.com/info/conference.asp

     

粤北山区多孔菌科的三个新种

本文发表了广东省北部山区的多孔菌科的三个新种,它们是:薄淀粉孔菌Amylonotus tenuis Zheng et Bi;近烟色赖特卧孔菌Wrighto-poria subadusta Bi et Zheng;和迷路状粉孢菌Amylosporus daedali-formis Zheng et Bi。     

CisML: an XML-based format for sequence motif detection software

SUMMARY: CisML is an XML-based format for sequence motif detection software. This proposed standard is applicable to many types of sequence motif detection programs. It is intended to facilitate the integration of data and the comparison of results from different software packages, and to simplify the development of downstream tools. XSL stylesheets are provided for easy generation of text, html and graphical reports from CisML-formatted data. AVAILABILITY: http://zlab.bu.edu/CisML/ SUPPLEMENTARY INFORMATION: Example CisML-formatted data and XSL stylesheets for report generation are available along with the sample output.     

中国金鞘蛾属Goniodoma－新种记述(鳞翅目：鞘蛾科)

记述我国鞘蛾科一新种：中华金鞘蛾Goniodoma sinica sp. nov.。这是金鞘蛾属在我国的首次报道,对属征和世界名录进行了扼要介绍。     

Does Clinical Depression Affect the Accuracy of Self‐reported Height and Weight in Obese Women?

Objective: Recent research from a self‐report survey showed a strong association between obesity and clinical depression in women. The present analysis assessed whether differential bias in self‐reports of height and weight as a function of depression influences the apparent strength of the association. Methods: Accuracy of self‐reported height and weight was assessed in 250 obese (mean BMI=38.7 kg/m²) women, 135 of whom met the American Psychiatric Association DSM‐IV diagnostic criteria for clinical depression. Results: Depressed and non‐depressed women underreported their weight by 1.5 and 1.2 kg, respectively. They underreported their height by 0.002 and 0.003 m, respectively. Discussion: Bias in self‐reports of body weight and height is similar in depressed and non‐depressed obese women. The underreporting of weight in both groups is similar in magnitude to that seen in normal weight women. Thus, using self‐reports of height and weight seems unlikely to bias estimates of the association between obesity and clinical depression in women.     

Impact of covert duplicate publication on meta-analysis: a case study.

OBJECTIVE: To quantify the impact of duplicate data on estimates of efficacy. DESIGN: Systematic search for published full reports of randomised controlled trials investigating ondansetron''s effect on postoperative emesis. Abstracts were not considered. DATA SOURCES: Eighty four trials (11,980 patients receiving ondansetron) published between 1991 and September 1996. MAIN OUTCOME MEASURES: Percentage of duplicated trials and patient data. Estimation of antiemetic efficacy (prevention of emesis) of the most duplicated ondansetron regimen. Comparison between the efficacy of non-duplicated and duplicated data. RESULTS: Data from nine trials had been published in 14 further reports, duplicating data from 3335 patients receiving ondansetron; none used a clear cross reference. Intravenous ondansetron 4 mg versus placebo was investigated in 16 reports not subject to duplicate publication, three reports subject to duplicate publication, and six duplicates of those three reports. The number needed to treat to prevent vomiting within 24 hours was 9.5 (95% confidence interval 6.9 to 15) in the 16 non-duplicated reports and 3.9 (3.3 to 4.8) in the three reports which were duplicated (P < 0.00001). When these 19 were combined the number needed to treat was 6.4 (5.3 to 7.9). When all original and duplicate reports were combined (n = 25) the apparent number needed to treat improved to 4.9 (4.4 to 5.6). CONCLUSIONS: By searching systematically we found 17% of published full reports of randomised trials and 28% of the patient data were duplicated. Trials reporting greater treatment effect were significantly more likely to be duplicated. Inclusion of duplicated data in meta-analysis led to a 23% overestimation of ondansetron''s antiemetic efficacy.     

WIPER: Weighted in-Path Edge Ranking for biomolecular association networks

Background: In network biology researchers generate biomolecular networks with candidate genes or proteins experimentally-derived from high-throughput data and known biomolecular associations. Current bioinformatics research focuses on characterizing candidate genes/proteins, or nodes, with network characteristics, e.g., betweenness centrality. However, there have been few research reports to characterize and prioritize biomolecular associations (“edges”), which can represent gene regulatory events essential to biological processes.Method: We developed Weighted In-Path Edge Ranking (WIPER), a new computational algorithm which can help evaluate all biomolecular interactions/associations (“edges”) in a network model and generate a rank order of every edge based on their in-path traversal scores and statistical significance test result. To validate whether WIPER worked as we designed, we tested the algorithm on synthetic network models.Results: Our results showed WIPER can reliably discover both critical “well traversed in-path edges”, which are statistically more traversed than normal edges, and “peripheral in-path edges”, which are less traversed than normal edges. Compared with other simple measures such as betweenness centrality, WIPER provides better biological interpretations. In the case study of analyzing postanal pig hearts gene expression, WIPER highlighted new signaling pathways suggestive of cardiomyocyte regeneration and proliferation. In the case study of Alzheimer’s disease genetic disorder association, WIPER reports SRC:APP, AR:APP, APP:FYN, and APP:NES edges (gene-gene associations) both statistically and biologically important from PubMed co-citation.Conclusion: We believe that WIPER will become an essential software tool to help biologists discover and validate essential signaling/regulatory events from high-throughput biology data in the context of biological networks.Availability: The free WIPER API is described at discovery.informatics.uab.edu/wiper/     

Pregnancy outcomes after maternal exposure to simvastatin and lovastatin

BACKGROUND: Our objective was to determine the frequency of adverse outcomes after maternal exposure to simvastatin and/or lovastatin during pregnancy in postmarketing experience. METHODS: We reviewed the Merck & Co., Inc. (West Point, PA) pharmacovigilance database for reports of exposure to simvastatin or lovastatin during pregnancy. The reports were classified as prospective (reported prior to pregnancy outcome) or retrospective (reported after pregnancy outcome) and were evaluated for timing of exposure, outcome, congenital anomalies, and other events. Outcome rates were calculated for prospective pregnancies. RESULTS: We identified 477 reports (386 prospective and 91 retrospective) with 225 prospective outcomes reported: 154 live born infants, 49 elective abortions, 18 spontaneous abortions, and 4 fetal deaths. Six congenital anomalies were reported: chromosomal translocation, trisomy 18, hypospadias, duodenal atresia, cleft lip, and skin tag. The rate of congenital anomalies (congenital anomalies/live births plus fetal deaths) was 3.8%, which is similar to the background population rate (3.2%; relative ratio, 1.21; 95% 1-sided upper confidence interval [CI], 2.02). There were 13 retrospective reports describing a range of congenital anomalies. No specific pattern of anomalies was identified in either the prospective or retrospective reports. Rates for other outcomes were similar to background rates. CONCLUSIONS: Although the number of reports was relatively small, there was no evidence of a notable increase in congenital anomalies in women exposed to simvastatin or lovastatin versus the general population. Greater reporting of congenital abnormalities in the retrospective cohort is not unexpected and may reflect a reporting bias. Drugs should be used during pregnancy only if the benefits outweigh the risks. Simvastatin and lovastatin remain contraindicated during pregnancy.     

Improving case ascertainment of a population-based birth defects registry in New York State using hospital discharge data

BACKGROUND: The assessment of the data quality of population-based registration systems is essential to understanding the reliability and usefulness of disease surveillance and research findings resulting from the use of registry data. Since the New York State Congenital Malformations Registry (CMR) uses passive case ascertainment, the completeness of the registry data is an important aspect of the quality of information. This paper presents the results of hospital audits, which were conducted to capture the unreported cases using hospital discharge files, and evaluates the effectiveness of the audits. METHODS: Children age 2 years or younger and diagnosed with reportable birth defects for the birth years 1998-2000 were selected from hospital discharge files of all reporting hospitals in the New York Statewide Planning and Research Cooperative System (SPARCS) and matched to the CMR database for the same birth year period.The unmatched reports from the SPARCS hospital discharge files that the CMR possibly missed were sent to hospitals, requesting submission of the missed reports. Two audits on all reporting hospitals in New York State were conducted: 1) 1998 and 1999 birth cohorts audited from June 2000 to March 2002, and 2) 2000 birth cohort audited from November 2001 to November 2002. RESULTS: Hospital audits using SPARCS hospital discharge data identified 5,460 reports that the CMR missed for the selected 66 hospitals analyzed. About 86% of these reports had reportable conditions and were added to the CMR, which comprised 21.4% of all reports from the 66 hospitals for the birth years 1998-2000. The number of reports that would have been missed without audits decreased from the 1998 and 1999 birth cohort (25.1%) to the 2000 birth cohort (13.9%). Low reporting rates and, thus, a high percent of added reports, were found for hospitals with a relatively small number of annual reports and for some specific birth defects such as chromosomal anomalies, anencephalus and congenital anomalies of the urinary system. CONCLUSION: The current study demonstrates that using hospital discharge data to improve case ascertainment is a valuable and effective method of enhancing birth defect surveillance, particularly for those hospitals with low reporting rates.     

Fatty acid and lipid compositions of Conidiobolus

The fatty acid composition of the total lipids from two Conidiobolus species was studied by gas—liquid chromatography. The major fatty acids of C. lamprauges were palmitic acid (C_16:0), oleic acid (C_18:1), linolenic acid (C_18:3), and arachidonic acid (C_20:4). For C. eurymitus , myristic acid (C_14:0), C_16:0, and linoleic acid (C_18:2) were the most abundant acids. The fatty acid composition of C. eurymitus was quite different from that of the Conidiobolus species as mentioned in other reports. The lipid composition of the total lipids of C. lamprauges and C. eurymitus was also studied by thinchrography on quartz rods. Triglycerides and phospholipids were the major components in the two Conidiobolus species.     

PLMItRNA, a database for higher plant mitochondrial tRNAs and tRNA genes.

The PLMItRNA database contains information and multialignments of tRNA genes and molecules detected in higher plant mitochondria. It has been developed from a previous compilation of higher plant mitochondrial tRNA genes [Sagliano,A., Volpicella,M., Gallerani,R. and Ceci,L.R. (1998) Nucleic Acids Res., 26, 154-155] and implemented with data and sequences of tRNA molecules retrieved from the literature. The current version of the database reports information on 171 genes and 16 tRNA molecules from 24 plants. PLMItRNA is accessible via WWW at http://bio-www.ba.cnr.it:8000/srs/     

A systematic review and meta-analysis of the association of transforming growth factor β receptor I 6A/9A gene polymorphism with ovarian cancer risk

Abstract

Ovarian cancer is the leading cause of cancer-related death in women. This meta-analysis was conducted to evaluate the association of transforming growth factor β receptor I (TβR-I) 6A/9A gene polymorphism with ovarian cancer risk. The association literatures were identified from PubMed and Cochrane Library on 1 October 2013, and eligible reports were recruited and synthesized. Four reports were recruited into this meta-analysis for the association of TβR-I 6A/9A gene polymorphism with ovarian cancer risk. 6A allele and 6A/6A genotype of TβR-I were associated with the ovarian cancer risk (6A: OR?=?1.24, 95% CI: 1.02–1.51, p?=?0.03; 6A/6A: OR?=?2.30, 95% CI: 1.01–5.22, p?=?0.05). However, TβR-I 9A/9A genotype was not associated with the risk of ovarian cancer (OR?=?0.82, 95% CI: 0.66–1.02, p?=?0.08). In conclusion, TβR-I 6A allele and 6A/6A genotype are associated with the ovarian cancer risk. However, more studies should be performed to confirm this relationship in the future.     

Review of cervical smears from 76 women with invasive cervical cancer: cytological findings and medicolegal implications

OBJECTIVE: To review cervical smears from 76 women which were taken prior to the diagnosis of invasive cervical cancer and to determine the appropriateness of the cytology reports issued on the smears. METHODS: Cervical smears, clinical records, cervical smear history and cytology reports from 76 women with invasive cervical cancer were reviewed. After microscopic review of the cervical smears, the cases were divided into two groups: Group 1 comprised 50 women who were found to have had at least one false-negative (F/N) smear report prior to the diagnosis of invasive cervical cancer. Group 2 comprised 26 women for whom no evidence of F/N reporting was found. RESULTS: A total of 209 cervical smears from the 50 women in group 1 were available for review (range 2-12 smears per woman); 100 of the 209 smears were considered to have been reported appropriately. Ninety-seven smears which had been reported originally as negative or inadequate were found, on review, to contain numerous severely dyskaryotic cells and were reclassified as F/N smears. All of the 50 women had at least one F/N smear and 29 had two or more. Twelve smears from eight women contained only a few (<200 severely dyskaryotic cells). Forty women developed invasive squamous carcinoma and 10 developed invasive adenocarcinoma. The stage at diagnosis ranged from 1A to stage 4. Seventy-one smears from the 24 women in group 2 were available for review (range 1-15 smears per woman). In two cases included in group 2, no smears were provided for review as the smears had been lost or mislaid. Review of the 71 smears confirmed the accuracy of the original cytological classification of the smear. Nineteen women were diagnosed with squamous cancer, two microinvasive cancer, one glassy cell, two adenocarcinomas, and one with adenosquamous carcinoma. One women was found to have an embryonal rhabdomyosarcoma of the corpus uteri involving the cervix. DISCUSSION/CONCLUSION: The medicolegal implications are discussed in the light of the above findings. Evidence of breach of duty of care was presented in all 50 cases in group I although causation was not established in every case. There was no evidence of failure of duty of care in terms of the standard of the cervical cytology reports issued or standard of clinical management in 17 of the 26 cases in group 2. However, in seven of the 26 cases in group 2, clinical management of the case was substandard due to failure to investigate symptoms of irregular bleeding regardless of a negative cytology report (two cases), failure to act upon a suspicious smear report or consecutive inadequate smear reports (two cases), failure of follow-up after treatment of CIN3 (two cases) and histological misdiagnosis (one case).     

Implant-supported palatal lift prosthesis in a patient with velopharyngeal incompetence: a case report

doi: 10.1111/j.1741‐2358.2011.00561.x Implant‐supported palatal lift prosthesis in a patient with velopharyngeal incompetence: a case report Objective: To describe the use of dental implants in the treatment of velopharyngeal incompetence. Background: Velopharyngeal incompetence is characterized by the inability to contract the tissues of the soft palate. The most common causes are neuromuscular problems resulting from concussion and degenerative conditions of the central nervous system. Materials and methods: The treatment using palatal lift prosthesis is well established in the literature; however, reports on the use of osseointegrated implants are scarce. Rehabilitation using only this type of fibromucosal support is difficult in edentulous patients, since the prosthesis has a palatal lift extension. Results: The implants provided retention and stability to the prosthesis, improving swallowing and speech and contributing to improve the patient’s quality of life. Conclusion: This article reports the rehabilitation of a patient with a totally edentulous maxilla with velopharyngeal incompetence using an implant‐retained palatal lift prosthesis.     

The Drosophila wings apart Gene Anchors a Novel,Evolutionarily Conserved Pathway of Neuromuscular Development

wings apart (wap) is a recessive, semilethal gene located on the X chromosome in Drosophila melanogaster, which is required for normal wing-vein patterning. We show that the wap mutation also results in loss of the adult jump muscle. We use complementation mapping and gene-specific RNA interference to localize the wap locus to the proximal X chromosome. We identify the annotated gene CG14614 as the gene affected by the wap mutation, since one wap allele contains a non-sense mutation in CG14614, and a genomic fragment containing only CG14614 rescues the jump-muscle phenotypes of two wap mutant alleles. The wap gene lies centromere-proximal to touch-insensitive larva B and centromere-distal to CG14619, which is tentatively assigned as the gene affected in introverted mutants. In mutant wap animals, founder cell precursors for the jump muscle are specified early in development, but are later lost. Through tissue-specific knockdowns, we demonstrate that wap function is required in both the musculature and the nervous system for normal jump-muscle formation. wap/CG14614 is homologous to vertebrate wdr68, DDB1 and CUL4 associated factor 7, which also are expressed in neuromuscular tissues. Thus, our findings provide insight into mechanisms of neuromuscular development in higher animals and facilitate the understanding of neuromuscular diseases that may result from mis-expression of muscle-specific or neuron-specific genes.     

Two female siblings with a previously unreported MCA/MR syndrome: pre- and postnatal growth retardation, iris colobomata, spasticity, facial dysmorphism and dilated ventricles.

We report two siblings from non consanguineous parents with a similar MCA/MR syndrome: Pre- and postnatal growth retardation, microcephaly, mental retardation, iris colobomata, facial dysmorphism, spasticity, dilated ventricles and abnormal immunoglobulin levels. Review of published reports and the use of the London Dysmorphology Database suggests that these siblings may present a new syndrome.