In situ trace metal analysis of Neoarchaean--Ordovician shallow-marine microbial-carbonate-hosted pyrites

Pre-Cambrian atmospheric and oceanic redox evolutions are expressed in the inventory of redox-sensitive trace metals in marine sedimentary rocks. Most of the currently available information was derived from deep-water sedimentary rocks (black shale/banded iron formation). Many of the studied trace metals (e.g. Mo, U, Ni and Co) are sensitive to the composition of the exposed land surface and prevailing weathering style, and their oceanic inventory ultimately depends on the terrestrial flux. The validity of claims for increased/decreased terrestrial fluxes has remained untested as far as the shallow-marine environment is concerned. Here, the first systematic study of trace metal inventories of the shallow-marine environment by analysis of microbial carbonate-hosted pyrite, from ca. 2.65-0.52 Ga, is presented. A petrographic survey revealed a first-order difference in preservation of early diagenetic pyrite. Microbial carbonates formed before the 2.4 Ga great oxygenation event (GOE) are much richer in pyrite and contain pyrite grains of greater morphological variability but lesser chemical substitution than samples deposited after the GOE. This disparity in pyrite abundance and morphology is mirrored by the qualitative degree of preservation of organic matter (largely as kerogen). Thus, it seems that in microbial carbonates, pyrite formation and preservation were related to presence and preservation of organic C. Several redox-sensitive trace metals show interpretable temporal trends supporting earlier proposals derived from deep-water sedimentary rocks. Most notably, the shallow-water pyrite confirms a rise in the oceanic Mo inventory across the pre-Cambrian-Cambrian boundary, implying the establishment of efficient deep-ocean ventilation. The carbonate-hosted pyrite also confirms the Neoarchaean and early Palaeoproterozoic ocean had higher Ni concentration, which can now more firmly be attributed to a greater proportion of magnesian volcanic rock on land rather than a stronger hydrothermal flux of Ni. Additionally, systematic trends are reported for Co, As, and Zn, relating to terrestrial flux and oceanic productivity.

Evaluation of DNA extraction methods for the detection of Cytomegalovirus in dried blood spots

BACKGROUND

Dried blood spots (DBS) are collected universally from newborns and may be valuable for the diagnosis of congenital Cytomegalovirus (CMV) infection. The reported analytical sensitivity for DBS testing compared to urine or saliva varies greatly across CMV studies. The purpose of this study was to directly compare the performance of various DNA extraction methods for identification of CMV in DBS including those used most often in CMV studies.

STUDY DESIGN

Whatman(®) Grade 903 filter paper cards were spotted with blood samples from 25 organ transplant recipients who had confirmed CMV viremia. Six DNA extraction methods were compared for relative yield of viral and cellular DNA: 2 manual solution-based methods (Gentra Puregene, thermal shock), 2 manual silica column-based methods (QIAamp DNA Mini, QIAamp DNA Investigator), and 2 automated methods (M48 MagAttract Mini, QIAcube Investigator). DBS extractions were performed in triplicate followed by real-time quantitative PCR (qPCR).

RESULTS

For extraction of both viral and cellular DNA, two methods (QIAamp DNA Investigator and thermal shock) consistently gave the highest yields, and two methods (M48 MagAttract Mini and QIAamp DNA Mini) consistently gave the lowest yields. There was an average 3-fold difference in DNA yield between the highest and lowest yield methods.

CONCLUSION

The choice of DNA extraction method is a major factor in the ability to detect low levels of CMV in DBS and can largely account for the wide range of DBS sensitivities reported in studies to date.

Abstract P1-02-09: Positive predictive value (PPV) of the diagnosis of atypia in breast core biopsies: An audit of MSKCC breast pathology service

Percutaneous needle core biopsy is the standard of care in the assessment of suspicious breast lesions. The diagnostic term “Atypia” is used in breast biopsy reporting when histologic appearances are suspicious but not diagnostic of malignancy. Multiple histopathological appearances are encompassed by the umbrella term “atypia”, including atypical ductal hyperplasia (ADH), columnar cell change with atypia (CCCWA), which is also known as flat epithelial atypia (FEA), and a miscellaneous group of diagnoses, known as atypia NOS.

A pathologic diagnosis of “atypia” in breast core biopsies usually leads to a recommendation to surgically excise the lesion. Many studies have correlated the diagnosis of “atypia” in core biopsies with the subsequent finding of carcinoma in the surgical excisions, and the percentage of carcinoma found represents the positive predictive value (PPV) of the diagnosis. To date, there is no agreed target PPV for the diagnosis of breast atypia on biopsy, but the most studies have demonstrated a PPV of 20- 40%. Individual “atypia” diagnoses such as CCCWA have an even lower PPV of 10-15%.

One method of performance review is an audit of the average breast-atypia PPV within individual pathology departments, which then can be monitored and studied over time, to detect trends and “diagnostic drift” at an early stage. In addition, assessment of the individual PPV of each breast pathologist allows for analysis of the consistency of the diagnostic practice of each individual with their colleagues. Surprisingly, there have been no major studies assessing the intradepartmental range of PPVs for breast atypia diagnoses to date. In contrast, the American College of Radiology has designed the BIRADS classification system in order to audit and monitor the PPV of breast imaging in diagnosing malignancy.

We undertook to measure the departmental PPV for malignancy following a biopsy diagnosis of breast atypia, and performed an anonymized subanalysis in order to establish the range of PPVs of atypia diagnoses between the sub-specialized breast pathologists within the department.

This study established that the baseline PPV in our department is comparable to previously reported studies at 24%, while the range of PPV for an atypia diagnosis between pathologists is between 22.8 and 25% for 5 of 6 pathologists, with one pathologist demonstrating a higher PPV of 36.8%. ADH was the most common diagnosis of the atypia subtypes, and the PPV for ADH alone was 29.9%. 15% of ADH diagnoses were described as “ADH bordering on low grade DCIS”; within this subgroup the PPV was 48.5%. The PPV for a diagnosis of CCCWA alone was 10%.

This study demonstrates that the PPV for breast atypia in a major tertiary cancer center is approximately 24%. We have demonstrated very reproducible use of this diagnostic term within the department. We plan to use the findings of this study to identify subgroups of patients with a sufficiently low PPV to justify a decision not to proceed to surgical intervention. We aim to develop an algorithm for use in the clinical setting in order to direct further patient management. The ultimate aim of this research is to reduce the number of patients undergoing unnecessary surgical interventions.

Citation Information: Cancer Res 2013;73(24 Suppl): Abstract nr P1-02-09.

Abstract P2-16-20: Biomarkers to predict response to the CDK 4/6 inhibitor, palbociclib (PD 0332991) in a single-agent phase II trial in advanced breast cancer

Background: The Cyclin D1-CDK4/6 complex is critical in regulating the G1/S checkpoint and phosphorylation of retinoblastoma protein (Rb); palbociclib is a highly-selective CDK 4/6 inhibitor. CCND1, the gene encoding Cyclin D1, is amplified in 15% of breast tumors; p16, the endogenous inhibitor of the complex is lost in up to half of breast tumors. We hypothesized that breast tumors containing either alteration or a high proliferative rate would have enhanced sensitivity to palbociclib. We conducted a single-agent, phase II trial of palbociclib in patients with advanced breast cancer (UPCC03909). In this trial, the clinical benefit rate (partial response [PR] + stable disease ≥6 months [6mSD]) was 17% (DeMichele, ASCO, 2013). The current analysis was a secondary endpoint to determine whether Rb expression, p16 loss, Ki-67 index or CCND1 amplification predicted response in the phase II trial.

Methods: Enrollment on UPCC03909 required archival tumor collection from either primary tumor or metastatic lesions. Fresh frozen paraffin-embedded (FFPE) tumor sections were tested for expression of Rb, Ki-67 and p16 by immunohistochemistry (IHC), and CCND1 amplification by fluorescence in situ hybridization. Categorical variables based on% tumor staining and intensity scores (negative defined as 0 or 1+ intensity staining, equivocal defined as 2+ staining or 3+ in <30%, or positive defined as 3+ staining intensity in 30%) were generated for Rb and p16 nuclear staining. Fisher's Exact test was used to test for associations between nominal factors, the Cochran-Mantel-Hænszel test for associations between ordinal factors, and the Cox proportional hazard model for association of progression-free survival (PFS) with biomarkers.

Results: Thirty-seven patients were enrolled; response evaluation is available in 36/37. All had FFPE tumor available for Rb, 33/37 (89%)for CCND1 amplification and 29/37 (78%) for Ki-67 and p16 analyses. For complete results see Table 1.

Conclusions: These results provide preliminary evidence that breast tumors more likely to respond to palbociclib may have higher Rb nuclear expression, lower Ki67 indices and/or loss of p16. Larger studies are needed to confirm these results.

Table 1: Biomarker Summary and ResponseBiomarkerBiomarker CategoizationFrequency (%)Response Rate PR+6mSD/total (%)PFS Hazard Ratio (95%CI)Overall Population (n = 37)  6/36 (17%) Ki-67 (n = 29)≤ 10 (n = 20)69%4/19 (21%)1.00 > 10 (n = 9)31%1/9 (11%)1.20 (0.50, 2.88)Rb (n = 37)Nuclear Score: Negative (n = 11)30%0/11 (0%)1.00 Equivocal (n = 15)40%2/14 (14.3%)0.72 (0.28, 1.84) Positive (n = 11)30%4/11 (36.4%)0.71 (0.28, 1.80)p16 (n = 29)Loss or Low Expression (n = 16)55%4/16 (25%)1.00 Moderate or High Expression (n = 13)45%1/12 (8.3%)1.08 (0.47, 2.49)CCND1 Amplification (n = 34)Non-amplified (n = 25)88%4/25 (16%)1.00 Amplified (n = 9)12%1/8 (12.5%)1.06 (0.46, 2.4)

Citation Information: Cancer Res 2013;73(24 Suppl): Abstract nr P2-16-20.

Persistent Rhodococcus equi infection in a renal transplant patient: case report and review of the literature

Rhodococcus equi is a pathogen that mainly causes infection in immunocompromised hosts. We report a case of relapsing R. equi pulmonary infection in a 57-year-old male renal transplant recipient who was treated with 12 months of antibiotics, adjunctive surgery, and a reduction in his immunosuppression. He suffered from relapsing disease, treatment-related complications, and ultimately died of Pneumocystis pneumonia. Case reports in the literature portray a good cure rate for transplant-related R. equi infections, with shorter durations of antibiotics. The case illustrates the difficulties in the management of R. equi infections. Forty cases from the literature were reviewed and compared in terms of epidemiology, location of infection, transplant type, immunosuppression used, treatment used, outcomes, and possible exposures.

Using landscape topology to compare continuous metaheuristics: a framework and case study on EDAs and ridge structure

In this paper we extend a previously proposed randomized landscape generator in combination with a comparative experimental methodology to study the behavior of continuous metaheuristic optimization algorithms. In particular, we generate two-dimensional landscapes with parameterized, linear ridge structure, and perform pairwise comparisons of algorithms to gain insight into what kind of problems are easy and difficult for one algorithm instance relative to another. We apply this methodology to investigate the specific issue of explicit dependency modeling in simple continuous estimation of distribution algorithms. Experimental results reveal specific examples of landscapes (with certain identifiable features) where dependency modeling is useful, harmful, or has little impact on mean algorithm performance. Heat maps are used to compare algorithm performance over a large number of landscape instances and algorithm trials. Finally, we perform a meta-search in the landscape parameter space to find landscapes which maximize the performance between algorithms. The results are related to some previous intuition about the behavior of these algorithms, but at the same time lead to new insights into the relationship between dependency modeling in EDAs and the structure of the problem landscape. The landscape generator and overall methodology are quite general and extendable and can be used to examine specific features of other algorithms.

P1-17-06: A Phase II Trial of the CDK 4/6 Inhibitor PD0332991 in Women with Advanced Breast Cancer

Background: Dysregulation of the G1/S checkpoint of the cell cycle is a feature of many breast cancers. PD0332991, a potent oral inhibitor of cyclin-dependent kinases (CDKs) 4 and 6 is well-tolerated and has demonstrated activity in a phase I trial in a variety of solid tumors at a phase II dose of 125 mg daily on a 3 week on/1 week off schedule. Preclinical data suggest that this agent is most active in ER+ (luminal) breast cancers. We are performing a phase II study of PD0332991 in women with advanced breast cancer, one of several parallel disease cohorts under study.

Methods: Patients with histologically-confirmed stage IV breast cancer were eligible if they had primary or metastatic tumor which stained positive for retinoblastoma (Rb) protein by immunohistochemistry, disease measureable by RECIST criteria and adequate organ function/performance status. Treatment was initiated with PD0332991 at 125 mg orally, days 1 - 21 of a 28-day treatment cycle. Tumor assessments occurred after every 2 cycles (8-week intervals). The primary objective was to determine the safety and response rates in cohorts of 15 patients per tumor type; 15 patients per arm provided 80% power to detect a 15% (1/15) response rate per disease that would lead to further cohort expansion. Secondary objectives include PK, PD and predictive biomarker assessment.

Results: 36 patients were screened, 32 (89%) stained positive for Rb, and 14 have enrolled on study. The only reported toxicites are neutropenia (7 patients, 4 grade 3/4), thrombocytopenia (1 patient, grade 1) and fatigue (1 patient, grade 2). 3 patients (23%) have had dose interruptions and 5 (38%) have had dose-reduction for neutropenia, though no episodes of febrile neutropenia have occurred. Among 11 patients assessable for response to date, there is 1(7%) partial response (PR), 6 (43%) with stable disease (SD) and 4 (29%) with progressive disease (PD). 3 of 6 patients with stable disease have received greater than 6 months of therapy, and these sustained responses have occurred with dosing as low as 50 mg/day. All PR/SD have occurred in patients with ER+ tumors; all PD have been in patients with triple negative (ER-/PR-/Her2-) disease. The cyclin D1 status of all patients are being assessed. Of the 10 ER+ patients, 3 are cyclin D1 amplified, 5 are non-amplified and 2 are pending assessment. 2 in 4 cyclin D1 non-amplified patients had SD, while 2 of 2 evaluable patients with amplification had SD. PK and PD analyses are in progress.

Conclusions: PD 0332991 is an extremely well-tolerated, oral CDK 4/6 inhibitor that demonstrates prolonged single-agent activity in ER+ breast cancer patients who have progressed on hormonal therapy. These data have prompted expansion of this breast cancer cohort to further delineate activity and translational studies examining predictors of response are underway.

Citation Information: Cancer Res 2011;71(24 Suppl):Abstract nr P1-17-06.

Epinephrine auto-injector use in adolescents at risk of anaphylaxis: a qualitative study in Scotland, UK

BACKGROUND

Adolescents with severe allergies are at particular risk of severe and fatal anaphylactic reactions. Epinephrine (adrenaline) is known to be under-utilized by teenagers.

OBJECTIVE

We sought to gain knowledge of adolescents' attitudes towards and experience of epinephrine auto-injectors in order to inform improvements in patient education.

METHODS

A qualitative study of adolescents in Scotland, UK with a history of anaphylaxis and their parents. In-depth interviews explored adolescents' accounts of anaphylactic reactions, including issues related to using epinephrine auto-injectors. Focus groups with adolescents and parents were used to discuss interventions to improve adolescent self-management of anaphylaxis.

RESULTS

Twenty-six adolescents and 28 parents were interviewed. Eight adolescents and 10 parents participated in separate focus groups. Most adolescents had not used the auto-injector in an anaphylactic emergency. We identified multi-faceted barriers to use, including: failure to recognize anaphylaxis; uncertainty about auto-injector technique and when to administer it; fear of using the auto-injector. Most adolescents reported carrying auto-injectors some of the time, though several found this inconvenient due to the size; only one reported non-use of an auto-injector because it had not been carried.

CONCLUSION AND CLINICAL RELEVANCE

Adolescents and parents reported under-use of epinephrine auto-injectors. Carriage is insufficient to ensure that auto-injectors are used. Barriers to use are multiple and complex, and unlikely to be overcome using simple educational interventions. Auto-injector training currently offered is often inadequate preparation for an emergency. A more comprehensive approach is needed, addressing the psychosocial dimensions of anaphylactic emergencies as well as treatment. Training should ideally be provided by specialist allergists or nurses, but can also be provided and reinforced in primary care.

Modelling of The Intramolecular Structure Of Monolayer C60 Molecules Observed with Scanning Tunneling Microscopy

Images of monolayer coverages of C60 on gold substrates, using scanning tunneling microscopy, reveal intermolecular arrangement and intramolecular features. In this paper we concentrate on the interpretation of these internal features, present a model showing that they arise from local charge density variations of high-lying π orbitals on approximately every other carbon atom, and discuss also other possible mechanisms for this effect.