Extending the boundaries of cancer therapeutic complexity with literature text mining

Drug combination therapy is a main pillar of cancer therapy. As the number of possible drug candidates for combinations grows, the development of optimal high complexity combination therapies (involving 4 or more drugs per treatment) such as RCHOP-I and FOLFIRINOX becomes increasingly challenging due to combinatorial explosion. In this paper, we propose a text mining (TM) based tool and workflow for rapid generation of high complexity combination treatments (HCCT) in order to extend the boundaries of complexity in cancer treatments. Our primary objectives were: (1) Characterize the existing limitations in combination therapy; (2) Develop and introduce the Plan Builder (PB) to utilize existing literature for drug combination effectively; (3) Evaluate PB's potential in accelerating the development of HCCT plans. Our results demonstrate that researchers and experts using PB are able to create HCCT plans at much greater speed and quality compared to conventional methods. By releasing PB, we hope to enable more researchers to engage with HCCT planning and demonstrate its clinical efficacy.

Occurrence and distribution of sequence types among Legionella pneumophila strains isolated from patients in Germany: common features and differences to other regions of the world

A total of 105 unrelated clinical isolates of Legionella pneumophila were randomly selected from the German National Legionella strain collection and typed by monoclonal antibody (MAb) subgrouping and a seven-gene locus sequence-based typing (SBT) scheme. According to the case definitions of the European Working Group for Legionella Infections, 19 of the isolates tested were travel-associated, 38 were community-acquired and 48 were of nosocomial origin. Eighty-four of these strains belonged to serogroup 1, 20 belonged to other serogroups, and one isolate could not be serogrouped. The majority of strains among the travel-associated and community-acquired cases were MAb3-1-positive. The most common sequence type (1, 4, 3, 1, 1, 1, 1) was found in 20 isolates in 11 cities; other allelic profiles also found in Europe (2, 3, 9, 10, 2, 1, 6), (1, 3, 9, 10, 2, 1, 6), (2, 6, 17, 14, 13, 11, 11) and (3, 4, 1, 1, 1, 9, 1) were detected among the German isolates but at a low frequency. In contrast, some SBT are unique to Germany, including (3, 4, 1, 3, 35, 9, 11), which was found among five isolates from patients in Berlin. In concordance with European data, a significant portion of the L. pneumophila strains isolated from patients in Germany belong to clones that occur throughout the world and which are responsible for the majority of clinical cases.

[Incidence of resistance and risk factors for resistance in Mycobacterium tuberculosis. A retrospective study of 1,055 patients of a specialty hospital 1984 to 1993]

For the past decade, there have been no data on the time course of drug-resistant tuberculosis and on risk factors for drug resistance in former West Germany. We reviewed the medical records of all patients with positive cultures for Mycobacterium tuberculosis from 1984 until 1993 in a hospital near Hamburg. Drug-susceptibility testing was performed for isoniazid, rifampicin, ethambutol, and streptomycin, using the modified proportion method. Of 1,055 patient, 9.6% had isolates resistant to one or more drugs. Of the isolates, 5.8% showed resistance to isoniazid or rifampicin and 1.8% to both isoniazid and rifampicin. There was no significant change of the resistance rate during the study period. Twenty six percent of 89 patients from South America, Africa or Asia had isolates resistant to one or more drugs, compared with 7.6% of 799 patients born in Germany (odds ratio (OR) 4.2; 95% confidence interval (95% CI) 2.5-7.3). Among patients born in Germany, 32% of 101 patients with a history of prior antituberculosis drug therapy had resistant organisms, versus 4.2% of 698 patients without prior therapy (OR 10.7; 95% CI 6.1-18.7). Resistance orates for 35 patients, who had been treated within the last 5 yrs, and for 65 patients, who had been treated more than 5 yrs ago, were 57 and 17%, respectively (OR 6.6; 95% CI 2.9-16.6). Our results suggest that there is no increase in the proportion of drug-resistant tuberculosis in our hospital, and that patients with a recent history of antituberculosis drug therapy and patients from South America, Africa, or Asia are at high risk for drug resistance.

Drug-resistant tuberculosis in northern Germany: a retrospective hospital-based study of 1,055 patients from 1984 until 1993

For the past decade, there have been no data on the time course of drug resistant tuberculosis and on risk factors for drug resistance in former West Germany. We reviewed the medical records of all patients with positive cultures for Mycobacterium tuberculosis from 1984 until 1993 in a hospital near Hamburg. Drug-susceptibility testing was performed for isoniazid, rifampicin, ethambutol, and streptomycin, using the modified proportion method. Of 1,055 patients, 9.6% had isolates resistant to one or more drugs. Of the isolates, 5.8% showed resistance to isoniazid or rifampicin and 1.8% to both isoniazid and rifampicin. There was no significant change of the resistance rate during the study period. Twenty six percent of 89 patients from South America, Africa or Asia had isolates resistant to one or more drugs, compared with 7.6% of 799 patients born in Germany (odds ratio (OR) 4.2; 95% confidence interval (95% CI) 2.5-7.3). Among patients born in Germany, 32% of 101 patients with a history of prior anti-tuberculosis drug therapy had resistant organisms, versus 4.2% of 698 patients without prior therapy (OR 10.7; 95% CI 6.1-18.7). Resistance rates for 35 patients, who had been treated within the last 5 yrs, and for 65 patients, who had been treated more than 5 yrs ago, were 57 and 17%, respectively (OR 6.6; 95% CI 2.9-16.6). Our results suggest that there is no increase in the proportion of drug-resistant tuberculosis in our hospital, and that patients with a recent history of antituberculosis drug therapy and patients from South America, Africa, or Asia are at high risk for drug resistance.