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Biomedical subjects

P Antal

Publications and source records attributed to P Antal.

6 recordsLinked to original sources
PubMed2003

Evaluation of the vector space representation in text-based gene clustering.

Thanks to its increasing availability, electronic literature can now be a major source of information when developing complex statistical models where data is scarce or contains much noise. This raises the question of how to deeply integrate information from domain literature with experimental data. Evaluating what kind of statistical text representations can integrate literature knowledge in clustering still remains an unsufficiently explored topic. In this work we discuss how the bag-of-words representation can be used successfully to represent genetic annotation and free-text information coming from different databases. We demonstrate the effect of various weighting schemes and information sources in a functional clustering setup. As a quantitative evaluation, we contrast for different parameter settings the functional groupings obtained from text with those obtained from expert assessments and link each of the results to a biological discussion.

Artificial Intelligence↗
PubMed2003

Probabilistic graphical models for computational biomedicine.

BACKGROUND: As genomics becomes increasingly relevant to medicine, medical informatics and bioinformatics are gradually converging into a larger field that we call computational biomedicine. OBJECTIVES: Developing a computational framework that is common to the different disciplines that compose computational biomedicine will be a major enabler of the further development and integration of this research domain. METHODS: Probabilistic graphical models such as Hidden Markov Models, belief networks, and missing-data models together with computational methods such as dynamic programming, Expectation-Maximization, data-augmentation Gibbs sampling, and the Metropolis-Hastings algorithm provide the tools for an integrated probabilistic approach to computational biomedicine. RESULTS AND CONCLUSIONS: We show how graphical models have already found a broad application in different fields composing computational biomedicine. We also indicate several challenges that lie at the interface between medical informatics, statistical genomics, and bioinformatics. We also argue that graphical models offer a unified framework making it possible to integrate in a statistically meaningful way multiple models ranging from the molecular level to cellular and to clinical levels. Because of their versatility and firm statistical underpinning, we assert that probabilistic graphical models can serve as the lingua franca for many computationally intensive approaches to biology and medicine. As such, graphical models should be a foundation of the curriculum of students in these fields. From such a foundation, students could then build towards specific computational methods in medical informatics, medical image analysis, statistical genetics, or bioinformatics while keeping the communication open between these areas.

Computational Biology↗
PubMed1998

Is the incidence of appendicitis reduced in patients with sickle cell disease?

BACKGROUND: Patients with sickle cell disease (SCD) often present with abdominal pain, usually attributable to vasoocclusion. Experience at a single institution suggested that appendicitis was a rare cause of abdominal symptoms in this population. OBJECTIVE: We sought to determine whether the incidence of appendicitis was significantly lower in patients with SCD than in the population at large. METHODS: A 17-year retrospective chart review was performed at Rainbow Babies and Children's Hospital, Cleveland, OH, to determine the approximate incidence of acute appendicitis (AA) in patients with SCD. In addition, we performed a statistical analysis comparing the incidence of AA among SCD patients enrolled in the Cooperative Study of Sickle Cell Disease with that in the general population. RESULTS: Only two patients with SCD with pathologically confirmed AA were identified among approximately 200 patients followed at our institution during a 17-year period ( approximately 3500 patient-years), yielding an incidence rate of 5.7 cases per 10 000 patient-years. Among 3765 patients with SCD enrolled in the Cooperative Study of Sickle Cell Disease followed for a mean of 5.3 years (19 886 patient-years), a maximum of 9 cases of AA were identified, yielding an incidence rate of 4.5 cases per 10 000 patient-years. Based on data from the National Hospital Discharge Survey of 1978 to 1981, the incidence rate of AA in the general population (0 to 44 years of age) is approximately 16 per 10 000 patient-years. Paired t test analysis demonstrated a highly significant difference (P < .001) when comparing the incidence of AA among patients enrolled in the Cooperative Study of Sickle Cell Disease and the population at large. CONCLUSION: AA is an unusual event in patients with SCD. The likelihood of developing appendicitis in SCD patients is less than one third of that for the population at large. Conservative therapy is warranted in the large majority of patients with SCD who present with acute abdominal pain. Surgical exploration is best limited to patients with clear evidence of potential surgical pathology or progressive findings during a period of observation. The biologic basis of our findings remains unknown.

Acute Disease↗
PubMed1995

Flow cytometric assay of phagocytic activity of human neutrophils and monocytes in whole blood by neutral red uptake.

In a new, simple, and fast flow-cytometric method for the simultaneous measurement of phagocytic activity of human neutrophils and monocytes in whole blood, the fluorescence capability of the well-known vital stain, neutral red was used. The incubation of 0.5 ml heparinized human blood with the phagocytic stimulus of zymosan dose- and time-dependently increased the percentage and the red fluorescence intensity of both neutrophils (4.3 +/- 1.2 times) and monocytes (2.7 +/- 0.7 times) measured cytofluorimetrically. Decreased uptake of neutral red was observed in a patient with phagocytic disorder, based upon impaired engulfment of particles and production of reactive oxygen species. In a patient with chronic granulomatosis, however, no decrease of neutral red uptake was measured. Platelet activating factor and phorbol myristate acetate were also able to increase the uptake of neutral red by both monocytes and neutrophils, but to a lesser extent than zymosan. The advantage of this method is the possibility for the simultaneous measurement of phagocytic activities of monocytes and neutrophils stimulated by either particles or soluble activators. This method is suitable for the selective measurement of activation processes not related to the production of free radicals in the phagocytes.

Adolescent↗
PubMed1994

Adjuvant Quil A improves protection in mice and enhances opsonic capacity of antisera induced by pneumococcal polysaccharide conjugate vaccines.

The adjuvant effect of Quil A on the primary antibody response of mice to pneumococcal capsular polysaccharide conjugates was examined. Quil A increased the anti-capsular polysaccharide antibody titres, the protection against Streptococcus pneumoniae, and the opsonic capacity of the antibodies as measured in a newly developed in vitro phagocytosis assay, using the mouse macrophage cell line J774.

Adjuvants, Immunologic↗