Leveraging Quantitative Imaging and Machine Learning to Differentiate Radionecrosis from Disease Recurrence in Patients with Brain Metastases

PURPOSE/OBJECTIVE(S)

Radiation necrosis can be difficult to non-invasively discern from tumor progression after stereotactic radiosurgery (SRS). In this work, we investigate the utility of radiomics (computerized features) and machine learning to capture per-voxel lesion heterogeneity on routine MRI scans, to differentiate radionecrosis from tumor recurrence in patients with brain metastases treated with SRS.

MATERIALS/METHODS

A retrospective analysis was conducted of patients with brain metastases treated with SRS. Eighty-three lesions (n = 56 intact; n = 27 surgical cavity) from 69 patients were identified with median age 68.8 years (range 40.2 - 91.0), of whom 53.6% were male and 33.3% received prior whole-brain radiotherapy (WBRT). Lesion histology included lung (60.2%), renal cell (15.7%), melanoma (10.8%), breast (9.6%), and other (3.6%). Pathologic confirmation was available in 73.5% of lesions. Both intact and resection cavity lesions were included and individually segmented. Image preprocessing and radiomic feature extraction were done using ANTsPy and open-source software. A total of 210 features were extracted from post-contrast T1-weighted (T1w) and T2/FLAIR MRIs. Highly correlated features were removed. Univariate logistic regression was conducted on the remaining T1w and T2/FLAIR features as well as on clinical variables. Multivariate analysis was implemented with various classifiers (Random Forest, Ridge, Lasso, Support Vector Machine [SVM]) on the top-performing features found on univariate logistic regression. Models were assessed using cross-validation to select the best model by area under ROC curve (AUC). Specificity and sensitivity were calculated.

RESULTS

On univariate analysis, the top 10 radiomics features consisted of 6 T1w features and 4 T2/FLAIR features (4 GLCM, 3 first order, 1 GLSZM, 1 GLRLM, and 1 shape feature). Age, gender, disease site, prior WBRT, prior fractionated SRS, planning tumor volume, brain-GTV V12 Gy, and immunotherapy before or after SRS were not predictive (AUC less than 62.0%) on univariate analysis compared to radiomic features. Multivariate analysis of top performing radiomic features on both intact and surgical cavities yielded an AUC of 72.0% (standard deviation [SD] ±8.8%). Multivariate analysis of top features on intact lesions alone improved the AUC to 80.5% (SD ±10.8%), with sensitivity of 77.8%, specificity of 72.4%, and positive likelihood ratio of 2.82 in differentiating radionecrosis from recurrence.

CONCLUSION

Radiomics and machine learning tools may improve diagnostic ability of distinguishing radiation necrosis from tumor recurrence after SRS. Further work is needed to deploy this in a larger multi-institutional cohort and prospectively evaluate its efficacy as a decision-support tool to personalize care in patients with brain metastases.

Longitudinal Radiomics-Based Prediction of Local Recurrence after Stereotactic Body Radiation Therapy for Early-Stage Non-Small Cell Lung Cancer

PURPOSE/OBJECTIVE(S)

Computed tomography (CT)-based radiomic analysis is an emerging tool that can help predict recurrence after radiation in non-small cell lung cancer (NSCLC). Most studies have focused on using radiomic features obtained from pre-treatment CT scans but not on post-treatment CTs. Our goal was to determine if radiomic features derived from post-treatment CTs perform better than those from pre-treatment CTs in predicting local recurrence after stereotactic body radiation therapy (SBRT) in patients with early-stage NSCLC.

MATERIALS/METHODS

Patients with T1/T2 N0 early-stage NSCLC were retrospectively reviewed. Criteria for selection included patients with biopsy-proven NSCLC, non-ground glass solid lesions, 4-5 fraction SBRT treatments, and non-contrast thin-slice CTs available at pre-treatment baseline and at 3 and 6 months post-SBRT. Clinical and tumor characteristics were compared using Chi-square and Student's t-tests. CT image pre-processing was performed and 107 radiomic features were extracted using 3D Slicer and open-source software. Univariate analysis for local recurrence was determined by Cox regression with death as a competing risk. The Benjamini-Hochberg Procedure was applied to control the false discovery rate. Pearson correlation analysis was used to exclude redundant features (r > 0.8), and multivariate analysis was conducted with Random Forest on the top-performing features found on univariate logistic regression. Models were trained on a class-balanced loss to account for class imbalance. Twenty iterations of stratified 3 k-fold cross-validation were used to select the best model by the area under the receiver operating characteristic curve (AUC).

RESULTS

We identified and analyzed 86 patient tumors, including 76 non-local recurrences and 10 local recurrences (49 males, 37 females; age, median 72, range 52-91 years). No differences in age, histology, standardized uptake values on positron emission tomography scans, gross tumor volume, and radiation dose were found between patients with and without local recurrence (all p >0.05). The median time to local recurrence was 18.9 months (range 5.5-45.6 months). At the baseline, 3-month, and 6-month timepoints, 2, 10, and 10 radiomic features predicted local recurrence on Cox regression univariate analysis, respectively (all q <0.01). On multivariate analysis of top-performing radiomic features, the 3-month timepoint performed the best with a mean (±standard deviation) AUC score of 0.82 (±0.13) compared to a mean AUC of 0.73 (±0.086) at baseline and a mean AUC of 0.74 (±0.10) at 6 months.

CONCLUSION

Post-treatment radiomic features at 3 months outperformed pre-treatment radiomic features in predicting local recurrence after SBRT for NSCLC. These results suggest radiomic data from follow-up CTs may be helpful when developing radiomic models to predict local recurrence in patients with NSCLC.

CAR T in patients with large B-cell lymphoma not fit for autologous transplant

Large B-cell lymphoma (LBCL) patients with comorbidities and/or advanced age are increasingly considered for treatment with CD19 CAR T, but data on the clinical benefit of CAR T in the less fit patient population are still limited. We analysed outcomes of consecutive patients approved for treatment with axicabtagene ciloleucel (axi-cel) or tisagenlecleucel (tisa-cel) by the UK National CAR T Clinical Panel, according to fitness for autologous stem cell transplant (ASCT). 81/404 (20%) of approved patients were deemed unfit for ASCT. Unfit patients were more likely to receive tisa-cel versus axi-cel (52% vs. 48%) compared to 20% versus 80% in ASCT-fit patients; p < 0.0001. The drop-out rate from approval to infusion was significantly higher in the ASCT-unfit group (34.6% vs. 23.5%; p = 0.042). Among infused patients, response rate, progression-free and overall survival were similar in both cohorts. CAR T was well-tolerated in ASCT-unfit patients with an incidence of grade ≥3 cytokine release syndrome and neurotoxicity of 2% and 11%, respectively. Results from this multicentre real-world cohort demonstrate that CD19 CAR T can be safely delivered in carefully selected older patients and patients with comorbidities who are not deemed suitable for transplant.

Gut microbe-targeted choline trimethylamine lyase inhibition improves obesity via rewiring of host circadian rhythms

Obesity has repeatedly been linked to reorganization of the gut microbiome, yet to this point obesity therapeutics have been targeted exclusively toward the human host. Here, we show that gut microbe-targeted inhibition of the trimethylamine N-oxide (TMAO) pathway protects mice against the metabolic disturbances associated with diet-induced obesity (DIO) or leptin deficiency (Lep^ob/ob). Small molecule inhibition of the gut microbial enzyme choline TMA-lyase (CutC) does not reduce food intake but is instead associated with alterations in the gut microbiome, improvement in glucose tolerance, and enhanced energy expenditure. We also show that gut microbial CutC inhibition is associated with reorganization of host circadian control of both phosphatidylcholine and energy metabolism. This study underscores the relationship between microbe and host metabolism and provides evidence that gut microbe-derived trimethylamine (TMA) is a key regulator of the host circadian clock. This work also demonstrates that gut microbe-targeted enzyme inhibitors have potential as anti-obesity therapeutics.

Improved methods for biomarker analysis of the big five mycotoxins enables reliable exposure characterization in a population of childbearing age women in Rwanda

Of the five agriculturally important mycotoxins, AFB₁, FB₁, DON, ZEA and OTA, a well-characterized biomarker of exposure in blood is only available for aflatoxin. Working with a population of 139 women of childbearing age in Rwanda, we undertook a comprehensive assessment of their dietary mycotoxin exposure. Using high-resolution LC-MS/MS with stable isotope dilution analysis, the albumin-aflatoxin adduct was quantitated in plasma. Similarly, AFM₁, AFB₁, AFG₁, FB₁ and B₂, OTA, zearalenone, α-zearalenol, deoxynivalenol, deoxynivalenol-15-glucuronide and deoxynivalenol-3-glucuronide were quantitated in urine. AFB₁-Lys was detected in plasma from 81% of the women, indicative of exposures 1-2 orders of magnitude above current guidance. Zearalenone and/or α-zearalenol were detected in the urine of 61% of the women, the majority of whom had estimated exposures 2-5 times the PMTDI, with one third more than an order of magnitude above. Urinary deoxynivalenol or the two glucuronide conjugates were found in 77% of the participants. Of these, 60% were below the PMTDI, 28% were twice and 12% were >10x the PMTDI. Fumonisin B₁ (30%) and ochratoxin A (71%) were also detected in urine. Exposures observed in these Rwandan women raise serious food safety concerns and highlight the need for authorities to help manage multiple mycotoxins in their diet.

Combinatorial morphogenetic and mechanical cues to mimic bone development for defect repair

Endochondral ossification during long bone development and natural fracture healing initiates by mesenchymal cell condensation, directed by local morphogen signals and mechanical cues. Here, we aimed to mimic development for regeneration of large bone defects. We hypothesized that engineered human mesenchymal condensations presenting transforming growth factor-β1 (TGF-β1) and/or bone morphogenetic protein-2 (BMP-2) from encapsulated microparticles promotes endochondral defect regeneration contingent on in vivo mechanical cues. Mesenchymal condensations induced bone formation dependent on morphogen presentation, with BMP-2 + TGF-β1 fully restoring mechanical function. Delayed in vivo ambulatory loading significantly enhanced the bone formation rate in the dual morphogen group. In vitro, BMP-2 or BMP-2 + TGF-β1 initiated robust endochondral lineage commitment. In vivo, however, extensive cartilage formation was evident predominantly in the BMP-2 + TGF-β1 group, enhanced by mechanical loading. Together, this study demonstrates a biomimetic template for recapitulating developmental morphogenic and mechanical cues in vivo for tissue engineering.

Impact of intended and relative dose intensity of R-CHOP in a large, consecutive cohort of elderly diffuse large B-cell lymphoma patients treated with curative intent: no difference in cumulative incidence of relapse comparing patients by age

BACKGROUND

The increasing incidence of diffuse large B-cell lymphoma (DLBCL) in ageing populations places a significant burden on healthcare systems. Co-morbidity, frailty, and reduced organ and physiological reserve contribute to treatment-related complications. The optimal dose intensity of R-CHOP to optimize outcome across different ages with variable frailty and comorbidity burden is unclear.

OBJECTIVES AND METHODS

We examined the influence of intended (IDI) and relative (RDI) dose intensity of the combination of cyclophosphamide and doxorubicin, age and comorbidity on outcomes for DLBCL patients ≥70 years in a representative, consecutive cohort across eight UK centres (2009-2018). We determined predictors of survival using multivariable Cox regression, and predictors of recurrence before death using competing risks regression.

RESULTS

Porgression-free survival (PFS) and overall survival (OS) were significantly inferior in patients ≥80 vs. 70-79 years (P < 0.001). In contrast, 2-year cumulative relapse incidence, when accounting for non-relapse mortality as a competing risk, was no different between 70-79 vs. ≥80 years (P = 0.27) or comorbidity status (CIRS-G: 0-6 vs. >6) (P = 0.27). In 70-79 years, patients with an IDI ≥80% had a significantly improved PFS and OS (P < 0.001) compared to IDI < 80%. Conversely, in patients ≥80 years, there was no difference in PFS (P = 0.88) or OS (P = 0.75) according to IDI <80% vs. ≥80%. On multivariable analysis, when comparing by age, there was a significantly higher cumulative relapse rate for patients aged 70-79 years with an IDI <80% (vs. >80%) (P = 0.04) but not for patients ≥80 years comparing IDI (P = 0.32).

CONCLUSION

'R-mini-CHOP' provides adequate lymphoma-specific disease control and represents a reasonable treatment option in elderly patients ≥80 years aiming for cure.

Pilot assessment of probiotics for pregnant women in Rwanda

Background

While the global market for probiotics is soon to reach in excess of US$50 billion, the continent of Africa has been largely ignored, despite these products having the ability to reduce the burden of disease and death.

Trial design

The present randomised, blinded, placebo-controlled clinical trial was undertaken in Rwanda, a country devoid of well-documented probiotics. The primary outcome aim was to examine receptivity and compliance for orally administered probiotic capsules containing Lactobacillus rhamnosus GR-1 and Lactobacillus reuteri RC-14 in pregnant women and assess any initial side effects or changes to the vaginal microbiome.

Methods

Pregnant women between the ages of 18 and 55 were recruited from the Nyamata District Hospital in Rwanda and randomly assigned to receive probiotic or placebo capsules for one month. Clinicians were blinded to the treatments.

Results

The drop-out rate was 21%, with 13 of 18 women in the placebo group and 17 of 20 in the probiotic group completing the study. Only 13 women returned for birthing and additional sample collection. No side effects of either treatment group were reported. Microbiota and metabolomics data showed similar findings to those reported in the literature, with low bacterial diversity and Lactobacillus dominance associated with a healthy vagina, and birthing associated with high diversity. Despite the small sample size and lack of changes in the microbiota, women in the placebo arm were significantly more likely to give birth pre-term.

Conclusion

Overall women were receptive to the probiotic concept, but the lack of information on such products and logistical and economical challenges pose problems for wider population engagement.

Trial registration

ClinicalTrials.gov NCT02150655

Central nervous system relapse of diffuse large B-cell lymphoma in the rituximab era: results of the UK NCRI R-CHOP-14 versus 21 trial

Background

Central nervous system (CNS) relapse of diffuse large B-cell lymphoma (DLBCL) is associated with a dismal prognosis. Here, we report an analysis of CNS relapse for patients treated within the UK NCRI phase III R-CHOP (rituximab, cyclophosphamide, doxorubicin, vincristine and prednisolone) 14 versus 21 randomised trial.

Patients and methods

The R-CHOP 14 versus 21 trial compared R-CHOP administered two- versus three weekly in previously untreated patients aged ≥18 years with bulky stage I–IV DLBCL (n = 1080). Details of CNS prophylaxis were retrospectively collected from participating sites. The incidence and risk factors for CNS relapse including application of the CNS-IPI were evaluated.

Results

177/984 patients (18.0%) received prophylaxis (intrathecal (IT) methotrexate (MTX) n = 163, intravenous (IV) MTX n = 2, prophylaxis type unknown n = 11 and IT MTX and cytarabine n = 1). At a median follow-up of 6.5 years, 21 cases of CNS relapse (isolated n = 11, with systemic relapse n = 10) were observed, with a cumulative incidence of 1.9%. For patients selected to receive prophylaxis, the incidence was 2.8%. Relapses predominantly involved the brain parenchyma (81.0%) and isolated leptomeningeal involvement was rare (14.3%). Univariable analysis demonstrated the following risk factors for CNS relapse: performance status 2, elevated lactate dehydrogenase, IPI, >1 extranodal site of disease and presence of a ‘high-risk’ extranodal site. Due to the low number of events no factor remained significant in multivariate analysis. Application of the CNS-IPI revealed a high-risk group (4-6 risk factors) with a 2- and 5-year incidence of CNS relapse of 5.2% and 6.8%, respectively.

Conclusion

Despite very limited use of IV MTX as prophylaxis, the incidence of CNS relapse following R-CHOP was very low (1.9%) confirming the reduced incidence in the rituximab era. The CNS-IPI identified patients at highest risk for CNS recurrence.

ClinicalTrials.gov

ISCRTN number 16017947 (R-CHOP14v21); EudraCT number 2004-002197-34.

Aflatoxin exposure in Nigerian children with severe acute malnutrition

Aflatoxin exposure is an important public health concern in sub-Saharan Africa as well as parts of Latin America and Asia. In addition to hepatocellular carcinoma, chronic aflatoxin exposure is believed to play a role in childhood growth impairment. The most reliable biomarker of chronic aflatoxin exposure is the aflatoxin-albumin adduct, as measured by ELISA or isotope dilution mass spectrometry (IDMS). In this report, we have used high resolution LC-MS/MS with IDMS to quantitate AFB₁-lysine in an extremely vulnerable population of Nigerian children suffering from severe acute malnutrition. To increase the sensitivity and reliability of the analyses, a labelled AFB₁-¹³C₆¹⁵N₂-lysine internal standard was synthesized. AFB₁-lysine concentrations in this population ranged between 0.2 and 59.2 pg/mg albumin, with a median value of 2.6 pg/mg albumin. AFB₁-lysine concentrations were significantly higher in stunted children (median = 4.6 pg/mg) compared to non-stunted (1.2 pg/mg), as well as in children with severe acute malnutrition (4.3 pg/mg) compared to controls (0.8 pg/mg). The median concentrations were also higher in children with kwashiorkor (6.3 pg/mg) compared to those suffering from marasmus (0.9 pg/mg). This is the first report of the use of high-resolution mass spectrometry to quantitate AFB₁-lysine in humans.

Outcome of elderly patients with diffuse large B-cell lymphoma treated with R-CHOP: results from the UK NCRI R-CHOP14v21 trial with combined analysis of molecular characteristics with the DSHNHL RICOVER-60 trial

BACKGROUND

There is an on-going debate whether 2- or 3-weekly administration of R-CHOP is the preferred first-line treatment for elderly patients with diffuse large B-cell lymphoma (DLBCL). The UK NCRI R-CHOP14v21 randomized phase 3 trial did not demonstrate a difference in outcomes between R-CHOP-14 and R-CHOP-21 in newly diagnosed DLBCL patients aged 19-88 years, but data on elderly patients have not been reported in detail so far. Here, we provide a subgroup analysis of patients ≥60 years treated on the R-CHOP14v21 trial with extended follow-up.

PATIENTS AND METHODS

Six hundred and four R-CHOP14v21 patients ≥60 years were included in this subgroup analysis, with a median follow-up of 77.7 months. To assess the impact of MYC rearrangements (MYC-R) and double-hit-lymphoma (DHL) on outcome in elderly patients, we performed a joint analysis of cases with available molecular data from the R-CHOP14v21 (N = 217) and RICOVER-60 (N = 204) trials.

RESULTS

Elderly DLBCL patients received high dose intensities with median total doses of ≥98% for all agents. Toxicities were similar in both arms with the exception of more grade ≥3 neutropenia (P < 0.0001) and fewer grade ≥3 thrombocytopenia (P = 0.05) in R-CHOP-21 versus R-CHOP-14. The elderly patient population had a favorable 5-year overall survival (OS) of 69% (95% CI: 65-73). We did not identify any subgroup of patients that showed differential response to either regimen. In multivariable analysis including individual factors of the IPI, gender, bulk, B2M and albumin levels, only age and B2M were of independent prognostic significance for OS. Molecular analyses demonstrated a significant impact of MYC-R (HR = 1.96; 95% CI: 1.22-3.16; P = 0.01) and DHL (HR = 2.21; 95% CI: 1.18-4.11; P = 0.01) on OS in the combined trial cohorts, independent of other prognostic factors.

CONCLUSIONS

Our data support equivalence of both R-CHOP application forms in elderly DLBCL patients. Elderly MYC-R and DHL patients have inferior prognosis and should be considered for alternative treatment approaches.

TRIAL NUMBERS

ISCRTN 16017947 (R-CHOP14v21); NCT00052936 (RICOVER-60).

Abstract P2-03-02: Differential mutation pattern between neoadjuvant and metastatic settings in breast cancer patients

Background: Dysregulated signaling pathways occur in human cancers including breast cancer, making it a rational target for novel genome guided combinatorial personalized therapies. The aim of the present study was to investigate the different genetic mutation pattern between neoadjuvant and metastatic settings in breast cancer patients to guide research and clinical treatment.

Material and Methods: 150 breast cancer patients were involved in this study. 38 patients were receiving neoadjuvant treatment and 112 patients were in the metastatic setting. Tumor specimens obtained from the 150 patients were subjected to genetic mutation testing by FoundationOne. Genetic alterations detected by FoundationOne test were collected and analyzed.

Results: 96 and 149 different genes where reported by FoundationOne in neoadjuvant and metastatic setting respectively. The average number of non-synonymous mutation was five per case in the neoadjuvant setting and six per case in the metastatic setting. TP53 (58%), MYC (32%), PIK3CA (29%), PTEN (16%), CDH1 (13%), CCND1 (11%), EMSY (11%), LYN (11%) and ZNF703 (11%) were the most seen mutations in neoadjuvant setting. TP53 (40%), PIK3CA (39%), MYC (22%), CCND1 (21%), FGF19 (21%), FGF4 (21%), CDH1 (20%), FGF3 (19%), ERBB2 (17%), ESR1 (14%), FGFR1 (14%), ZNF703 (14%), GATA3 (13%), MYST3 (11%), PTEN (11%), EMSY (10%), NF1 (10%) and ZNF217 (10%) were the most seen mutations in metastatic setting. ESR1 and GATA3, which are seen in 14% and 13% of metastatic breast cancer patients, were not reported in neoadjuvant breast patients. Moreover, among the 16 metastatic breast cancer patients who has ESR1 mutation, 9 (56%) of them presented with PIK3CA or other genetic mutations which are directly involved in the phosphoinositide 3-kinase (PI3K)/AKT pathway.

Conclusion: A significantly more mutation in Receptor Tyrosine Kinases (RTKs)/ Growth Factor Signaling ( especially ERBB and FGFR pathways) was reported in the metastatic setting compare to the neoadjuvant setting, suggesting a critical role of the RTKs in metastatic breast cancer patients. The coexisting of ESR1 and PI3K/AKT pathway alteration and the absence of ESR1 in neoadjuvant setting also suggested that in early stage breast cancer patients who have a PI3K pathway alterations; there is a higher chance to develop ESR1 mutation with disease progression.

Citation Format: Xu B, Williams C, De P, Dey N, Klein J, Williams K, McMillan A, Leyland-Jones B. Differential mutation pattern between neoadjuvant and metastatic settings in breast cancer patients [abstract]. In: Proceedings of the 2016 San Antonio Breast Cancer Symposium; 2016 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2017;77(4 Suppl):Abstract nr P2-03-02.

Experimental verification of multipartite entanglement in quantum networks

Multipartite entangled states are a fundamental resource for a wide range of quantum information processing tasks. In particular, in quantum networks, it is essential for the parties involved to be able to verify if entanglement is present before they carry out a given distributed task. Here we design and experimentally demonstrate a protocol that allows any party in a network to check if a source is distributing a genuinely multipartite entangled state, even in the presence of untrusted parties. The protocol remains secure against dishonest behaviour of the source and other parties, including the use of system imperfections to their advantage. We demonstrate the verification protocol in a three- and four-party setting using polarization-entangled photons, highlighting its potential for realistic photonic quantum communication and networking applications.

Multipartite entangled states are a fundamental resource for quantum information processing tasks; it is thus important to verify their presence. Here the authors present and demonstrate a protocol that allows any party in a network to verify if an untrusted source is distributing multipartite entangled states.

Post-acquisition filtering of salt cluster artefacts for LC-MS based human metabolomic studies

Liquid chromatography-high resolution mass spectrometry (LC-MS) has emerged as one of the most widely used platforms for untargeted metabolomics due to its unparalleled sensitivity and metabolite coverage. Despite its prevalence of use, the proportion of true metabolites identified in a given experiment compared to background contaminants and ionization-generated artefacts remains poorly understood. Salt clusters are well documented artefacts of electrospray ionization MS, recognized by their characteristically high mass defects (for this work simply generalized as the decimal numbers after the nominal mass). Exploiting this property, we developed a method to identify and remove salt clusters from LC-MS-based human metabolomics data using mass defect filtering. By comparing the complete set of endogenous metabolites in the human metabolome database to actual plasma, urine and stool samples, we demonstrate that up to 28.5 % of detected features are likely salt clusters. These clusters occur irrespective of ionization mode, column type, sweep gas and sample type, but can be easily removed post-acquisition using a set of R functions presented here. Our mass defect filter removes unwanted noise from LC-MS metabolomics datasets, while retaining true metabolites, and requires only a list of m/z and retention time values. Reducing the number of features prior to statistical analyses will result in more accurate multivariate modeling and differential feature selection, as well as decreased reporting of unknowns that often constitute the largest proportion of human metabolomics data.

Employing an Innovation Strategy in Racially Diverse Workforces

This study explored racial diversity’s influence on firm performance. A national sample of 177 banks was used to first test competing hypotheses supported by the resource-based view of the firm and social identity theory that posited positive and negative direct effects, respectively, of racial diversity on organizational performance. No support was found for either prediction. However, a contingency theory-based hypothesis was supported. A moderation effect indicated that racial diversity’s association with performance was contingent on firms’ level of innovation. Specifically, racial diversity enhanced performance for banks pursuing an innovation strategy, whereas for banks low in innovation, performance declined. The results suggest that a racially diverse workforce in conjunction with an innovation-focused business strategy may provide firms a competitive advantage. This study thus supports a contingency/resource-based perspective that states that racial diversity, as a knowledge-based resource, needs to be set in an appropriate context to fully realize its potential benefits.

The uptake of HIV testing among patients with chlamydial or gonococcal infections attending a genitourinary medicine clinic

Bacterial sexually transmitted infections (STIs) may be markers of high-risk sexual activity. Counselling for these infections provides an opportunity for promoting HIV testing.

The aim of the present study was to compare the uptake of HIV testing between patients with gonorrhoea or chlamydial infections and those without a bacterial STI. A study on patients screened for chlamydial or gonococcal infections in the Department of Genitourinary (GU) Medicine, Edinburgh between 1 July 2002 and 30 June 2003. The overall uptake of HIV testing among patients screened for chlamydial and gonococcal infections was 2263 (37%) of 6184 and 2012 (44%) of 4583, respectively ( P < 0.0002). Uptake of HIV testing was significantly higher among uninfected patients: for chlamydial infection, 17% of 1857 infected patients versus 45% of 4327 uninfected patients ( P < 0.0002); and for gonococcal infection, 24% of 256 infected patients versus 45% of 4327 uninfected patients ( P < 0.0002).

The policy of pre-test counselling needs to be redesigned in order to improve the uptake of HIV testing among patients with high-risk sexual activity.

Heterosexual men and women with HIV test positive at a later stage of infection than homo- or bisexual men

The current strategy of offering HIV testing to individuals with known risk has had no impact on the reduction in the number of patients diagnosed with immune suppression of infection. A prospective observational study to compare the baseline CD4+ T-cell counts in HIV-infected homosexual/bisexual men, intravenous drug users, heterosexual men and women diagnosed in GUM/RIDU and that of patients diagnosed during routine maternal screening for HIV between December 1999 and January 2003 was carried out at the Departments of Genitourinary Medicine (GUM), Regional Infectious Disease Unit (RIDU) and Obstetrics in Edinburgh.

Late presentation was defined as positive HIV test with baseline CD4+ T-cell count of less than 200 cells/mL.

During the study period, 189 patients tested in GUM/RIDU setting and 13 screened women were diagnosed with HIV infection. Thirty-four percent of the former and 38% of the latter group had CD4+ T-cell count of less than 200 cells/mL by the time of diagnosis. Heterosexual individuals contributed to 78% of HIV tests in the GUM/RIDU setting. Amongst the 78 HIV-infected heterosexual individuals diagnosed in GUM/RIDU 45% were late presenters. Significantly fewer homosexual men were late presenters. There was no difference between the proportion of late presenters amongst women screened at the antenatal (5/13) compared to heterosexual patients diagnosed in GUM/RIDU (35/78). A significant number of HIV infected heterosexual patients are late presenters in the HIV testing at GUM/RIDU. HIV screening programmes for heterosexual individuals in any medical encounter may reduce the number of late presenters.

The three-year positivity rate of sexually transmitted infections among a group of HIV-infected men attending the Department of Genitourinary Medicine, Edinburgh, UK

The aim of this study was to investigate the prevalence of sexually transmitted infections (STI) among patients at the time of and subsequent to the diagnosis of HIV, and possible immunological or virological features of patients with STI. An observational study was carried out on the results of annual STI screenings conducted on consecutive HIV-infected men in the Department of Genitourinary Medicine, Edinburgh between 1 January 1999 and 1 January 2003. Patients were tested for syphilis, gonococcal, and chlamydial infections.

Among the 79 male patients in the study cohort, the frequencies of all STI rose within the study period. The three-year positivity rates of episodes of gonorrhoea, chlamydia, and syphilis were (42/131) 32%, (21/127) 16%, and (13/150) 9%, respectively. Patients with STI had significantly higher median CD4+ T-cells ( P<0.02) and lower median viral loads ( P<0.0001), and a higher proportion of them were on highly active anti-retroviral therapy (HAART) ( P<0.0002) compared with those without an STI. Routine screening for STI and counselling for safe sex should be part of care for all HIV-infected patients.

Concurrent gonococcal and chlamydial infections among men attending a sexually transmitted diseases clinic

The aim of this retrospective study was to determine the prevalence of Chlamydia trachomatis co-infection in men with gonorrhoea attending a sexually transmitted diseases clinic in Edinburgh, Scotland. During the study period, there were 660 cases of culture-proven gonorrhoea. Chlamydial DNA was detected in the urethra in 79 (31%; 95% confidence interval [CI], 25–37%) heterosexual men who have sex with women (MSW); the median age was significantly lower than those with gonorrhoea alone (24.0 versus 30.0; P < 0.0005). The prevalence of urethral chlamydial infection among MSW was significantly higher than among men who have sex with men (MSM) (32 [12%; 95% CI, 8–16%] of 268 MSM) (χ2 = 27.21; P < 0.001). Sixteen (24%; 95% CI, 14–34%) of 68 MSM with rectal gonorrhoea had concurrent rectal chlamydial infection. The high prevalence of concurrent gonorrhoea and chlamydiae therefore warrants empirical treatment and/or testing for chlamydia in all men with urethral gonorrhoea.

The sensitivity of syphilis assays in detecting different stages of early syphilis

Our aim was to determine the sensitivity of the Murex ICE enzyme immunoassay (EIA) as a screening test for early syphilis and to determine how many additional cases of infection were detected by performing additional tests when requested on clinical grounds.

This was an observational study on consecutive patients diagnosed with syphilis in the Department of Genitourinary Medicine, Edinburgh between January 1st 2004 and April 1st 2005. Additional tests were performed on sera that gave a positive or equivocal EIA on screening as well as by clinical request on sera from contacts of syphilis, and those with clinical signs of syphilis. Additional tests included a Venereal Diseases Research Laboratory (VDRL) carbon antigen test, a Treponema pallidum particle agglutination (TPPA) test, INNO-LIA line immunoblot assay, and an EIA specific for anti-treponemal IgM.

A total of 105 patients were diagnosed with syphilis: primary (50), secondary (26), early latent (8), and of unknown duration (21). The TPPA was the most sensitive test in primary syphilis and had a sensitivity of 96% (48/50), which was significantly higher ( P <0.05) than the sensitivity of 84% (42/50) for the screening EIA: seven of the EIA negatives were detected by EIA–IgM, six by TPPA, five by immunoblot, and two by VDRL. EIA–IgM was negative in six primaries; all were positive by TPPA and immunoblot.

We conclude that, in order to maximize the serological detection of primary syphilis a specific EIA–IgM test and a TPPA test should be performed whenever there is a clinical suspicion of primary infection. This is particularly important when an EIA such as Murex ICE is used as a single screening test as it is less sensitive than the TPPA in primary infection.

Post-exposure prophylaxis for human immunodeficiency virus infection in the Royal Infirmary of Edinburgh - an audit

The purpose of the audit was to assess the implementation of the protocols developed by Lothian University National Health Service Trust for post-exposure prophylaxis (PEP) against blood-borne virus infections.

Patients at risk of infection after an injury were referred to the Department of Genitourinary Medicine (GUM) Edinburgh Royal Infirmary for assessment. A brief description of the incident, the time of the incident, the time of referral and the decision made was documented. The notes of these patients were reviewed 12 months later for the results of prospective HIV test after each incident.

There were 76 referrals to the GUM Department in year 2001. Occupational Health (OH) and the Accident and Emergency (A&E) Departments each made 35 referrals. The latter cases were exposures in community settings. Amongst A&E referrals the time interval between the incident and assessment was significantly longer than for OH referrals ( P = 0.001). Female health workers reported exposure incidents sooner than their male counterparts ( P = 0.01). Post-exposure prophylaxis for HIV was offered to 22 (29%) of 76 referred individuals, and was accepted by 13 (59%) persons. The course of PEP drugs was discontinued by five (38%) of the 13 individuals after consented postincident HIV testing of the source patients showed that they were HIV-seronegative. Five of eight individuals completed the course of PEP medication. Only 11 (14%) persons attended for serological testing for blood-borne virus infection three or more months after exposure. None of these 11 persons, one of whom had been given PEP medication, had become infected.

Further training and emphasis on the necessity of immediate reporting of occupational incidents and consented post-incident HIV testing of the source patient is needed. The current guidelines appear to work fairly well, but further counselling of those with significant injuries to undertake HIV serological testing after appropriate time interval is required.

Non-chlamydial non-gonococcal urethritis or undiagnosed chlamydial urethritis?

The aim of this study is to investigate the prevalence of sexually transmitted infections (STI) in the partners of men with non-chlamydial, non-gonococcal urethritis (NCNGU).

Observational study of the sexual partners of men with NCNGU diagnosed in the Department of Genitourinary Medicine, Edinburgh between 1 June 2002 and 31 December 2003. The diagnosis of chlamydial infection was based on ligase chain reaction (LCx) between June 2002 and March 2003, and on polymerase chain reaction (PCR) thereafter. Gonococcal infection was diagnosed with culture method.

Sexual partners of 99 (25%) of the 403 heterosexual men diagnosed with NCNGU were screened. Chlamydial infection was detected in 19 (19%) of the female sexual partners. Higher proportion of female partners of symptomatic men (15/51) had chlamydial infection compared with that of partners of asymptomatic men (4/48) ( P < 0.005).

NCNGU may be related to false-negative results of chlamydial diagnostic tests. Screening and treatment of sexual partners of men with NCNGU is therefore necessary.

The outcome of treatment of early latent syphilis and syphilis with undetermined duration in HIV-infected and HIV-uninfected patients

The aim of the study was to compare the outcome of syphilis treatment in HIV-infected and -uninfected patients. An observational study on patients diagnosed with early syphilis in three genitourinary clinics in the UK between January 2003 and June 2005 was conducted. Failure of the initial Venereal Disease Research Laboratory (test) (VDRL) titre to decrease four-fold within 12 months in the absence of history of re-infection was considered as treatment failure. During the study period, 190 HIV-uninfected and 129 HIV-infected patients were diagnosed, and 161 (84%) HIV-uninfected and 100 (77.5%) HIV-positive patients with diagnosis of syphilis who had 24 months follow-up syphilis serology results were included in the study ( P = 0.10). There were 381 and 508 follow-up episodes for HIV-infected and -uninfected patients, respectively, within 24 months. One HIV-infected patient was diagnosed with neuro-syphilis. After 12 months, 102 (63%) HIV-uninfected and 76 (70%) HIV-infected patients were treated ( P = 0.04). On Cox proportional hazard model, successful treatment after 12 months was associated with having VDRL titre more than 1:6 (hazard ratio [HR] 1.011; 95% confidence interval [CI], 1.004–1.019; P = 0.002). Those with negative immunoglobulin M enzyme immunoassay were less likely to have been successfully treated after 12 months (HR 0.676 [95% CI 0.518–0.883]; P = 0.004). HIV sero-status, age, sex group and treatment regimen were not associated with success of treatment. In conclusion, HIV sero-status did not play a role in the outcome of syphilis treatment. Treatment failure in a proportion of HIV-infected patients is due to a slower decline in VDRL titre rather than lack of response to treatment.

1-(Ethoxymethyl)-6-(Phenylselenenyl)Pyrimidines with Activity against Human Immunodeficiency Virus Types 1 and 2

The reaction of chloromethyl ethyl ether with bis(trimethylsilyl)uracil derivatives yield 1-(ethoxymethyl)pyrimidines 1a–d in good yield. Lithiation of 1a–d with lithium diisopropylamide at −78°C, followed by reaction with diphenyl diselenide as an electrophile, gave 1-(ethoxymethyl)-6-(phenylselenenyl)ura-cils 2a–d in 70–80% yield. The 6-phenylselenenyl acyclic pyrimidines 2b and 2d exhibited selective in vitro activity against HIV-1 and HIV-2 in primary human lymphocytes. The most potent compound was 1-(ethoxymethyl)-6-(phenylselenenyl)-5-ethyluracil 2d with a median effective concentration of 17 nM in primary human lymphocytes and no discernable cytotoxicity in these cells or rapidly dividing CEM and Vero cells. Well characterized AZT-resistant virus was modestly (3 to 12-fold increase) cross-resistant to compounds 2b and 2d.

A multi-platform metabolomics approach identifies highly specific biomarkers of bacterial diversity in the vagina of pregnant and non-pregnant women

Bacterial vaginosis (BV) increases transmission of HIV, enhances the risk of preterm labour, and is associated with malodour. Clinical diagnosis often relies on microscopy, which may not reflect the microbiota composition accurately. We use an untargeted metabolomics approach, whereby we normalize the weight of samples prior to analysis, to obtained precise measurements of metabolites in vaginal fluid. We identify biomarkers for BV with high sensitivity and specificity (AUC = 0.99) in a cohort of 131 pregnant and non-pregnant Rwandan women, and demonstrate that the vaginal metabolome is strongly associated with bacterial diversity. Metabolites associated with high diversity and clinical BV include 2-hydroxyisovalerate and γ-hydroxybutyrate (GHB), but not succinate, which is produced by both Lactobacillus crispatus and BV-associated anaerobes in vitro. Biomarkers associated with high diversity and clinical BV are independent of pregnancy status, and were validated in a blinded replication cohort from Tanzania (n = 45), where we predicted clinical BV with 91% accuracy. Correlations between the metabolome and microbiota identified Gardnerella vaginalis as a putative producer of GHB, and we demonstrate production by this species in vitro. This work illustrates how changes in community structure alter the chemical composition of the vagina, and identifies highly specific biomarkers for a common condition.

A systems biology approach investigating the effect of probiotics on the vaginal microbiome and host responses in a double blind, placebo-controlled clinical trial of post-menopausal women

A lactobacilli dominated microbiota in most pre and post-menopausal women is an indicator of vaginal health. The objective of this double blinded, placebo-controlled crossover study was to evaluate in 14 post-menopausal women with an intermediate Nugent score, the effect of 3 days of vaginal administration of probiotic L. rhamnosus GR-1 and L. reuteri RC-14 (2.5×10⁹ CFU each) on the microbiota and host response. The probiotic treatment did not result in an improved Nugent score when compared to when placebo. Analysis using 16S rRNA sequencing and metabolomics profiling revealed that the relative abundance of Lactobacillus was increased following probiotic administration as compared to placebo, which was weakly associated with an increase in lactate levels. A decrease in Atopobium was also observed. Analysis of host responses by microarray showed the probiotics had an immune-modulatory response including effects on pattern recognition receptors such as TLR2 while also affecting epithelial barrier function. This is the first study to use an interactomic approach for the study of vaginal probiotic administration in post-menopausal women. It shows that in some cases multifaceted approaches are required to detect the subtle molecular changes induced by the host to instillation of probiotic strains.

Trial Registration

ClinicalTrials.gov NCT02139839

A multicenter phase II study of pazopanib in patients with advanced gastrointestinal stromal tumors (GIST) following failure of at least imatinib and sunitinib

BACKGROUND

Advanced GISTs are incurable, but often treatable for years with tyrosine kinase inhibitors (TKIs). The majority of GISTs harbor an oncogenic activating mutation in KIT or PDGFRA. Inhibition of this activating mutation with TKIs most often leads to durable disease control for many patients. However, almost all patients develop resistance to these TKIs, typically due to the development of secondary mutations, heralding the need for new therapeutic options. We conducted a phase II study evaluating the efficacy and toxicity of pazopanib, a broad spectrum TKI inhibiting KIT, VEGFRs (-1, -2, and -3), and PDGFR (-α and-β) in patients with advanced GIST following failure of at least imatinib and sunitinib.

METHODS

Patients received pazopanib 800 mg orally once daily. All patients were assessed for efficacy with CT scans every 8 weeks (two cycles). Patients continued pazopanib until progression or unacceptable toxicity. The primary end point was the 24-week nonprogression [complete response+partial response+stable disease (SD)] rate (NPR) per RECIST 1.1. Secondary end points included PFS, OS, and toxicity.

RESULTS

Between August 2011 and September 2012, a total of 25 patients were treated at two institutions. Median number of prior therapy was 3 (range 2-7). A total of 90 cycles of pazopanib were administered, with a median of two cycles (range 1 to 17+) per patient. Best response of SD at any time was observed in 12 (48%) patients. The NPR was 17% [95% confidence interval (CI) 4.5-37]. All but one patient discontinued protocol either due to PD (n = 19) or intolerance (n = 4). One patient with succinate dehydrogenase (SDH)-deficient GIST exhibited continuing disease control after 17 cycles. The median PFS for the entire cohort was 1.9 months (95% CI 1.6-5.2), and the median OS was 10.7 months (95% CI 3.9-NR).

CONCLUSIONS

Pazopanib was reasonably well tolerated with no unexpected toxicities. Pazopanib as a single agent has marginal activity in unselected heavily pretreated patients with advanced GIST.

Effect of chemotherapy on the microbiota and metabolome of human milk, a case report

BACKGROUND

Human milk is an important source of bacteria for the developing infant and has been shown to influence the bacterial composition of the neonatal gut, which in turn can affect disease risk later in life. Human milk is also an important source of nutrients, influencing bacterial composition but also directly affecting the host. While recent studies have emphasized the adverse effects of antibiotic therapy on the infant microbiota, the effects of maternal chemotherapy have not been previously studied. Here we report the effects of drug administration on the microbiota and metabolome of human milk.

METHODS

Mature milk was collected every two weeks over a four month period from a lactating woman undergoing chemotherapy for Hodgkin's lymphoma. Mature milk was also collected from healthy lactating women for comparison. Microbial profiles were analyzed by 16S sequencing and the metabolome by gas chromatography-mass spectrometry.

FINDINGS

Chemotherapy caused a significant deviation from a healthy microbial and metabolomic profile, with depletion of genera Bifidobacterium, Eubacterium, Staphylococcus and Cloacibacterium in favor of Acinetobacter, Xanthomonadaceae and Stenotrophomonas. The metabolites docosahexaenoic acid and inositol known for their beneficial effects were also decreased.

CONCLUSION

With milk contents being critical for shaping infant immunity and development, consideration needs to be given to the impact of drugs administered to the mother and the long-term potential consequences for the health of the infant.

Harnessing microbiome and probiotic research in sub-Saharan Africa: recommendations from an African workshop

To augment capacity-building for microbiome and probiotic research in Africa, a workshop was held in Nairobi, Kenya, at which researchers discussed human, animal, insect, and agricultural microbiome and probiotics/prebiotics topics. Five recommendations were made to promote future basic and translational research that benefits Africans.

Characterizing long-term contaminant mass discharge and the relationship between reductions in discharge and reductions in mass for DNAPL source areas

The objective of this study was to characterize the temporal behavior of contaminant mass discharge, and the relationship between reductions in contaminant mass discharge and reductions in contaminant mass, for a very heterogeneous, highly contaminated source-zone field site. Trichloroethene is the primary contaminant of concern, and several lines of evidence indicate the presence of organic liquid in the subsurface. The site is undergoing groundwater extraction for source control, and contaminant mass discharge has been monitored since system startup. The results show a significant reduction in contaminant mass discharge with time, decreasing from approximately 1 to 0.15 kg/d over five years. Two methods were used to estimate the mass of contaminant present in the source area at the initiation of the remediation project. One was based on a comparison of two sets of core data, collected 3.5 years apart, which suggests that a significant (~80%) reduction in aggregate sediment-phase TCE concentrations occurred between sampling events. The second method was based on fitting the temporal contaminant mass discharge data with a simple exponential source-depletion function. Relatively similar estimates, 784 and 993 kg, respectively, were obtained with the two methods. These data were used to characterize the relationship between reductions in contaminant mass discharge (CMDR) and reductions in contaminant mass (MR). The observed curvilinear relationship exhibits a reduction in contaminant mass discharge essentially immediately upon the initiation of mass reduction. This behavior is consistent with a system wherein significant quantities of mass are present in hydraulically poorly accessible domains for which mass removal is influenced by rate-limited mass transfer. The results obtained from the present study are compared to those obtained from other field studies to evaluate the impact of system properties and conditions on mass-discharge and mass-removal behavior. The results indicate that factors such as domain scale, hydraulic-gradient status (induced or natural), and flushing-solution composition had insignificant impact on the CMDR-MR profiles and thus on underlying mass-removal behavior. Conversely, source-zone age, through its impact on contaminant distribution and accessibility, was implicated as a critical factor influencing the nature of the CMDR-MR relationship.

Adhesion of Lactobacillus iners AB-1 to human fibronectin: a key mediator for persistence in the vagina?

Lactobacillus iners is prominent in the human vagina and is able to persist despite development of bacterial vaginosis and treatment with antibiotics. A probable factor in its persistent survival is its ability to be retained in the vaginal epithelia. Genome sequencing of the strain showed an organism deplete of many metabolic pathways, yet equipped with fibronectin (Fn)-binding adhesins. The objective of the present study was to assess the ability of L iners AB-1 to bind immobilized Fn. Results showed that the organism superiorly bound the protein compared to other species of Lactobacillus and known binders such as Staphylococcus aureus. Treatment of L iners cells by protease rendered its binding abilities to Fn nonfunctional. The findings indicate a mechanism of vaginal persistence for a Lactobacillus species, with implications for reproductive health.