Constructing Reference Sets from Unstructured, Ungrammatical Text

Vast amounts of text on the Web are unstructured and ungrammatical, such as classified ads, auction listings, forum postings, etc. We call such text “posts.” Despite their inconsistent structure and lack of grammar, posts are full of useful information. This paper presents work on semi-automatically building tables of relational information, called “reference sets,” by analyzing such posts directly. Reference sets can be applied to a number of tasks such as ontology maintenance and information extraction. Our reference-set construction method starts with just a small amount of background knowledge, and constructs tuples representing the entities in the posts to form a reference set. We also describe an extension to this approach for the special case where even this small amount of background knowledge is impossible to discover and use. To evaluate the utility of the machine-constructed reference sets, we compare them to manually constructed reference sets in the context of reference-set-based information extraction. Our results show the reference sets constructed by our method outperform manually constructed reference sets. We also compare the reference-set-based extraction approach using the machine-constructed reference set to supervised extraction approaches using generic features. These results demonstrate that using machine-constructed reference sets outperforms the supervised methods, even though the supervised methods require training data.

Expanding CEP290 mutational spectrum in ciliopathies

Ciliopathies are an expanding group of rare conditions characterized by multiorgan involvement, that are caused by mutations in genes encoding for proteins of the primary cilium or its apparatus. Among these genes, CEP290 bears an intriguing allelic spectrum, being commonly mutated in Joubert syndrome and related disorders (JSRD), Meckel syndrome (MKS), Senior-Loken syndrome and isolated Leber congenital amaurosis (LCA). Although these conditions are recessively inherited, in a subset of patients only one CEP290 mutation could be detected. To assess whether genomic rearrangements involving the CEP290 gene could represent a possible mutational mechanism in these cases, exon dosage analysis on genomic DNA was performed in two groups of CEP290 heterozygous patients, including five JSRD/MKS cases and four LCA, respectively. In one JSRD patient, we identified a large heterozygous deletion encompassing CEP290 C-terminus that resulted in marked reduction of mRNA expression. No copy number alterations were identified in the remaining probands. The present work expands the CEP290 genotypic spectrum to include multiexon deletions. Although this mechanism does not appear to be frequent, screening for genomic rearrangements should be considered in patients in whom a single CEP290 mutated allele was identified.

A defect in the thymidine kinase 2 gene causing isolated mitochondrial myopathy without mtDNA depletion

Isolated mitochondrial myopathies (IMM) are either due to primary defects in mtDNA, in nuclear genes that control mtDNA abundance and structure such as thymidine kinase 2 (TK2), or due to CoQ deficiency. Defects in the TK2 gene have been found to be associated with mtDNA depletion attributed to a depleted mitochondrial dNTP pool in non-dividing cells. We report an unusual case of IMM, homozygous for the H90N mutation in the TK2 gene but unlike other cases with the same mutation, does not demonstrate mtDNA depletion. The patient's clinical course is relatively mild and a muscle biopsy showed ragged red muscle fibers with a mild decrease in complexes I and an increase in complexes IV and II activities. This report extends the phenotypic expression of TK2 defects and suggests that all patients who present with an IMM even with normal quantities of mtDNA should be screened for TK2 mutations.

Creating Relational Data from Unstructured and Ungrammatical Data Sources

In order for agents to act on behalf of users, they will have to retrieve and integrate vast amounts of textual data on the World Wide Web. However, much of the useful data on the Web is neither grammatical nor formally structured, making querying difficult. Examples of these types of data sources are online classifieds like Craigslist and auction item listings like eBay. We call this unstructured, ungrammatical data "posts." The unstructured nature of posts makes query and integration difficult because the attributes are embedded within the text. Also, these attributes do not conform to standardized values, which prevents queries based on a common attribute value. The schema is unknown and the values may vary dramatically making accurate search difficult. Creating relational data for easy querying requires that we define a schema for the embedded attributes and extract values from the posts while standardizing these values. Traditional information extraction (IE) is inadequate to perform this task because it relies on clues from the data, such as structure or natural language, neither of which are found in posts. Furthermore, traditional information extraction does not incorporate data cleaning, which is necessary to accurately query and integrate the source. The two-step approach described in this paper creates relational data sets from unstructured and ungrammatical text by addressing both issues. To do this, we require a set of known entities called a "reference set." The first step aligns each post to each member of each reference set. This allows our algorithm to define a schema over the post and include standard values for the attributes defined by this schema. The second step performs information extraction for the attributes, including attributes not easily represented by reference sets, such as a price. In this manner we create a relational structure over previously unstructured data, supporting deep and accurate queries over the data as well as standard values for integration. Our experimental results show that our technique matches the posts to the reference set accurately and efficiently and outperforms state-of-the-art extraction systems on the extraction task from posts.

Inborn errors of metabolism: a cause of abnormal brain development

Brain malformations are caused by a disruption in the sequence of normal development by various environmental or genetic factors. By modifying the intrauterine milieu, inborn errors of metabolism may cause brain dysgenesis. However, this association is typically described in single case reports. The authors review the relationship between brain dysgenesis and specific inborn errors of metabolism. Peroxisomal disorders and fatty acid oxidation defects can produce migration defects. Pyruvate dehydrogenase deficiency, nonketotic hyperglycinemia, and maternal phenylketonuria preferentially cause a dysgenetic corpus callosum. Abnormal metabolism of folic acid causes neural tube defects, whereas defects in cholesterol metabolism may produce holoprosencephaly. Various mechanisms have been proposed to explain abnormal brain development in inborn errors of metabolism: production of a toxic or energy-deficient intrauterine milieu, modification of the content and function of membranes, or disturbance of the normal expression of intrauterine genes responsible for morphogenesis. The recognition of a metabolic disorder as the cause of the brain malformation has implications for both the care of the patient and for genetic counseling to prevent recurrence in subsequent pregnancies.

Urinary organic acid screening in children with developmental language delay

The prevalence of 3-methylglutaconic aciduria was evaluated among children with developmental language disorders. A urine specimen was obtained from 40 children referred for developmental language delay to the Tel-Aviv Child Development Center during 12/96-6/97 and from 50 age-matched controls. Urine organic acids were analysed by gas chromatography-mass spectrometry. Urinary 3-methylglutaconic acid was quantified. A mildly increased excretion of 3-methylglutaconic acid was found in 8 children with developmental language delay. The combined excretion of 3-methylglutaconic and 3-methylglutaric acid was increased in 9 patients. There were no differences in the excretion of other organic acids. The patients with elevated 3-methylglutaconic acid did not differ from the other patients with developmental language disorders in any of the parameters evaluated. Mildly elevated urinary levels of 3-methylglutaconic acid may be a marker of a still undefined metabolic disorder presenting with developmental language delay. A further study in large groups of children with different developmental disorders is mandatory.

Polyadenylic-polyuridylic acid as adjuvant in the treatment of operable breast cancer: recent results

A randomized trial of polyadenylic-polyuridylic acid (Poly(A).Poly(U) given as an adjuvant in the treatment of operable breast cancer, has included 300 patients of the Institut Gustave-Roussy from September 1972 to December 1979; 145 patients were allocated to conventional treatment alone and 155 to conventional treatment plus Poly(A).Poly(U). Reviews after mean periods of follow-up of 50 and 87 months were previously published. The present review performed after a mean follow-up period of 111 months confirmed a significant increase in the overall survival of patients with invaded nodes treated with Poly(A).Poly(U). The best results were achieved in the subset of patients with up to three affected nodes who showed a significant increase of both overall and relapse-free survival. The benefit seemed to be greater in postmenopausal women (P = 0.07). Present status of other ongoing trials of adjuvant Poly(A).Poly(U) is presented.

A phase I clinical tolerance study of polyadenylic-polyuridylic acid in cancer patients

Polyadenylic-polyuridylic acid [poly(A) X poly(U)], an immunomodulator, has been shown to have antitumor effects in rodents and in a randomized clinical trial as an adjuvant to surgery in patients with operable breast cancer. The purpose of the present study was to determine the following: (a) clinical tolerance and safety of poly(A) X poly(U) in 13 patients with advanced cancer receiving a single dose of this duplex, using increasing amounts per intravenous injection of 90, 180, 300, and 450 mg; (b) if such high doses increased the level of interferon-mediated protein kinase and enhanced natural killer (NK) cell activity as observed previously with lower doses; and (c) if circulating interferon could be detected. No toxicity was observed in the 13 patients by close observation of clinical parameters, hemogram, and renal and liver functions. Increases of interferon-mediated protein kinase and of NK cell activity were observed, but there was no correlation between the magnitude of the responses and the dose of poly(A) X poly(U). No circulating interferon was detected. We conclude that poly(A) X poly(U) is not toxic in humans, at least up to a dose of 450 mg.

Enhancement of natural killer cell activity and 2-5A synthetase in operable breast cancer patients treated with polyadenylic; polyuridylic acid

Treatment of operable breast cancer patients with a single injection of 60 mg poly(A); poly(U) (polyadenylic, polyuridylic acid) resulted in an enhancement of natural killer (NK) cell cytotoxicity against human myeloid K562 target cells. Furthermore, the level of 2-5A synthetase in peripheral blood lymphocytes of such patients was increased after the treatment. Both of these effects, measured 24 and 48 hours after the injection of poly(A); poly(U), were statistically significant compared to their respective levels before the treatment. These events, therefore, may be used as markers to monitor the immediate response of patients toward treatment with this synthetic double-stranded RNA.

Adjuvant treatment with polyadenylic-polyuridylic acid in operable breast cancer: updated results of a randomised trial

The results of a randomised trial of polyadenylic-polyuridylic acid given as adjuvant treatment for operable breast cancer were reviewed after a mean follow up period of 87 months. Of the 300 patients included in the original trial, 145 had been allocated to conventional treatment alone and served as controls. At the time of review the overall survival of the group given polyadenylic-polyuridylic acid was significantly improved (p less than 0.05) as compared with that of the controls given conventional treatment alone. Significant benefit (p less than 0.02) was also observed among patients with evidence of disease in lymph nodes, the best results occurring in those with up to three invaded nodes, who showed a significant increase in both overall and relapse free survival. No evidence of toxicity was recorded. These findings confirm the value of polyadenylic-polyuridylic acid as adjuvant treatment for operable breast cancer. Results in an experimental model and in patients receiving the adjuvant suggested a possible role of interferon and natural killer (NK) cells in the mechanism of action.

Mortality among young black women using contraceptives

Data on the risk of death associated with various contraceptive methods are incomplete. Therefore, we analyzed the mortality rates for young, black inner-city women who used one of four methods of contraception--oral contraceptives, depomedroxyprogesterone acetate, intrauterine (contraceptive) devices, and barrier methods. The subjects were 30,580 15- to 44-year-old women who enrolled at a family planning clinic between 1967 and 1972 and who were observed by monitoring death certificates through the end of 1977. Forty percent of the 218 deaths observed were from accidents and violence. Use of this family planning clinic greatly reduced the risk of death from childbearing; only two deaths were associated with pregnancy and childbirth, compared with the 24 deaths expected. Overall, users of the four methods died at similar, low rates. Given that this study involves considerable loss to follow-up, possible acute effects of contraceptives (eg, infections or thrombosis) are more accurately estimated than possible long-term effects (eg, cancer).

A new adjuvant treatment with polyadenylic-polyuridylic acid in operable breast cancer

Adjuvant treatment with polyadenylic-polyuridylic acid poly A-poly U was tested in 300 patients with operable breast cancer who had all received the same locoregional treatment. They were randomized into two groups; 155 patients receiving 30 mg poly A-poly U i.v. once a week for 6 weeks and 145 controls. Overall survival was significantly improved in the poly A-Poly U group (P less than 0.05). The most striking difference (less than 0.03) was observed in the group of positive node patients, who had a 5-year relapse-free actuarial survival rate of 71% versus 47% in the controls.

Enhancement of interferon-mediated protein kinase in mouse and human plasma in response to treatment with polyadenylic-polyuridylic acid (poly A:poly U)

Interferon-treated mouse and human cells show enhanced levels of kinase activity manifested by the phosphorylation of endogenous 67,000 (p67K kinase) and 72,000 (p72K kinase) molecular weight proteins, respectively. Both the p67K kinase and the p72K activities are detectable in mouse and human plasma. We have previously shown that the p67K kinase in the plasma of mice may serve as a marker for the presence and action of interferon. Here we show that these kinase activities are enhanced in mice and in patients treated with polyadenylic-polyuridylic acid (Poly A:Poly U) at doses (0.4-0.6 mg/kg body weight) which do not lead to detectable amount of circulating interferon. Mice injected with higher doses of Poly A:Poly U (2-10 mg/kg body weight) show detectable levels of circulating interferon in addition to enhanced levels of p67K kinase in their plasma. Interferon produced under these conditions is acid stable.

[Increase in dismutase activity in splenic leukocytes of mice sensitive to BCG and Mycobacterium lepraemurium]

A marked enhancement of superoxide dismutase activity was evidenced when Mice receptive to BCG and Mycobacterium lepraemurium were infected. Such increase was not found in non receptive Mice. This seems related to a genetic factor of the breed of Mice studied.

Adjuvant treatment with polyadenylic-polyuridylic acid (Polya.Polyu) in operable breast cancer

Adjuvant immunotherapy with polyadenylic-polyuridylic acid (PolyA.PolyU) was tested in a randomised trial on 300 patients with operable breast cancer, all of whom were treated by surgery with or without radiotherapy. They were randomly divided into an experimental group of 155 patients who were treated with 30 mg PolyA.PolyU intravenously per week for 6 weeks and a control group of 145 patients who received normal saline intravenously on the same schedule. The mean follow-up time was more than 50 months in both groups. The overall survival was significantly higher in the treated group (p less than or equal to 0.05), in whom the 5-year "relapse-free" surival was also increased. In node-positive patients, treatment increased the relapse-free survival (p less than or equal to 0.03) and overall survival (p less than or equal to 0.07). No side-effects were noted. Thus, immunotherapy with PolyA.PolyU appears to be a simple, non-toxic, and efficient adjuvant treatment in operable breast cancer.