Artificial intelligence for detection of microsatellite instability in colorectal cancer-a multicentric analysis of a pre-screening tool for clinical application.

BACKGROUND: Microsatellite instability (MSI)/mismatch repair deficiency (dMMR) is a key genetic feature which should be tested in every patient with colorectal cancer (CRC) according to medical guidelines. Artificial intelligence (AI) methods can detect MSI/dMMR directly in routine pathology slides, but the test performance has not been systematically investigated with predefined test thresholds. METHOD: We trained and validated AI-based MSI/dMMR detectors and evaluated predefined performance metrics using nine patient cohorts of 8343 patients across different countries and ethnicities. RESULTS: Classifiers achieved clinical-grade performance, yielding an area under the receiver operating curve (AUROC) of up to 0.96 without using any manual annotations. Subsequently, we show that the AI system can be applied as a rule-out test: by using cohort-specific thresholds, on average 52.73% of tumors in each surgical cohort [total number of MSI/dMMR = 1020, microsatellite stable (MSS)/ proficient mismatch repair (pMMR) = 7323 patients] could be identified as MSS/pMMR with a fixed sensitivity at 95%. In an additional cohort of N = 1530 (MSI/dMMR = 211, MSS/pMMR = 1319) endoscopy biopsy samples, the system achieved an AUROC of 0.89, and the cohort-specific threshold ruled out 44.12% of tumors with a fixed sensitivity at 95%. As a more robust alternative to cohort-specific thresholds, we showed that with a fixed threshold of 0.25 for all the cohorts, we can rule-out 25.51% in surgical specimens and 6.10% in biopsies. INTERPRETATION: When applied in a clinical setting, this means that the AI system can rule out MSI/dMMR in a quarter (with global thresholds) or half of all CRC patients (with local fine-tuning), thereby reducing cost and turnaround time for molecular profiling.

Clinical and molecular characteristics and treatment outcomes of advanced right-colon, left-colon and rectal cancers: data from 1180 patients in a phase III trial of panitumumab with an extended biomarker panel.

BACKGROUND: Primary tumour location (PTL) is being adopted by clinicians to guide treatment decisions in metastatic colorectal cancer (mCRC). Here we test PTL as a predictive marker for panitumumab efficacy, and examine its relationship with an extended biomarker profile. We also examine rectal tumours as a separate location. PATIENTS AND METHODS: mCRC patients from the second-line PICCOLO trial of irinotecan versus irinotecan/panitumumab (IrPan). PTL was classified as right-PTL, left-PTL or rectal-PTL. PTL was assessed as a predictive biomarker for IrPan effect in RAS-wild-type (RAS-wt) patients (compared with irinotecan alone), then tested for independence alongside an extended biomarker profile (BRAF, epiregulin/amphiregulin (EREG/AREG) and HER3 mRNA expression). RESULTS: PTL data were available for 1180 patients (98.5%), of whom 558 were RAS-wt. High HER3 expression was independently predictive of panitumumab overall survival improvement, but PTL and EREG/AREG were not. IrPan progression-free survival (PFS) improvement compared with irinotecan was seen in left-PTL [hazard ratio (HR) = 0.61, P = 0.002) but not right-PTL (HR = 0.98, P = 0.90) (interaction P = 0.05; RAS/BRAF-wt interaction P = 0.10), or in rectal-PTL (HR = 0.82, P = 0.20) (interaction P = 0.14 compared with left-PTL; RAS/BRAF-wt interaction P = 0.04). Patients with right-PTL and high EREG/AREG or HER3 expression, had IrPan PFS improvement (high EREG/AREG HR = 0.20, P = 0.04; high HER3 HR = 0.33, P = 0.10) compared with irinotecan. Similar effect was seen for rectal-PTL patients (high EREG/AREG HR = 0.44, P = 0.03; high HER3 HR = 0.34, P = 0.05). CONCLUSIONS: RAS-wt patients with left-PTL are more likely to have panitumumab PFS advantage than those with right-PTL or rectal-PTL. However, an extended biomarker panel demonstrated significant heterogeneity in panitumumab PFS effect within a tumour location. AREG/EREG and HER3 mRNA expression identifies patients with right-PTL or rectal-PTL who achieve similar PFS effect with panitumumab as left-colon patients. Testing could provide a more reliable basis for clinical decision making. Further validation and development of these biomarkers is required to optimise routine patient care. CLINICAL TRIAL REGISTRATION: ISRCTN identifier: ISRCTN93248876.

Investigating the poor outcomes of BRAF-mutant advanced colorectal cancer: analysis from 2530 patients in randomised clinical trials.

Background: To improve strategies for the treatment of BRAF-mutant advanced colorectal cancer (aCRC) patients, we examined individual data from patients treated with chemotherapy alone in three randomised trials to identify points on the treatment pathway where outcomes differ from BRAF wild-types. Patients and methods: 2530 aCRC patients were assessed from three randomised trials. End-points were progression-free survival, response rate, disease control rate, post-progression survival (P-PS) and overall survival. Treatments included first-line oxaliplatin/fluorouracil (OxFU) and second-line irinotecan. Clinicians were unaware of BRAF-status. Results: 231 patients (9.1%) had BRAF-mutant tumours. BRAF-mutation conferred significantly worse survival independent of associated clinicopathological factors known to be prognostic. Compared with wild-type, BRAF-mutant patients treated with first-line OxFU had similar DCR (59.2% versus 72%; adjusted OR = 0.76, P = 0.24) and PFS (5.7 versus 6.3 months; adjusted HR = 1.14, P = 0.26). Following progression on first-line chemotherapy, BRAF-mutant patients had a markedly shorter P-PS (4.2 versus 9.2 months, adjusted HR = 1.69, P < 0.001). Fewer BRAF-mutant patients received second-line treatment (33% versus 51%, P < 0.001), but BRAF-mutation was not associated with inferior second-line outcomes (RR adjusted OR = 0.56, P = 0.45; PFS adjusted HR = 1.01, P = 0.93). Significant clinical heterogeneity within the BRAF-mutant population was observed: a proportion (24.3%) had good first-line PFS and P-PS (both >6 months; OS = 24.0 months); however, 36.5% progressed rapidly through first-line chemotherapy and thereafter, with OS = 4.7 months. Conclusions: BRAF-mutant aCRC confers a markedly worse prognosis independent of associated clinicopathological features. Chemotherapy provides meaningful improvements in outcome throughout treatment lines. Post-progression survival is markedly worse and vigilance is required to ensure appropriate delivery of treatment after first-line progression.

Macrochimerism in Intestinal Transplantation: Association With Lower Rejection Rates and Multivisceral Transplants, Without GVHD.

Blood chimerism has been reported sporadically among visceral transplant recipients, mostly in association with graft-vs-host disease (GVHD). We hypothesized that a higher degree of mixed chimerism would be observed in multivisceral (MVTx) than in isolated intestinal (iITx) and isolated liver transplant (iLTx) recipients, regardless of GVHD. We performed a longitudinal prospective study investigating multilineage blood chimerism with flow cytometry in 5 iITx and 4 MVTx recipients up to one year posttransplant. Although only one iITx patient experienced GVHD, T cell mixed chimerism was detected in 8 out of 9 iITx/MVTx recipients. Chimerism was significantly lower in the four subjects who displayed early moderate to severe rejection. Pre-formed high-titer donor-specific antibodies, bound in vivo to the circulating donor cells, were associated with an accelerated decline in chimerism. Blood chimerism was also studied in 10 iLTx controls. Among nonsensitized patients, MVTx recipients exhibited greater T and B cell chimerism than either iITx or iLTx recipients. Myeloid lineage chimerism was present exclusively among iLTx and MVTx (6/13) recipients, suggesting that its presence required the hepatic allograft. Our study demonstrates, for the first time, frequent T cell chimerism without GVHD following visceral transplantation and a possible relationship with reduced rejection rate in MVTx recipients.

Anti-JC virus (JCV) antibody prevalence in the JCV Epidemiology in MS (JEMS) trial.

BACKGROUND AND PURPOSE: Progressive multifocal leukoencephalopathy (PML) is caused by reactivation of JC virus (JCV) infection due to combined host and viral factors. Anti-JCV antibodies provide a means to assess JCV exposure and stratify PML risk. The reported seroprevalence of anti-JCV antibodies varies from 39% to 91% depending on assay methodology and population studied. A two-step anti-JCV antibody assay (STRATIFY JCV™; Focus Diagnostics, Cypress, CA, USA) detected anti-JCV antibodies in approximately 55% of multiple sclerosis (MS) patients. This study describes the prevalence of anti-JCV antibodies in a large, multinational MS population. METHODS: This cross-sectional epidemiology study was designed to enroll a minimum of 2000 patients with an MS diagnosis of any type, irrespective of treatment, from Europe, Canada and Australia. Anti-JCV antibody prevalence was determined by STRATIFY JCV; the effects of demographic and disease characteristics were evaluated. RESULTS: A total of 7724 patients from 10 countries participated in the study. Overall anti-JCV antibody prevalence was 57.1% (95% confidence interval 56.0%-58.2%). Seroprevalence was significantly associated with increasing age, gender and country of current residence (P < 0.0001). No significant differences in anti-JCV antibody prevalence were associated with MS disease characteristics, including duration and type of MS and number and duration of MS therapies. CONCLUSIONS: Overall seroprevalence of anti-JCV antibodies in MS patients from Europe, Canada and Australia was consistent with previous studies using the STRATIFY JCV assay. Anti-JCV prevalence differed significantly by age, gender and country, but no geographical pattern was evident. Disease and treatment type were not associated with differences in anti-JCV antibody status.

A feasibility study testing four hypotheses with phase II outcomes in advanced colorectal cancer (MRC FOCUS3): a model for randomised controlled trials in the era of personalised medicine?

BACKGROUND: Molecular characteristics of cancer vary between individuals. In future, most trials will require assessment of biomarkers to allocate patients into enriched populations in which targeted therapies are more likely to be effective. The MRC FOCUS3 trial is a feasibility study to assess key elements in the planning of such studies. PATIENTS AND METHODS: Patients with advanced colorectal cancer were registered from 24 centres between February 2010 and April 2011. With their consent, patients' tumour samples were analysed for KRAS/BRAF oncogene mutation status and topoisomerase 1 (topo-1) immunohistochemistry. Patients were then classified into one of four molecular strata; within each strata patients were randomised to one of two hypothesis-driven experimental therapies or a common control arm (FOLFIRI chemotherapy). A 4-stage suite of patient information sheets (PISs) was developed to avoid patient overload. RESULTS: A total of 332 patients were registered, 244 randomised. Among randomised patients, biomarker results were provided within 10 working days (w.d.) in 71%, 15 w.d. in 91% and 20 w.d. in 99%. DNA mutation analysis was 100% concordant between two laboratories. Over 90% of participants reported excellent understanding of all aspects of the trial. In this randomised phase II setting, omission of irinotecan in the low topo-1 group was associated with increased response rate and addition of cetuximab in the KRAS, BRAF wild-type cohort was associated with longer progression-free survival. CONCLUSIONS: Patient samples can be collected and analysed within workable time frames and with reproducible mutation results. Complex multi-arm designs are acceptable to patients with good PIS. Randomisation within each cohort provides outcome data that can inform clinical practice.

KRAS mutation analysis on low percentage of colon cancer cells: the importance of quality assurance.

KRAS mutation testing is mandatory for patients with metastatic colorectal cancer who are eligible for treatment with an epidermal growth factor receptor targeting agent, since tumors with a mutation are not sensitive to the drug. Several methods for mutation testing are in use and the need for external quality assurance has been demonstrated. An often little addressed but important issue in external quality assurance schemes is a low percentage of tumor cells in the test samples, where the analytical sensitivity of most tests becomes critical. Using artificial samples based on a mixture of cell lines with known mutation status of the KRAS gene, we assessed the reliability of a series of commonly used methods (Sanger sequencing, high resolution melting, pyrosequencing, and amplification refractory mutation system-polymerase chain reaction) on samples with 0, 2.5, 5, 10, and 15 % mutated cells. Nine laboratories throughout Europe participated and submitted a total of ten data sets. The limit of detection of each method differed, ranging from >15-5 % tumor cells. All methods showed a decreasing correct mutation call rate proportionally with decreasing percentage of tumor cells. Our findings indicate that laboratories and clinicians need to be aware of the decrease in correct mutation call rate proportionally with decreasing percentage of tumor cells and that external quality assurance schemes need to address the issue of low tumor cell percentage in the test samples.

Single-chain VαVß T-cell receptors function without mispairing with endogenous TCR chains.

Transduction of exogenous T-cell receptor (TCR) genes into patients' activated peripheral blood T cells is a potent strategy to generate large numbers of specific T cells for adoptive therapy of cancer and viral diseases. However, the remarkable clinical promise of this powerful approach is still being overshadowed by a serious potential consequence: mispairing of the exogenous TCR chains with endogenous TCR chains. These 'mixed' heterodimers can generate new specificities that result in graft-versus-host reactions. Engineering TCR constant regions of the exogenous chains with a cysteine promotes proper pairing and reduces the mispairing, but, as we show here, does not eliminate the formation of mixed heterodimers. By contrast, deletion of the constant regions, through use of a stabilized Vα/Vß single-chain TCR (scTv), avoided mispairing completely. By linking a high-affinity scTv to intracellular signaling domains, such as Lck and CD28, the scTv was capable of activating functional T-cell responses in the absence of either the CD3 subunits or the co-receptors, and circumvented mispairing with endogenous TCRs. Such transduced T cells can respond to the targeted antigen independent of CD3 subunits via the introduced scTv, without the transduced T cells acquiring any new undefined and potentially dangerous specificities.

KRAS and BRAF mutations in Nigerian colorectal cancers.

PURPOSE: Activation of the KRAS oncogene is implicated in colorectal carcinogenesis and mutations have been reported in 30-50% of cases. BRAF mutation, though less common, is also reported and importantly associated with shorter progression-free interval. This study aims to determine the KRAS and BRAF mutation statuses of Nigerian colorectal cancers (CRC). METHODS: Mutation analysis was carried out on archival paraffin-embedded blocks of CRC tissues. KRAS codons 12, 13 and 61 and BRAF V600E were assessed by pyrosequencing after DNA extraction from 200 cases at the Leeds Institute of Molecular Medicine, St. James's University Hospital, UK. Mutation rates and the spectra were determined. RESULTS: Pyrosequencing was successful in 112 of 200 cases. KRAS mutation in codons 12 and 13 was demonstrated in 23 of 112 cases (21%); none in codon 61. BRAF mutation in codon 600 was demonstrated in 4.5%. CONCLUSION: This study shows that 21% of Nigerian CRC patients carry a KRAS mutation; half the rate in Caucasians; and that BRAF mutation also occurs in Nigerian CRC cancers.

Clinical outcomes of natalizumab-associated progressive multifocal leukoencephalopathy.

OBJECTIVE: Natalizumab, a therapy for multiple sclerosis (MS), has been associated with progressive multifocal leukoencephalopathy (PML), a rare opportunistic infection of the CNS associated with the JC virus. We assessed clinical outcomes and identified variables associated with survival in 35 patients with natalizumab-associated PML. METHODS: Physicians provided Karnofsky scores and narrative descriptions of clinical status. Data were supplemented by the natalizumab global safety database. RESULTS: At the time of analysis, 25 patients (71%) had survived. Survivors were younger (median 40 vs 54 years) and had lower pre-PML Expanded Disability Status Scale scores (median 3.5 vs 5.5) and a shorter time from symptom onset to diagnosis (mean 44 vs 63 days) compared with individuals with fatal cases. Of patients with nonfatal cases, 86% had unilobar or multilobar disease on brain MRI at diagnosis, whereas 70% of those with fatal cases had widespread disease. Gender, MS duration, natalizumab exposure, prior immunosuppressant use, and CSF JC viral load at diagnosis were comparable. Most patients were treated with rapid removal of natalizumab from the circulation. The majority of patients developed immune reconstitution inflammatory syndrome and were treated with corticosteroids. Among survivors with at least 6 months follow-up, disability levels were evenly distributed among mild, moderate, and severe, based on physician-reported Karnofsky scores. CONCLUSIONS: Natalizumab-associated PML has improved survival compared with PML in other populations. Disability in survivors ranged from mild to severe. A shorter time from symptom onset to diagnosis and localized disease on MRI at diagnosis were associated with improved survival. These data suggest that earlier diagnosis through enhanced clinical vigilance and aggressive management may improve outcomes.

What can the molecular pathologist offer for optimal decision making?

As a consequence of new innovative therapies and therapeutic combinations, the treatment of advanced colorectal cancer is becoming increasingly complex. Validated molecular biomarkers could contribute to patient management, but until recently, none has been routinely used. With the recognition that activating mutations of the KRAS oncogene can predict resistance to anti-epidermal growth factor receptor agents, the clinical value of biomarkers in advanced colorectal cancer has been brought to the fore. Prognostic and predictive biomarkers that reflect the molecular and therapeutic complexities of advanced colorectal cancer may provide valuable information regarding likely clinical outcome and therapeutic response and thus may improve patient management and therapeutic agent selection. Such biomarkers are discussed herein.

Ezrin is a key element in the human vagina.

OBJECTIVE: The vagina is a complex tubular structure that has reproductive, support and barrier functions. These depend on the cytoarchitecture of the vaginal cells, which is controlled by key proteins. Cytoskeletal proteins determine cell polarity and membrane specializations by integrating the actin cytoskeleton with cell membranes. This integration is the domain of cytoskeletal proteins including the MERM protein family (moesin-ezrin-radixin-Merlin). Nothing is known about the cyto-localization of the MERM's in the vaginal epithelium or how it influences the cytoarchitecture of the vaginal epithelium and stroma. DESIGN: Full-thickness human vaginal fornix samples were obtained from 20 normal human specimens obtained at surgery for pelvic relaxation. Light- and electron microscopical immunohistochemistry (IHC) were used to identify and study activation and cellular localization of immuno-reactive-ezrin (ir-ezrin), a prototypical MERM. RESULTS: Ir-ezrin was identified in the stratified squamous vaginal epithelium and connective tissue (fibroblasts, blood vessels and leucocytes). "H" scoring indicated that ir-ezrin staining is denser in the vaginal epithelium than in other layers, that the ir-ezrin staining was associated with increased keratinization and with the size of the tight junctions (p<0.01). Both the amounts and localization of ir-ezrin were associated with high levels of estrogen, identified by the menstrual history and keratinization of the superficial vaginal epithelium. The density of stromal ir-ezrin was increased in the presence of dense epithelial keratinization. Immuno-reactive-ezrin staining was most pronounced near the cell membranes of both keratinized and non-keratinized epithelium, indicating that ezrin activation (unfolding and movement to the membrane) had occurred. Ultra-structural examination of the epithelium showed intra-cellular ir-ezrin to be localized to junctional complexes that have been associated with decreased mucosal penetration by microorganisms. Ir-ezrin was widely distributed throughout stromal fibro-muscular cell, vessels and immunocytes. CONCLUSIONS: MERM's, represented by ezrin, are widely present in the vaginal wall. This has implications for the strength and resilience of this tubular structure and may be the case in other internal genital tissues. Ezrin's localization and association with cell specializations indicate that in the vagina, as in other tissues, ezrin likely modulates vaginal cell-cell interactions including the changing vaginal cellular interface with the external environment, the regulation of the elasticity of the vagina, and the regulation of microbial and chemical traffic that determine the pH and microbial environment of the vagina. In other work we have shown that ezrin expression is induced by estradiol. The increase of ir-ezrin staining during the appearance of keratinization and maturation of the vaginal cytology indicates that estrogen may regulate vaginal ezrin and thereby the properties of the vaginal wall and epithelium.

The incidence and risk factors associated with postoperative delirium in geriatric patients undergoing surgery for suspected gynecologic malignancies.

BACKGROUND: The incidence of postoperative delirium (PD) in the elderly ranges between 3-60% but has never been examined in gynecologic oncology. Our goal was to identify pre, intra, and postoperative risk factors associated with the development of PD. METHODS: English speaking women of 60 years and above undergoing major surgery for suspected gynecologic malignancies were invited to participate. Enrolled patients were administered a pre and postoperative Mini-Mental State Exam (MMSE), and the postoperative Confusion Assessment Method was used to diagnosis PD. Pre, intra, and postoperative clinicopathology parameters were collected. Statistics included the Pearson chi-squared tests and multivariate logistic regression. RESULTS: Eighteen of a total of 103 patients (17.5%) developed PD. Univariate analysis revealed significant associations (p<0.05) between the development of delirium and age, albumin level, Charlson comorbidity index, performance status, dementia, level of education, number of pre and postoperative medications, prolonged oxygen or Foley catheter usage (>2 d), increased narcotic use (above standard regimens), postoperative transfusion, bed restriction and change in MMSE scores (pre vs. post). Using multivariate logistic regression analysis, older patients (p=0.0002), on multiple medications (p=0.008), given additional narcotic doses (p<0.0001) were at highest risk for the development of delirium. Intraoperative parameters were not correlated with outcome. CONCLUSIONS: PD is a common complication in older women undergoing major gynecologic surgery. Increased narcotics, age, and preoperative medications were strongly associated with this adverse event. Prevention needs to focus on i) identifying patients at higher risk for PD based on preoperative parameters, and ii) eliminating known postoperative risk factors.

Costs of diving by wing and foot propulsion in a sea duck, the white-winged scoter.

Most birds swim underwater by either feet alone or wings alone, but some sea ducks often use both. For white-winged scoters (Melanitta fusca), we measured costs (V(O2)) of dives to 2 m with descent by feet only versus wings + feet (only feet are used at the bottom). Dive costs repaid during the recovery period after a dive bout were an important fraction (27-44%) of total dive costs, and removing costs of extraneous surface behaviors increased resolution of differences between dive types. Scoters using wings + feet had 13% shorter descent duration, 18% faster descent speed, 31% fewer strokes/m, and 59% longer bottom duration than with feet only. The cost of time underwater for dives using wings + feet was 32-37% lower than with feet only (P = 0.09 to 0.15). When indirect methods were used to partition descent costs from costs of ascent and bottom phases, using wings + feet lowered descent cost by an estimated 34%. Thus, using wings + feet increases descent speed and lowers descent cost, leaving more time and energy for bottom foraging. For birds in cold water, the large savings may result from both biomechanical and thermoregulatory factors.

Development of a novel strategy for engineering high-affinity proteins by yeast display.

Yeast display provides a system for engineering high-affinity proteins using a fluorescent-labeled ligand and fluorescence-activated cell sorting (FACS). In cases where it is difficult to obtain purified ligands, or to access FACS instrumentation, an alternative selection strategy would be useful. Here we show that yeast expressing high-affinity proteins against a mammalian cell surface ligand could be rapidly selected by density centrifugation. Yeast cell-mammalian cell conjugates were retained at the density interface, separated from unbound yeast. High-affinity T cell receptors (TCRs) displayed on yeast were isolated using antigen presenting cells that expressed TCR ligands, peptides bound to products of the major histocompatibility complex (MHC). The procedure yielded 1000-fold enrichments, in a single centrifugation, of yeast displaying high-affinity TCRs. We defined the affinity limits of the method and isolated high-affinity TCR mutants against peptide variants that differed by only a single residue. The approach was applied to TCRs specific for class I or class II MHC, an important finding since peptide-class II MHC ligands have been particularly difficult to purify. As yeast display has also been used previously to identify antigen-specific antibodies, the method should be applicable to the selection of antibodies, as well as TCRs, with high-affinity for tumor cell-surface antigens.

Pharmacogenomic analysis: correlating molecular substructure classes with microarray gene expression data.

Genomic studies are producing large databases of molecular information on cancers and other cell and tissue types. Hence, we have the opportunity to link these accumulating data to the drug discovery processes. Our previous efforts at 'information-intensive' molecular pharmacology have focused on the relationship between patterns of gene expression and patterns of drug activity. In the present study, we take the process a step further-relating gene expression patterns, not just to the drugs as entities, but to approximately 27,000 substructures and other chemical features within the drugs. This coupling of genomic information with structure-based data mining can be used to identify classes of compounds for which detailed experimental structure-activity studies may be fruitful. Using a systematic substructure analysis coupled with statistical correlations of compound activity with differential gene expression, we have identified two subclasses of quinones whose patterns of activity in the National Cancer Institute's 60-cell line screening panel (NCI-60) correlate strongly with the expression patterns of particular genes: (i) The growth inhibitory patterns of an electron-withdrawing subclass of benzodithiophenedione-containing compounds over the NCI-60 are highly correlated with the expression patterns of Rab7 and other melanoma-specific genes; (ii) the inhibitory patterns of indolonaphthoquinone-containing compounds are highly correlated with the expression patterns of the hematopoietic lineage-specific gene HS1 and other leukemia genes. As illustrated by these proof-of-principle examples, we introduce here a set of conceptual tools and fluent computational methods for projecting directly from gene expression patterns to drug substructures and vice versa. The analysis is presented in terms of the NCI-60 cell lines and microarray-based gene expression patterns, but the concept and methods are broadly applicable to other large-scale pharmacogenomic database sets as well. The approach (SAT for Structure-Activity-Target) provides a systematic way to mine databases for the design of further structure-activity studies, particularly to aid in target and lead identification.

A new determination of G using two methods.

We present the results of a measurement of G made with a torsion-strip balance used in two substantially independent ways. The two results agree to within their respective uncertainties; the correlation coefficient of the two methods is -0.18. The result is G = 6.675 59(27)x10(-11) m(3) kg(-1) s(-2) with a standard uncertainty of 4.1 parts in 10(5). Our result is 2 parts in 10(4) higher than the recent result of Gundlach and Merkowitz.

The Mackworth Clock Test: a computerized version.

The Mackworth Clock Test (MCT; N. H. Mackworth, 1948) was developed to evaluate vigilance in British Air Force radar technicians during World War II. Homemade versions of the MCT have since varied with respect to both the characteristics of the device and the procedures of its administration. This article is a report on a computerized version of the MCT developed by the authors to closely emulate Mackworth's test. MCT data were collected from 25 undergraduate students; their performance was found to be equivalent to Mackworth's participants' data. This is the first MCT version that has been validated against the original.

Minority cancer patients and their providers: pain management attitudes and practice.

BACKGROUND: The goals of the current studies were: 1) to determine the pain treatment needs of socioeconomically disadvantaged African-American and Hispanic patients with recurrent or metastatic cancer and 2) to assess the attitudes of health care professionals who treat them. METHODS: In the first study 108 African-American and Hispanic patients with metastatic or recurrent cancer and pain completed a survey about their pain intensity, pain interference, and attitudes toward analgesic medications. Physicians also rated their patients' pain and the adequacy of the patients' current analgesic prescriptions was assessed. In the second study 55 physicians and nurses who treat these patients completed a questionnaire regarding cancer pain and its management in their practice settings. RESULTS: Approximately 28% of the Hispanic and 31% of the African-American patients received analgesics of insufficient strength to manage their pain. Although the majority of patients received appropriate analgesics, 65% reported severe pain. Physicians underestimated pain severity for 64% of the Hispanic and 74% of the African-American patients. Physicians were more likely to underestimate the pain severity of female patients than male patients. Inadequate pain assessment, patient reluctance to report pain, and lack of staff time were perceived as barriers to pain management. CONCLUSIONS: Although the data suggest recent improvements in analgesic prescribing practices for African-American and Hispanic cancer patients, the majority of patients reported high levels of pain and limited pain relief from analgesic medications. Inadequate pain assessment remains a major barrier to optimal cancer pain treatment.

Distortions of depth-order relations and parallelism in structure from motion.

Four experiments related human perception of depth-order relations in structure-from-motion displays to current Euclidean and affine theories of depth recovery from motion. Discrimination between parallel and nonparallel lines and relative-depth judgments was observed for orthographic projections of rigidly oscillating random-dot surfaces. We found that (1) depth-order relations were perceived veridically for surfaces with the same slant magnitudes, but were systematically biased for surfaces with different slant magnitudes. (2) Parallel (virtual) lines defined by probe dots on surfaces with different slant magnitudes were judged to be nonparallel. (3) Relative-depth judgments were internally inconsistent for probe dots on surfaces with different slant magnitudes. It is argued that both veridical performance and systematic misperceptions may be accounted for by a heuristic analysis of the first-order optic flow.