Subjective and objective sleep quality and aging in the sleep heart health study

OBJECTIVES

To examine the extent to which subjective and objective sleep quality are related to age independent of chronic health conditions.

DESIGN

Cross-sectional study.

SETTING

The Sleep Heart Health Study (SHHS) is a multicenter study designed to determine the cardiovascular consequences and the natural history of sleep disordered breathing.

PARTICIPANTS

Five thousand four hundred seven community-dwelling adults who participated in the SHHS (mean age 63, range 45-99; 52% women).

MEASUREMENTS

Unattended home polysomnography (PSG) and sleep questionnaires.

RESULTS

Older age was associated with shorter sleep time, diminished sleep efficiency, and more arousals in men and women. In men, age was independently associated with more Stage 1 and Stage 2 sleep and less slow-wave (Stage 3 to 4) and rapid eye movement sleep. In women, older age was less strongly associated according to linear trend with sleep stage. Conversely, poor subjective sleep quality was not associated with older age in men, but older women had more trouble falling asleep, and there was a trend toward older women having more problems with waking up during the night and waking up too early. Associations between self-report and directly measured sleep time and sleep latency were low to moderate across age groups (correlation coefficient=0.06-0.32).

CONCLUSION

Older age was more strongly associated with poorer sleep according to PSG in men than women, yet the subjective report of poor sleep with older age was stronger in women. The higher prevalence of chronic health conditions, including sleep apnea, in older adults did not explain changes of sleep parameters with aging and age-sex differences in these relationships.

Specific pan-neural crest expression of zebrafish Crestin throughout embryonic development

Zebrafish crestin was identified in a screen for genes dependent on cyclops function and is a member of a family of retroelements (Rubinstein et al. [2000] Genesis 26:86-97). We report here a detailed description of crestin mRNA expression during zebrafish embryogenesis. Crestin expression was first observed during the onset of somitogenesis in cells of the neural crest domain of the ectoderm. Crestin expression was subsequently observed in premigratory cranial and trunk neural crest cells and then in actively migrating crest cells. Cell counts of crestin-expressing premigratory trunk neural crest cells strongly suggest that crestin is expressed by all neural crest cells at this stage. Crestin expression co-localized with a battery of markers for premigratory neural crest cells, developmentally distinct neural crest-derived precursor sublineages, and overtly differentiated neural crest-derived cell types. Expression of crestin is gradually downregulated in overtly differentiated cells. Our results indicate that crestin is a specific pan-neural crest marker throughout zebrafish embryogenesis.

Sampling-based approaches to improve estimation of mortality among patient dropouts: experience from a large PEPFAR-funded program in Western Kenya

Background

Monitoring and evaluation (M&E) of HIV care and treatment programs is impacted by losses to follow-up (LTFU) in the patient population. The severity of this effect is undeniable but its extent unknown. Tracing all lost patients addresses this but census methods are not feasible in programs involving rapid scale-up of HIV treatment in the developing world. Sampling-based approaches and statistical adjustment are the only scaleable methods permitting accurate estimation of M&E indices.

Methodology/Principal Findings

In a large antiretroviral therapy (ART) program in western Kenya, we assessed the impact of LTFU on estimating patient mortality among 8,977 adult clients of whom, 3,624 were LTFU. Overall, dropouts were more likely male (36.8% versus 33.7%; p = 0.003), and younger than non-dropouts (35.3 versus 35.7 years old; p = 0.020), with lower median CD4 count at enrollment (160 versus 189 cells/ml; p<0.001) and WHO stage 3–4 disease (47.5% versus 41.1%; p<0.001). Urban clinic clients were 75.0% of non-dropouts but 70.3% of dropouts (p<0.001). Of the 3,624 dropouts, 1,143 were sought and 621 had their vital status ascertained. Statistical techniques were used to adjust mortality estimates based on information obtained from located LTFU patients. Observed mortality estimates one year after enrollment were 1.7% (95% CI 1.3%–2.0%), revised to 2.8% (2.3%–3.1%) when deaths discovered through outreach were added and adjusted to 9.2% (7.8%–10.6%) and 9.9% (8.4%–11.5%) through statistical modeling depending on the method used. The estimates 12 months after ART initiation were 1.7% (1.3%–2.2%), 3.4% (2.9%–4.0%), 10.5% (8.7%–12.3%) and 10.7% (8.9%–12.6%) respectively.

Conclusions/Significance Abstract

Assessment of the impact of LTFU is critical in program M&E as estimated mortality based on passive monitoring may underestimate true mortality by up to 80%. This bias can be ameliorated by tracing a sample of dropouts and statistically adjust the mortality estimates to properly evaluate and guide large HIV care and treatment programs.

Phase II study of ceralasertib (AZD6738) in combination with durvalumab in patients with advanced/metastatic melanoma who have failed prior anti-PD-1 therapy

BACKGROUND

Modulating the DNA damage response and repair (DDR) pathways is a promising strategy for boosting cancer immunotherapy. Ceralasertib (AZD6738) is an oral inhibitor of the serine/threonine protein kinase ataxia telangiectasia and Rad3-related protein, which is crucial for DDR.

PATIENTS AND METHODS

This phase II trial evaluated ceralasertib plus durvalumab for the treatment of patients with metastatic melanoma who had failed anti-programmed cell death protein 1 therapy.

RESULTS

Among the 30 patients, we observed an overall response rate of 31.0% and a disease control rate of 63.3%. Responses were evident across patients with acral, mucosal, and cutaneous melanoma. The median duration of response was 8.8 months (range, 3.8-11.7 months). The median progression-free survival was 7.1 months (95% confidence interval, 3.6-10.6 months), and the median overall survival was 14.2 months (95% confidence interval, 9.3-19.1 months). Common adverse events were largely hematologic and manageable with dose interruptions and reductions. Exploratory biomarker analysis suggested that tumors with an immune-enriched microenvironment or alterations in the DDR pathway were more likely to respond to the study treatment.

CONCLUSION

We conclude that ceralasertib in combination with durvalumab has promising antitumor activity among patients with metastatic melanoma who have failed anti-programmed cell death protein 1 therapy, and constitute a population with unmet needs.

Silicon enhances natural enemy attraction and biological control through induced plant defences

Silicon (Si) is known to have a role in constitutive plant defence against arthropod pests, and recent work has illustrated involvement in induced plant defences. The present tri-trophic study tested the hypothesis that Si increases natural enemy attraction to pest-infested plants and improves biological control. Cucumber plants treated with potassium silicate (Si+) and untreated control plants (Si-) were maintained in separately vented glasshouse compartments. Y-tube olfactometer studies showed that adult Dicranolaius bellulus were significantly more attracted to Si+ plants upon which Helicoverpa armigera larvae had fed compared with Si-, pest-infested plants. Predators were not significantly more attracted to Si+ plants when comparing uninfested cucumbers. In a field experiment, we placed H. armigera-infested and uninfested Si+ and Si- cucumber plants in a lucerne stand. Removal rates of H. armigera egg baits showed predation was greater for Si+ infested plants than for other treatments. Results suggest that Si applied to plants with a subsequent pest infestation increases the plants' attractiveness to natural enemies; an effect that was reflected in elevated biological control in the field.

Longitudinal evaluation of sleep-disordered breathing and sleep symptoms with change in quality of life: the Sleep Heart Health Study (SHHS)

STUDY OBJECTIVES

Findings from population studies evaluating the progression and incidence of sleep disordered breathing have shown evidence of a longitudinal increase in the severity of sleep disordered breathing. The present study evaluates the association among changes in sleep disordered breathing, sleep symptoms, and quality of life over time.

DESIGN

Prospective cohort study. Data were from the Sleep Heart Health Study.

SETTING

Multicenter study.

PARTICIPANTS

Three thousand seventy-eight subjects aged 40 years and older from the baseline and follow-up examination cycles were included.

MEASUREMENTS

The primary outcomes were changes in the Physical Component Summary and Mental Component Summary scales obtained from the Medical Outcomes Study Short-Form Health Survey. The primary exposure was change in the respiratory disturbance index obtained from unattended overnight polysomnograms performed approximately 5 years apart. Other covariates included measures of excessive daytime sleepiness and difficulty initiating and maintaining sleep.

RESULTS

Mean respiratory disturbance index increased from 8.1 +/- 11 SD at baseline to 10.9 +/- 14 (P < 0.0001) at follow-up. The mean Physical Component Summary and Mental Component Summary scores were 48.5 and 54.1 at baseline and 46.3 and 54.8 at follow-up. No associations between change in respiratory disturbance index and changes in Physical Component Summary or Mental Component Summary scores were seen. However, worsening of difficulty initiating and maintaining sleep and excessive daytime sleepiness were significantly associated with lower quality of life.

CONCLUSIONS

A slight increase in severity of sleep disordered breathing was seen over 5 years; this was not associated with worsening of quality of life. However, subjective symptoms of quality of sleep and daytime sleepiness were associated with declining quality of life.

Oral cancer-associated tertiary lymphoid structures: gene expression profile and prognostic value

Tertiary lymphoid structure (TLS) provides a local and critical microenvironment for both cellular and humoral immunity and supports effective antigen presentation and lymphocyte activation. However, the gene expression profile and prognostic significance of TLS in oral cancer remain largely unrevealed. In this study, we found the presence of both intratumoral and peritumoral TLSs in a series of 65 patients with oral cancer treated by surgical resection, with positive detection rates of 33.8 and 75.4%, respectively. The presence of intratumoral TLSs, but not peritumoral TLSs, was significantly associated with decreased P53 and Ki67 scores (P = 0·027 and 0·047, respectively). The survival analyses revealed that oral cancer patients with higher grades of TLSs was associated with improved disease-free survival (DFS) and overall survival (OS) (P = 0·037 and 0·031, respectively). Gene expression profiling analysis of the cytokines and chemokines responsible for lymph-node neogenesis identified a three-up-regulated-gene set, i.e. IL7, LTB and CXCL13, which was shown to be correlated with human oral cancer-associated TLSs. This study provides a framework for better understanding of oral cancer-associated TLSs and for delineating future innovative prognostic biomarkers and immune therapeutic strategies for oral cancer.

On-site field sampling and analysis of fragrance from living lavender (Lavandula angustifolia L.) flowers by solid-phase microextraction coupled to gas chromatography and ion-trap mass spectrometry

Solid-phase microextraction coupled to gas chromatography and mass spectrometry has been applied as a simple alternative method for the analysis of essential oil directly from lavender intact flowering spikes and genuine oils. All recognised major oil constituents were detected by this procedure, with results comparable to those given by a conventional method (organic solvent extraction). Distinctive chromatographic profiles were found for various species.

Differential gene expression of TGF beta inducible early gene (TIEG), Smad7, Smad2 and Bard1 in normal and malignant breast tissue

TGF beta/Smad signaling pathway members are potent tumor suppressors for many types of cancers. We hypothesize that breast tumors differentially express these genes and that this expression pattern plays a role in the proliferation of breast cancer. We examined the mRNA levels of TIEG, Smad7, Smad2, and Bard1 using real-time RT/PCR in 14 normal breast, five non-invasive, 57 invasive (including 29 with outcome data), and five metastatic breast tumor tissues. TIEG and Smad7 mRNA levels were lower in non-invasive tumors compared to normal breast tissues. TIEG, Bard1, and Smad2 mRNA levels were lower in invasive cancers compared to normal breast tissues. In addition, TIEG, Smad2, and Bard1, provided discriminatory ability to potentially distinguish between normal and tumor samples, N- and N+ tumors, and N-/good (no recurrence for at least 5 years) and N-/bad (recurrence within 3 years) outcome patients. TIEG mRNA levels accurately discriminated between normal breast tissue and primary tumors with a sensitivity and specificity of 96 and 93%, respectively. TIEG, in combination with Smad2, distinguished between N+ and N- primary tumors with a sensitivity and specificity of 75 and 85%, respectively. TIEG in combination with Bard1 discriminated between N-/bad outcome from N-/good tumors with a sensitivity and specificity of 83 and 82%, respectively. Our results support the hypothesis that the differential gene expression of TIEG, Smad2, and Bard1, which are tumor suppressor genes, plays a significant role in the proliferation of breast cancer. Further investigation is necessary to validate the ability of these genes to discriminate between different populations of breast cancer patients.

Allelochemicals in wheat (Triticum aestivum L.): variation of phenolic acids in shoot tissues

Seven known phenolic acids implicated in wheat allelopathy were analyzed in a worldwide collection of 58 wheat accessions by gas chromatography and tandem mass spectrometry (GC-MS-MS). Chemical analysis showed that accessions differed significantly in the production of p-hydroxybenzoic, vanillic, syringic, trans-p-coumaric, cis-p-coumaric, trans-ferulic, and cis-ferulic acids in the shoots of 17-day-old wheat seedlings. The concentrations of p-hydroxybenzoic, vanillic, cis-p-coumaric, and cis-ferulic acids were normally distributed in the 58 accessions. A binormal distribution was found for syringic and trans-ferulic acids and a skewed normal distribution for trans-p-coumaric acid. The concentration of each compound also varied with phenolic acids. The relative abundance of each phenolic acid was ordered decreasingly as trans-ferulic, vanillic, trans-p-coumaric, p-hydroxybenzoic, syringic, cis-ferulic, and cis-p-coumaric acids. The concentration of total identified phenolic acids varied from 93.2 to 453.8 mg/kg in the shoots of 58 accessions. The content of each phenolic acid or group was highly associated with others in the shoots of wheat seedlings. Wheat accessions with high levels of total identified phenolic acids in the shoots are generally strongly allelopathic to the growth of annual ryegrass.

Precision oncology: A new era of cancer clinical trials

Traditionally, site of disease and anatomic staging have been used to define patient populations to be studied in individual cancer clinical trials. In the past decade, however, oncology has become increasingly understood on a cellular and molecular level, with many cancer subtypes being described as a function of biomarkers or tumor genetic mutations. With these changes in the science of oncology have come changes to the way we design and perform clinical trials. Increasingly common are trials tailored to detect enhanced efficacy in a patient subpopulation, e.g. patients with a known biomarker value or whose tumors harbor a specific genetic mutation. Here, we provide an overview of traditional and newer biomarker-based trial designs, and highlight lessons learned through implementation of several ongoing and recently completed trials.

Simultaneous determination of phenolic acids and 2,4-dihydroxy-7-methoxy-1,4-benzoxazin-3-one in wheat (Triticum aestivum L.) by gas chromatography-tandem mass spectrometry

A procedure using gas chromatography and tandem mass spectrometry (GC-MS-MS) has been developed for the identification and quantification of some allelochemicals in wheat (Triticum aestivum L.). The quantities of allelochemicals in wheat shoots ranged from 2.9 to 110 mg per kilogram of dry shoot residues. Compared with gas chromatography-mass spectrometry (GC-MS), the GC-MS-MS technique significantly increased instrument selectivity and sensitivity, thereby providing more reliable quantitation results in the determination of the phytotoxic compounds examined during this allelopathy research.

Evaluation of alternate categorical tumor metrics and cut points for response categorization using the RECIST 1.1 data warehouse

PURPOSE

We sought to test and validate the predictive utility of trichotomous tumor response (TriTR; complete response [CR] or partial response [PR] v stable disease [SD] v progressive disease [PD]), disease control rate (DCR; CR/PR/SD v PD), and dichotomous tumor response (DiTR; CR/PR v others) metrics using alternate cut points for PR and PD. The data warehouse assembled to guide the Response Evaluation Criteria in Solid Tumors (RECIST) version 1.1 was used.

METHODS

Data from 13 trials (5,480 patients with metastatic breast cancer, non-small-cell lung cancer, or colorectal cancer) were randomly split (60:40) into training and validation data sets. In all, 27 pairs of cut points for PR and PD were considered: PR (10% to 50% decrease by 5% increments) and PD (10% to 20% increase by 5% increments), for which 30% and 20% correspond to the RECIST categorization. Cox proportional hazards models with landmark analyses at 12 and 24 weeks stratified by study and number of lesions (fewer than three v three or more) and adjusted for average baseline tumor size were used to assess the impact of each metric on overall survival (OS). Model discrimination was assessed by using the concordance index (c-index).

RESULTS

Standard RECIST cut points demonstrated predictive ability similar to the alternate PR and PD cut points. Regardless of tumor type, the TriTR, DiTR, and DCR metrics had similar predictive performance. The 24-week metrics (albeit with higher c-index point estimate) were not meaningfully better than the 12-week metrics. None of the metrics did particularly well for breast cancer.

CONCLUSION

Alternative cut points to RECIST standards provided no meaningful improvement in OS prediction. Metrics assessed at 12 weeks have good predictive performance.

Changes in the volatile profile of oats induced by processing

Samples of an Australian oat cultivar, Echidna, were pilot-scale processed. At each stage of the processing (raw oats, groats, kiln dried dehulled oats (KDHO), and rolled (flaked)) samples were removed for later sensory and GC-MS analysis of the flavor components. Mean taste panel scores from a trained taste panel were calculated according to attributes (cereal, burnt, toasted, floury, and yeasty). Attributes were generally similar for both KDHO and flaked oats except in the yeasty attributes. Panelists were able to differentiate between groats, KDHO, and flaked oats (raw oats were not included). The largest effects of heat processing were found for the attributes toasted and yeasty aroma; toasted, cereal, and yeasty flavor; and toasted and yeasty aftertaste. A multi-organoleptic sensor analyzer was able to differentiate all samples when the output was subjected to discriminant function analysis. A reintroduced sample was recognized with a confidence level better than 96%. Solid-phase microextraction (SPME) of headspace followed by GC--MS was used to identify volatiles after either dry or slurry heating. Several SPME fiber types were evaluated as to their ability to sorb oat volatiles. A 100-microm poly(dimethylsiloxane) SPME fiber was found to provide the best adsorption profile as measured by number of compounds sorbed and peak area response. A range of alcohols, aldehydes, alkyl benzenes, dienes, and ketones was identified in the processed samples.

Phytotoxicity of vulpia residues: III. Biological activity of identified allelochemicals from Vulpia myuros

Twenty compounds identified in vulpia (Vulpia myuros) residues as allelochemicals were individually and collectively tested for biological activity. Each exhibited characteristic allelochemical behavior toward the test plant, i.e., inhibition at high concentrations and stimulation or no effect at low concentrations, but individual activities varied. Allelopathins present in large quantities, such as syringic, vanillic, and succinic acids, possessed low activity, while those present in small quantities, such as catechol and hydrocinnamic acid, possessed strong inhibitory activity. The concept of a phytotoxic strength index was developed for quantifying the biological properties of each individual allelopathin in a concise, comprehensive, and meaningful format. The individual contribution of each allelopathin, assessed by comparing the phytotoxic strength index to the overall toxicity of vulpia residues, was variable according to structure and was influenced by its relative proportion in the residue. The majority of compounds possessed low or medium biological activity and contributed most of the vulpia phytotoxicity, while compounds with high biological activity were in the minority and only present at low concentration. Artificial mixtures of these pure allelochemicals also produced phytotoxicity. There were additive/synergistic effects evident in the properties of these mixtures. One such mixture, formulated from allelochemicals found in the same proportions as occur in vulpia extract, produced stronger activity than another formulated from the same set of compounds but in equal proportions. These results suggest that the exploration of the relative composition of a cluster of allelopathins may be more important than simply focusing on the identification of one or two compounds with strong biological activity and that synergism is fundamental to the understanding of allelopathy.

Clinical trial designs incorporating predictive biomarkers

Development of oncologic therapies has traditionally been performed in a sequence of clinical trials intended to assess safety (phase I), preliminary efficacy (phase II), and improvement over the standard of care (phase III) in homogeneous (in terms of tumor type and disease stage) patient populations. As cancer has become increasingly understood on the molecular level, newer "targeted" drugs that inhibit specific cancer cell growth and survival mechanisms have increased the need for new clinical trial designs, wherein pertinent questions on the relationship between patient biomarkers and response to treatment can be answered. Herein, we review the clinical trial design literature from initial to more recently proposed designs for targeted agents or those treatments hypothesized to have enhanced effectiveness within patient subgroups (e.g., those with a certain biomarker value or who harbor a certain genetic tumor mutation). We also describe a number of real clinical trials where biomarker-based designs have been utilized, including a discussion of their respective advantages and challenges. As cancers become further categorized and/or reclassified according to individual patient and tumor features, we anticipate a continued need for novel trial designs to keep pace with the changing frontier of clinical cancer research.

Principal stratification designs to estimate input data missing due to death

We consider studies of cohorts of individuals after a critical event, such as an injury, with the following characteristics. First, the studies are designed to measure "input" variables, which describe the period before the critical event, and to characterize the distribution of the input variables in the cohort. Second, the studies are designed to measure "output" variables, primarily mortality after the critical event, and to characterize the predictive (conditional) distribution of mortality given the input variables in the cohort. Such studies often possess the complication that the input data are missing for those who die shortly after the critical event because the data collection takes place after the event. Standard methods of dealing with the missing inputs, such as imputation or weighting methods based on an assumption of ignorable missingness, are known to be generally invalid when the missingness of inputs is nonignorable, that is, when the distribution of the inputs is different between those who die and those who live. To address this issue, we propose a novel design that obtains and uses information on an additional key variable-a treatment or externally controlled variable, which if set at its "effective" level, could have prevented the death of those who died. We show that the new design can be used to draw valid inferences for the marginal distribution of inputs in the entire cohort, and for the conditional distribution of mortality given the inputs, also in the entire cohort, even under nonignorable missingness. The crucial framework that we use is principal stratification based on the potential outcomes, here mortality under both levels of treatment. We also show using illustrative preliminary injury data that our approach can reveal results that are more reasonable than the results of standard methods, in relatively dramatic ways. Thus, our approach suggests that the routine collection of data on variables that could be used as possible treatments in such studies of inputs and mortality should become common.

Allelochemicals in wheat (Triticum aestivum L.): production and exudation of 2,4-dihydroxy-7-methoxy-1,4-benzoxazin-3-one

An analytical technique employing gas chromatography and tandem mass spectrometry (GC/MS/MS) was employed to systematically screen fifty-eight wheat accessions for their differential production of 2,4-dihydroxy-7-methoxy-1,4-benzoxazin-3-one (DIMBOA) from three consecutive sources, i.e., the shoots, roots, and in the associated agar growth medium (collected as root exudates) of 17-day-old wheat seedlings. DIMBOA content differed significantly in the shoots, roots, or in the agar growth medium between accessions. DIMBOA accumulated differentially within the plant, with roots containing more DIMBOA than the shoots. Only 19% of accessions were able to exude DIMBOA from living roots into their growth medium, indicating the exudation of DIMBOA is accession-specific. DIMBOA level in root tissues is expected to be high when a high level of DIMBOA content is detected in the shoots. Wheat seedlings did not release detectable amounts of DIMBOA when the DIMBOA level was low in the root tissues. The valuable genetic material with high levels of DIMBOA in the shoots or roots identified in the present research could be used to breed for wheat cultivars with elevated allelopathic activity.

Phytotoxicity of vulpia residues: IV. Dynamics of allelochemicals during decomposition of vulpia residues and their corresponding phytotoxicity

The behavior and dynamics of 20 identified allelochemicals in vulpia residues were both collectively and individually monitored, and their kinetic phytotoxicity was assessed. The total content of the identified allelochemicals in decaying vulpia residues increased from 0.31 to 1.24 mg/g dry residue over a 21-day decomposition period, while the total phenolic content increased from 1.86 to 2.16 mg/g dry residue. This corresponded to a phytotoxicity increase from 42% to 82% of radical inhibition. Allelochemicals changed in composition and quantity over the duration of the residue decomposition. Addition of soil to the residues reduced the total allelochemical contents extracted and altered the dynamic pattern. In the same period, the total content of allelochemicals declined from 0.061 to 0.046 mg/g residue + soil, with the total phenolics reduced from 0.20 to 0.11 mg/g residue + soil, corresponding to a radical length increase from 53% to 109% of control. Only 14 of the identified allelochemicals were detected in the mix of soil and residues, in contrast to 20 present in the residues alone. The implications of these findings are discussed.

Evaluation of the optimal number of lesions needed for tumor evaluation using the response evaluation criteria in solid tumors: a north central cancer treatment group investigation

PURPOSE In February 2000, the criteria for measuring tumor shrinkage as an indicator of antitumor activity were redefined by the Response Evaluation Criteria in Solid Tumors (RECIST). This resulted in simplifying bidimensional to unidimensional measurement of lesions. Under RECIST, all lesions, up to 10, must be measured. Scanning and measuring multiple lesions is costly, time-consuming, and a disincentive to participation in clinical trials. We investigated whether fewer than 10 lesions can be measured without compromising the accuracy of assessing a regimen's activity. PATIENTS AND METHODS Thirty-two North Central Cancer Treatment Group trials including 2,374 patients were analyzed. Twelve studies were conducted before RECIST; 20 were conducted post-RECIST. Agreement between objective status by cycle, confirmed response, overall response rate, and time to progression (TTP) was evaluated based on all 10 versus the largest one through five lesions. Results The median number of lesions reported on RECIST trials did not differ from pre-RECIST trials (median = 2.0). One lesion at baseline was reported in 49% of patients, two lesions in 28% of patients, three lesions in 12% of patients, four lesions in 6% of patients, and five lesions in 5% of patients in post-RECIST trials. Utilizing the largest two lesions produced excellent concordance with that using all lesions for all end points. In no trial did the overall response rate differ by more than 3% when two versus all lesions were considered. Evaluating more than two lesions did not significantly improve agreement. CONCLUSION Based on these trials, the assessment of more than two lesions did not alter the conclusions regarding a treatment's efficacy as judged by response rate or TTP.

Avian transitin expression mirrors glial cell fate restrictions during neural crest development

During development, trunk neural crest cells give rise to three primary classes of derivatives: glial cells, melanocytes, and neurons. As part of an effort to learn how neural crest diversification is regulated, we have produced monoclonal antibodies (MAbs) that recognize antigens expressed by neural crest cells early in development. One of these, MAb 7B3 (7B3), was found to recognize an avian transitin-like protein by co-immunostaining with a series of transitin-specific monoclonal antibodies and by Western blot analysis. In neural crest cell cultures, we found that 7B3 initially recognizes the majority of neural crest cells as they emerge from the neural tube. Subsequently, 7B3-immunoreactivity (IR) is progressively restricted to a smaller subpopulation of cells. In fully differentiated trunk neural crest cell cultures, 7B3-IR is expressed only by cells that do not express neuronal markers and lack melanin granules. During development in vivo, 7B3-IR is evident in neural crest cells on the medial, but not the lateral migration pathway, suggesting that it is not expressed by melanocyte precursors. Later, the antigen is detected in non-neuronal, presumptive glial cells in dorsal root ganglia (DRG) and sympathetic ganglia, as well as along ventral roots. Cultures of E5 DRG confirm that 7B3-IR is restricted to non-neuronal cells of ganglia, many of which closely associate with neuronal processes. Therefore, of the three major classes of differentiated trunk neural crest derivatives, 7B3 exclusively recognizes glial cells, including both satellite glia and Schwann cells. Since the pattern of 7B3 expression in vitro mirrors the pattern of glial cell fate-restrictions in the trunk neural crest lineage, and is expressed by neural crest-derived glia in vivo, we conclude that 7B3 is an early pan-glial marker for neural crest-derived glial cells and their precursors.

Comparison of continuous versus categorical tumor measurement-based metrics to predict overall survival in cancer treatment trials

PURPOSE

The categorical definition of response assessed via the Response Evaluation Criteria in Solid Tumors has documented limitations. We sought to identify alternative metrics for tumor response that improve prediction of overall survival.

EXPERIMENTAL DESIGN

Individual patient data from three North Central Cancer Treatment Group trials (N0026, n = 117; N9741, n = 1,109; and N9841, n = 332) were used. Continuous metrics of tumor size based on longitudinal tumor measurements were considered in addition to a trichotomized response [TriTR: response (complete or partial) vs. stable disease vs. progression). Cox proportional hazards models, adjusted for treatment arm and baseline tumor burden, were used to assess the impact of the metrics on subsequent overall survival, using a landmark analysis approach at 12, 16, and 24 weeks postbaseline. Model discrimination was evaluated by the concordance (c) index.

RESULTS

The overall best response rates for the three trials were 26%, 45%, and 25%, respectively. Although nearly all metrics were statistically significantly associated with overall survival at the different landmark time points, the concordance indices (c-index) for the traditional response metrics ranged from 0.59 to 0.65; for the continuous metrics from 0.60 to 0.66; and for the TriTR metrics from 0.64 to 0.69. The c-indices for TriTR at 12 weeks were comparable with those at 16 and 24 weeks.

CONCLUSIONS

Continuous tumor measurement-based metrics provided no predictive improvement over traditional response-based metrics or TriTR; TriTR had better predictive ability than best TriTR or confirmed response. If confirmed, TriTR represents a promising endpoint for future phase II trials.

Test on existence of histology subtype-specific prognostic signatures among early stage lung adenocarcinoma and squamous cell carcinoma patients using a Cox-model based filter

Background

Non-small cell lung cancer (NSCLC) is the predominant histological type of lung cancer, accounting for up to 85% of cases. Disease stage is commonly used to determine adjuvant treatment eligibility of NSCLC patients, however, it is an imprecise predictor of the prognosis of an individual patient. Currently, many researchers resort to microarray technology for identifying relevant genetic prognostic markers, with particular attention on trimming or extending a Cox regression model.

Adenocarcinoma (AC) and squamous cell carcinoma (SCC) are two major histology subtypes of NSCLC. It has been demonstrated that fundamental differences exist in their underlying mechanisms, which motivated us to postulate the existence of specific genes related to the prognosis of each histology subtype.

Results

In this article, we propose a simple filter feature selection algorithm with a Cox regression model as the base. Applying this method to real-world microarray data identifies a histology-specific prognostic gene signature. Furthermore, the resulting 32-gene (32/12 for AC/SCC) prognostic signature for early-stage AC and SCC samples has superior predictive ability relative to two relevant prognostic signatures, and has comparable performance with signatures obtained by applying two state-of-the art algorithms separately to AC and SCC samples.

Conclusions

Our proposal is conceptually simple, and straightforward to implement. Furthermore, it can be easily adapted and applied to a range of other research settings.

Reviewers

This article was reviewed by Leonid Hanin (nominated by Dr. Lev Klebanov), Limsoon Wong and Jun Yu.

Electronic supplementary material

The online version of this article (doi:10.1186/s13062-015-0051-z) contains supplementary material, which is available to authorized users.

Glyphosate biodegradation and potential soil bioremediation by Bacillus subtilis strain Bs-15

Glyphosate and glyphosate-containing herbicides have an adverse effect on mammals, humans, and soil microbial ecosystems. Therefore, it is important to develop methods for enhancing glyphosate degradation in soil through bioremediation. We investigated the potential of glyphosate degradation and bioremediation in soil by Bacillus subtilis Bs-15. Bs-15 grew well at high concentrations of glyphosate; the maximum concentration tolerated by Bs-15 reached 40,000 mg/L. The optimal conditions for bacterial growth and glyphosate degradation were less than 10,000 mg/L glyphosate, with a temperature of 35°C and a pH of 8.0. Optimal fermentation occurred at 180 rpm for 60 h with an inoculum ratio of 4%. Bs-15 degraded 17.65% (12 h) to 66.97% (96 h) of glyphosate in sterile soil and 19.01% (12 h) to 71.57% (96 h) in unsterilized soil. Using a BIOLOG ECO plate test, we observed no significant difference in average well color development values between the soil inoculated with Bs-15 and the control soil before 72 h, although there was a significant difference (P < 0.01) after 72 h. In the presence of Bs-15, the 5 functional diversity indices (Shannon index, Shannon uniformity, Simpson index, McIntosh index, and McIntosh uniformity) were greater (P < 0.01) compared with the control soil. These results indicate that Bs-15 could be used to alleviate contamination from glyphosate-containing herbicides, increasing the microbial functional diversity in glyphosate-contaminated soils and thus enhancing the bioremediation of glyphosate-contaminated soils.