Subgraphs of reduced chemical graphs as screens for substructure searching of specific chemical structures

Reduced chemical graphs are descriptions of chemical structures which summarize certain structural features, for instance, the ring or chain nature of components, and conserve certain topological relationships. They have proved valuable in representing and searching generic chemical structure informa tion.

The generation of all subgraphs of one type of reduced chemical graph and their use as screens for substructure searching of databases of specific chemical structures are de scribed. The subgraphs have the potential to provide a single key for each substructure search query which comprises a single connected fragment, with possible advantages in an inverted file substructure search system. The methods and costs of generating the subgraphs, and their effectiveness in search, are assessed.

Automatic extraction of citations from the text of English-language patents - an example of template mining

Methods for automatically isolating and extracting biblio graphic references from the full texts of patents are described and evaluated; these include citations both to patents and to other bibliographic sources. Patents are unusual as citing documents in that citations occur princi pally in the text of the abstracts or description parts of the documents, rather than as footnotes or in separate sections. A template mining approach has been developed for this purpose, to relieve patent examiners of the chore of doing this manually.

Information retrieval research in the Department of Information Studies, University of Sheffield: 1965-1985

This paper discusses research which was carried out at the Department of Information Studies, University of Sheffield in the period 1965 to 1985 into storage and retrieval techniques for databases of textual and chemical structure data. The research includes the development of methods for the auto matic production of printed subject indexes and for the inde xing and retrieval of chemical structures and chemical reac tions, the variety generation method for the analysis, characterization and storage of data in a range of types of textual database, the prediction of biological activity in chemical compounds, and the design of document retrieval systems.

An evaluation of methods for assessing the quality of case management for inpatients with malaria in Benin

To improve healthcare quality for hospitalized patients with malaria in Benin, a feasible and valid evaluation method is needed. Because observation of inpatients is challenging, chart abstraction is an attractive option. However, the quality of inpatient charts is unknown. We employed three methods in five hospitals to assess 11 signs of malaria and severe disease: 1) chart abstraction (probability sample of inpatients), 2) chart abstraction compared to interviews of inpatients and health workers (HWs), and 3) abstraction from charts of recently discharged inpatients compared to interviews with HWs. Method 1 showed that of 473 malaria signs (from 43 charts), 178 (38%, 95% confidence interval 24-51%) were documented. Method 2 showed that 96% (45 of 47) of documented signs were valid. Method 3 suggests that 65% (36 of 55) of non-documented signs were assessed (but not documented) by HWs. Chart abstraction was feasible and documented data were valid, but results should be interpreted cautiously in consideration of low levels of documentation.

Specific domains of Aβ facilitate aggregation on and association with lipid bilayers

A hallmark of Alzheimer's disease, a late-onset neurodegenerative disease, is the deposition of neuritic amyloid plaques composed of aggregated forms of the β-amyloid peptide (Aβ). Aβ forms a variety of nanoscale, toxic aggregate species ranging from small oligomers to fibrils. Aβ and many of its aggregate forms strongly interact with lipid membranes, which may represent an important step in several toxic mechanisms. Understanding the role that specific regions of Aβ play in regulating its aggregation and interaction with lipid membranes may provide insights into the fundamental interaction between Aβ and cellular surfaces. We investigated the interaction and aggregation of several Aβ fragments (Aβ1-11, Aβ1-28, Aβ10-26, Aβ12-24, Aβ16-22, Aβ22-35, and Aβ1-40) in the presence of supported model total brain lipid extract (TBLE) bilayers. These fragments represent a variety of chemically unique domains within Aβ, that is, the extracellular domain, the central hydrophobic core, and the transmembrane domain. Using scanning probe techniques, we elucidated aggregate morphologies for these different Aβ fragments in free solution and in the presence of TBLE bilayers. These fragments formed a variety of oligomeric and fibrillar aggregates under free solution conditions. Exposure to TBLE bilayers resulted in distinct aggregate morphologies compared to free solution and changes in bilayer stability dependent on the Aβ sequence. Aβ10-26, Aβ16-22, Aβ22-35, and Aβ1-40 aggregated into a variety of distinct fibrillar aggregates and disrupted the bilayer structure, resulting in altered mechanical properties of the bilayer. Aβ1-11, Aβ1-28, and Aβ12-24 had minimal interaction with lipid membranes, forming only sparse oligomers.

Typhoid fever in the United States, 1999-2006

CONTEXT

Typhoid fever in the United States has increasingly been due to infection with antimicrobial-resistant Salmonella ser Typhi. National surveillance for typhoid fever can inform prevention and treatment recommendations.

OBJECTIVE

To assess trends in infections with antimicrobial-resistant S. Typhi.

DESIGN

Cross-sectional, laboratory-based surveillance study.

SETTING AND PARTICIPANTS

We reviewed data from 1999-2006 for 1902 persons with typhoid fever who had epidemiologic information submitted to the Centers for Disease Control and Prevention (CDC) and 2016 S. Typhi isolates sent by participating public health laboratories to the National Antimicrobial Resistance Monitoring System Laboratory at the CDC for antimicrobial susceptibility testing.

MAIN OUTCOME MEASURES

Proportion of S. Typhi isolates demonstrating resistance to 14 antimicrobial agents and patient risk factors for antimicrobial-resistant infections.

RESULTS

Patient median age was 22 years (range, <1-90 years); 1295 (73%) were hospitalized and 3 (0.2%) died. Foreign travel within 30 days of illness was reported by 1439 (79%). Only 58 travelers (5%) had received typhoid vaccine. Two hundred seventy-two (13%) of 2016 isolates tested were resistant to ampicillin, chloramphenicol, and trimethoprim-sulfamethoxazole (multidrug-resistant S. Typhi [MDRST]); 758 (38%) were resistant to nalidixic acid (nalidixic acid-resistant S. Typhi [NARST]) and 734 NARST isolates (97%) had decreased susceptibility to ciprofloxacin. The proportion of NARST increased from 19% in 1999 to 54% in 2006. Five ciprofloxacin-resistant isolates were identified. Patients with resistant infections were more likely to report travel to the Indian subcontinent: 85% of patients infected with MDRST and 94% with NARST traveled to the Indian subcontinent, while 44% of those with susceptible infections did (MDRST odds ratio, 7.5; 95% confidence interval, 4.1-13.8; NARST odds ratio, 20.4; 95% confidence interval, 12.4-33.9).

CONCLUSION

Infection with antimicrobial-resistant S. Typhi strains among US patients with typhoid fever is associated with travel to the Indian subcontinent, and an increasing proportion of these infections are due to S. Typhi strains with decreased susceptibility to fluoroquinolones.

Recurrent multistate outbreak of Salmonella Newport associated with tomatoes from contaminated fields, 2005

Salmonella Newport causes more than an estimated 100,000 infections annually in the United States. In 2002, tomatoes grown and packed on the eastern shore of Virginia contaminated with a pan-susceptible S. Newport strain caused illness in 510 patients in 26 states. In July-November 2005, the same strain caused illness in at least 72 patients in 16 states. We conducted a case-control study during the 2005 outbreak, enrolling 29 cases and 140 matched neighbourhood controls. Infection was associated with eating tomatoes (matched odds ratio 9.7, 95% confidence interval 3.3-34.9). Tomatoes were traced back to the eastern shore of Virginia, where the outbreak strain was isolated from pond water used to irrigate tomato fields. Two multistate outbreaks caused by one rare strain, and identification of that strain in irrigation ponds 2 years apart, suggest persistent contamination of tomato fields. Further efforts are needed to prevent produce contamination on farms and throughout the food supply chain.

A Waterborne Outbreak of Gastroenteritis with Multiple Etiologies among Resort Island Visitors and Residents: Ohio, 2004

BACKGROUND

The implementation of treated municipal water systems in the 20th century led to a dramatic decrease in waterborne disease in the United States. However, communities with deficient water systems still experience waterborne outbreaks. In August 2004, we investigated an outbreak of gastroenteritis on South Bass Island, Ohio, an island of 900 residents that is visited by >500,000 persons each year.

METHODS

To identify the source of illness, we conducted a case-control study and an environmental investigation. A case was defined as diarrhea in a person who traveled to the island during the period from May 1 through 30 September 2004 and became ill within 2 weeks after the visit. Healthy travel companions served as matched control subjects. We also performed an environmental assessment and extensive testing of island water sources.

RESULTS

Among the 1450 persons reporting illness, Campylobacter jejuni, norovirus, Giardia intestinalis, and Salmonella enterica serotype Typhimurium were identified in 16, 9, 3, and 1 persons, respectively. We interviewed 100 case patients and 117 matched control subjects. Case patients were more likely to drink water on the island than control subjects (68% vs. 35%; matched odds ratio, 4.3; 95% confidence interval, 2.2-9.3). Sampling of ground water wells indicated contamination with multiple fecal microbes, including Escherichia coli, C. jejuni, Salmonella species, and Giardia species. Irregularities in sewage disposal practices that could have contaminated the underground aquifer were noted.

CONCLUSIONS

The combined epidemiological and environmental investigation indicated that sewage-contaminated ground water was the likely source of this large outbreak. Long-term changes to the island's water supply and sewage management infrastructure are needed.

Ethnic trends in survival curves and mortality

The nature of secular trends in survival curves has been widely debated. Fries (1984) has argued for increasing rectangularization, while Myers and Manton (1984a; 1984b) have observed increases in mean age at death with little or no change in standard deviation--arguing against rectangularization. We hypothesize that ethnic differences in mortality trends may shed light on this argument. Using California population data for 1970, 1980, and 1990, we examined ethnic differences in rectangularization using both visual and means and standard deviations analyses. The resulting patterns varied by ethnicity, gender, and type of analyses. Nearly all female groups demonstrated modest rectangularization, regardless of mean age of death, while most of the male groups did not.