I spent a few hours reviewing 200+ abstracts published in BiomedCentral that had the words
"sensitivity" and "specificity" in the title. There were four which had enough information in
the abstract to be used as teaching examples on how to calculate sensitivity, specificity,
positive predictive value, and/or negative predictive value.
1. Read the following abstracts. Calculate the values of sensitivity, specificity,
positive predictive value, or negative predictive value as requested. If you need a hint,
some helpful tables from the text of the articles is included below.
a. Frozen section is superior to imprint cytology for the intra-operative
assessment of sentinel lymph node metastasis in Stage I Breast cancer patients. Mori
M, Tada K, Ikenaga M, Miyagi Y, Nishimura S, Takahashi K, Makita M, Iwase T, Kasumi F,
Koizumi M. World Journal of Surgical Oncology 2006, 4:26 (17 May 2006)
[Abstract]
[Full Text]
[PDF] Background
A standard intra-operative procedure for assessing sentinel lymph node metastasis in
breast cancer patients has not yet been established. Patients and methods One
hundred and thirty-eight patients with stage I breast cancer who underwent sentinel node
biopsy using both imprint cytology and frozen section were analyzed. Results
Seventeen of the 138 patients had sentinel node involvement. Results of imprint cytology
included nine false negative cases (sensitivity, [[CALCULATE THIS VALUE]]).
In contrast, only two cases of false negatives were found on frozen section
(sensitivity, [[CALCULATE THIS VALUE]]). There were two false
positive cases identified by imprint cytology (specificity, [[CALCULATE THIS
VALUE]]). On the other hand, frozen section had 100% specificity.
Conclusion These findings suggest that frozen section is superior to imprint
cytology for the intra-operative determination of sentinel lymph node metastasis in
stage I breast cancer patients.
b. The Single Item Literacy Screener: Evaluation of a brief instrument to identify
limited reading ability. Morris NS, MacLean CD, Chew LD, Littenberg B. BMC Family
Practice 2006, 7:21 (24 March 2006)
[Abstract]
[Full text]
[PDF]
Background Reading skills are important for accessing health information, using
health care services, managing one's health and achieving desirable health outcomes. Our
objective was to assess the diagnostic accuracy of the Single Item Literacy Screener (SILS)
to identify limited reading ability, one component of health literacy, as measured by
the S-TOFHLA. Methods Cross-sectional interview with 999 adults with diabetes
residing in Vermont and bordering states. Participants were randomly recruited from
Primary Care practices in the Vermont Diabetes Information System June 2003 ' December
2004. The main outcome was limited reading ability. The primary predictor was the SILS.
Results Of the 999 persons screened, 169 (17%) had limited reading ability. The
sensitivity of the SILS in detecting limited reading ability was 54% [95% CI: 47%, 61%]
and the specificity was 83% [95% CI: 81%, 86%] with an area under the Receiver Operating
Characteristics Curve (ROC) of 0.73 [95% CI: 0.69, 0.78]. Seven hundred seventy (77%)
screened negative on the SILS and 692 of these subjects had adequate reading skills
(negative predictive value = [[CALCULATE THIS VALUE]] [95% CI: 0.88,
0.92]). Of the 229 who scored positive on the SILS, 92 had limited reading ability
(positive predictive value = [[CALCULATE THIS VALUE]] [95% CI: 0.34,
0.47]). Conclusion The SILS is a simple instrument designed to identify patients
with limited reading ability who need help reading health-related materials. The SILS
performs moderately well at ruling out limited reading ability in adults and allows
providers to target additional assessment of health literacy skills to those most in
need. Further study of the use of the SILS in clinical settings and with more diverse
populations is warranted.
c. Gait disorders are associated with non-cardiovascular falls in elderly people:
a preliminary study. Montero-Odasso M, Schapira M, Duque G, Soriano ER, Kaplan R,
Camera LA. BMC Geriatrics 2005, 5:15 (1 December 2005)
[Abstract]
[Full text]
[PDF]
Background The association between unexplained falls and cardiovascular causes is
increasingly recognized. Neurally mediated cardiovascular disorders and hypotensive
syndromes are found in almost 20 percent of the patients with unexplained falls.
However, the approach to these patients remains unclear. Gait assessment might be an
interesting approach to these patients as clinical observations suggests that those with
cardiovascular or hypotensive causes may not manifest obvious gait alterations. Our
primary objective is to analyze the association between gait disorders and a
non-cardiovascular cause of falls in patients with unexplained falls. A second objective
is to test the sensitivity and specificity of a gait assessment approach for detecting
non-cardiovascular causes when compared with intrinsic-extrinsic classification.
Methods Cross-sectional study performed in a falls clinic at a university hospital
in 41 ambulatory elderly participants with unexplained falls. Neurally mediated
cardiovascular conditions, neurological diseases, gait and balance problems were
assessed. Gait disorder was defined as a gait velocity < 0.8 m/s or Tinetti Gait Score
<9. An attributable etiology of the fall was determined in each participant. Comparisons
between the gait assessment approach and the attributable etiology regarding a neurally
mediated cardiovascular cause were performed. Fisher exact test was used to test the
association hypothesis. Sensitivity and specificity of gait assessment approach and
intrinsic-extrinsic classification to detect a non-cardiovascular mediated fall was
calculated with 95% confidence intervals (CI95%). Results A cardiovascular
etiology (orthostatic and postprandial hypotension, vasovagal syndrome and carotid sinus
hypersensitivity) was identified in 14% of participants (6/41). Of 35 patients with a
gait disorder, 34 had a non-cardiovascular etiology of fall; whereas in 5 out of 6
patients without a gait disorder, a cardiovascular diagnosis was identified (p < 0.001).
Sensitivity and specificity of the presence of gait disorder for identifying a
non-cardiovascular mediated cause was [[CALCULATE THIS VALUE]]
(CI95% = 85'99) and [[CALCULATE THIS VALUE]] (CI95% = 36'99),
respectively. Conclusion In community dwelling older persons with unexplained
falls, gait disorders were associated with non-cardiovascular diagnosis of falls. Gait
assessment was a useful approach for the detection of a non-cardiovascular mediated
cause of falls, providing additional value to this assessment.
d. Software PREP-Mt: predictive RNA editor for plant mitochondrial genes.
Mower JP. BMC Bioinformatics 2005, 6:96 (12 April 2005) [Abstract] [Full text] [PDF]
Background In plants, RNA editing is a process that converts specific cytidines to
uridines and uridines to cytidines in transcripts from virtually all mitochondrial
protein-coding genes. There are thousands of plant mitochondrial genes in the sequence
databases, but sites of RNA editing have not been determined for most. Accurate methods
of RNA editing site prediction will be important in filling in this information gap and
could reduce or even eliminate the need for experimental determination of editing sites
for many sequences. Because RNA editing tends to increase protein conservation across
species by "correcting" codons that specify unconserved amino acids, this principle can
be used to predict editing sites by identifying positions where an RNA editing event
would increase the conservation of a protein to homologues from other plants. PREP-Mt
takes this approach to predict editing sites for any protein-coding gene in plant
mitochondria. Results To test the general applicability of the PREP-Mt
methodology, RNA editing sites were predicted for 370 full-length or nearly full-length
DNA sequences and then compared to the known sites of RNA editing for these sequences.
Of 60,263 cytidines in this test set, PREP-Mt correctly classified 58,994 as either an
edited or unedited site (accuracy = 97.9%). PREP-Mt properly identified 3,038 of the
3,698 known sites of RNA editing (sensitivity = [[CALCULATE THIS VALUE]])
and 55,956 of the 56,565 known unedited sites (specificity = [[CALCULATE THIS
VALUE]]). Accuracy and sensitivity increased to 98.7% and 94.7%,
respectively, after excluding the 489 silent editing sites (which have no effect on
protein sequence or function) from the test set. Conclusion These results
indicate that PREP-Mt is effective at identifying C to U RNA editing sites in plant
mitochondrial protein-coding genes. Thus, PREP-Mt should be useful in predicting protein
sequences for use in molecular, biochemical, and phylogenetic analyses. In addition,
PREP-Mt could be used to determine functionality of a mitochondrial gene or to identify
particular sequences with unusual editing properties. The PREP-Mt methodology should be
applicable to any system where RNA editing increases protein conservation across
species.
Hint for 1a. Two tables from Frozen section is superior to imprint cytology for
the intra-operative assessment of sentinel lymph node metastasis in Stage I Breast
cancer patients that might help with your calculations.
Hint for 1b. One table from The Single Item Literacy Screener: Evaluation of a brief
instrument to identify limited reading ability that might help with your
calculations.
Hint for 1c. One table from Gait disorders are associated with non-cardiovascular
falls in elderly people: a preliminary study that might help with your calculations.
Hint for 1d. One table from Software PREP-Mt: predictive RNA editor for plant
mitochondrial genes that might help with your calculations.
[[Deleted material]]
07/08/2008.
