Regularized estimation for the accelerated failure time model

SUMMARY

In the presence of high-dimensional predictors, it is challenging to develop reliable regression models that can be used to accurately predict future outcomes. Further complications arise when the outcome of interest is an event time, which is often not fully observed due to censoring. In this article, we develop robust prediction models for event time outcomes by regularizing the Gehan's estimator for the accelerated failure time (AFT) model (Tsiatis, 1996, Annals of Statistics 18, 305-328) with least absolute shrinkage and selection operator (LASSO) penalty. Unlike existing methods based on the inverse probability weighting and the Buckley and James estimator (Buckley and James, 1979, Biometrika 66, 429-436), the proposed approach does not require additional assumptions about the censoring and always yields a solution that is convergent. Furthermore, the proposed estimator leads to a stable regression model for prediction even if the AFT model fails to hold. To facilitate the adaptive selection of the tuning parameter, we detail an efficient numerical algorithm for obtaining the entire regularization path. The proposed procedures are applied to a breast cancer dataset to derive a reliable regression model for predicting patient survival based on a set of clinical prognostic factors and gene signatures. Finite sample performances of the procedures are evaluated through a simulation study.

Krüppel-like factor 5 promotes breast cell proliferation partially through upregulating the transcription of fibroblast growth factor binding protein 1

The Krüppel-like factor 5 (KLF5) is a zinc-finger transcription factor promoting cell proliferation, cell-cycle progression and survival. A high expression level of KLF5 mRNA has been shown to be associated with shorter breast cancer patient survival. However, the mechanism of KLF5 action in breast cancer is still not clear. In this study, we found that both KLF5 and its downstream gene fibroblast growth factor binding protein 1 (FGF-BP) are co-expressed in breast cell lines and primary tumors. Manipulation of the KLF5 expression can positively regulate the FGF-BP mRNA and protein levels in multiple breast cell lines. In addition, the secreted FGF-BP protein in the conditional medium is also regulated by KLF5. Furthermore, we demonstrated that KLF5 binds and activates the FGF-BP promoter through a GC box by luciferase reporter, oligo pull down and chromatin immunoprecipitation (ChIP) assays. When FGF-BP is depleted by siRNA, KLF5 fails to promote cell proliferation in MCF10A, SW527 and TSU-Pr1. We further demonstrated that overexpression or addition of FGF-BP rescues the KLF5-knockdown-induced growth arrest in MCF10A cells. Finally, KLF5 significantly promotes MCF7 breast cancer cell xenograft growth in athymic nude mice. These findings suggest that KLF5 may promote breast cancer cell proliferation at least partially through directly activating the FGF-BP mRNA transcription. Understanding the mechanism of KLF5 action in breast cancer may result in useful diagnostic and therapeutic targets.

Foresight Infectious Diseases China Project--a novel approach to anticipating future trends in risk of infectious diseases in China: methodology and results from an initial application

The project devised a simple but novel methodology for identifying possible future trends in infectious diseases in animals and humans in China, of priority concern to the Chinese authorities. It used a model of disease drivers (social, economic, biological or environmental factors that affect disease outcomes, by changing the behaviour of diseases, sources or pathways) devised for the Foresight Programme in the United Kingdom. Nine families of drivers were adapted to Chinese circumstances and matrices were constructed to identify the likely relationship of single infectious diseases or families of diseases to the drivers. The likely future trends in those drivers in China were determined by interviews with 36 independent Chinese experts. These trends included not only potentially adverse animal and human movements but also opportunities for innovative surveillance methods, more use of hospitals, antimicrobials and vaccines. Some human behaviours and social trends were expected to increase the risk of infections (in particular sexually transmitted and healthcare-associated infections) while at the same time the experts thought the awareness of risk in the Chinese population would increase. The results suggested a number of areas where the Chinese authorities may experience difficulties in the future, such as rising numbers of healthcare-associated infections, zoonoses and other emerging diseases and sexually transmitted infections (including HIV). Not making firm predictions, this work identifies priority disease groups requiring surveillance and consideration of countermeasures as well as recommending strengthening basic surveillance and response mechanisms for unanticipatable zoonoses and other emerging disease threats.

Iron oxide nanoparticle platform for biomedical applications

Progress in nanosynthesis has succeeded in making nanoscale particles from iron oxide under precise quality control. Given the recent great advances in polymer manufacturing, antibody purification, DNA/RNA synthesis and magnetic resonance imaging (MRI), such iron oxide nanoparticles (IONPs) have been enriched with many variables and attracted great interest in studying their potential biomedical applications. After nearly two decades' effort, IONPs have become a powerful platform in many diverse aspects of biomedicine, including MRI, gene and drug delivery, and hyperthermia. While some studies are still at the proof-of-concept stage, others have now been widely used in clinics. With the on-going efforts to enhance their targeting ability and endow more functions, IONPs' future applications are highly expected.

A comparison of the role of two blue-green algae in THM and HAA formation

The contribution of two blue-green algae species, Anabaena flos-aquae and Microcystis aeruginosa, to the formation of trihalomethanes (THMs) and haloacetic acids (HAAs) was investigated. The experiments examined the formation potential of these disinfection by-products (DBPs) from both algae cells and extracellular organic matter (EOM) during four algal growth phases. Algal cells and EOM of Anabaena and Microcystis exhibited a high potential for DBP formation. Yields of total THMs (TTHM) and total HAAs (THAA) were closely related to the growth phase. Reactivity of EOM from Anabaena was slightly higher than corresponding cells, while the opposite result was found for Microcystis. Specific DBP yields (yield/unit C) of Anabaena were in the range of 2-11micromol/mmol C for TTHM and 2-17micromol/mmol C for THAA, while those of Microcystis were slightly higher. With regard to the distributions of individual THM and HAA compounds, differences were observed between the algae species and also between cells and EOM. The presence of bromide shifted the dominant compounds from HAAs to THMs.

Prognostic value of different B symptoms in upper aerodigestive tract NK/T-cell lymphoma

e19544

Background: Extranodal NK/T-cell lymphoma (ENKL) is a rare disease originated from NK or toxic T cells. ENKL arising from the upper aerodigestive tract (UNKTL) is a newly recognized subtype and commonly presents with B symptoms. This study is to investigate the prognostic value of different B symptoms in UNKTL. Methods: UNKTL cases with detailed clinical, pathological and prognostic data in our center since 2001 to 2007 were retrospectively analyzed with the major study endpoint of overall survival (OS). Central pathological review was performed. Survival curves were estimated by Kaplan-Meier method and tested by Log Rank method. Statistically significant factors in univariate analysis were then included in multivariate analysis. B symptoms were defined as fever, night sweat and weight loss according to the Ann Arbor Cotswolds meeting. The predictive values of survival for each type of B symptoms were studied independently. Results: 172 cases of UNKTL with a median follow-up duration of 27.4 months were included. 45 ladies and 127 gentlemen had a median age of 43 years. 98 cases were Ann Arbor stage I, 54 were stage II and the remaining 20 cases were stage III or IV. About half of the patients present B symptoms: 82 had fever, 5 had night sweat and 6 present weight loss. Totally 18 patients had ECOG PS larger than 1. The 5-year OS rate of the whole group is 41.8%. Patients with persistent fever before treatment indicated a poor outcome in the univariate analysis (p=.033) and its prognostic value was also confirmed by the Cox regression (p=.030) whereas those of night sweat and weight loss were not (p= .960 and .824 respectively). Conclusions: B symptoms were common in UNKTL patients. Our data suggested that only fever among the three types of B symptoms was independent prognostic factor for UNKTL but it still needs further confirmation.

No significant financial relationships to disclose.

Safety of bevacizumab in patients with metastases to the central nervous system

2007

Background:. The background rate of CNS hemorrhage (CH) in cancer patients with brain metastases not receiving bevacizumab (BV) treatment is 5%-29%, depending on tumor type. Patients with CNS metastases were routinely excluded from most BV late-stage clinical trials, following the occurrence of CH in one hepatocellular carcinoma patient with occult CNS metastasis in a BV phase I trial. In this particular tumour type, up to 87.5% has been reported as a background rate of CH without BV use. Available safety information in BV-treated patients with CNS metastases has been reviewed to determine whether the exclusion of these patients from trials is still justified. Methods: A retrospective exploratory analysis was conducted using safety data from three datasets: A.) 13 randomized controlled phase II or III trials (RCTs); B.) Two ongoing open-label trials MO19391 (ATHENA) and MO19390 (SAIL). While patients with known CNS metastases, based on imaging or clinical signs and symptoms, were excluded from trial in A and B datasets, patients who were found to have CNS lesions had either unrecognized CNS metastases at study entry or had developed these during the trial.; C.) 2 ongoing open-label studies AVF3752g and AVF3671g in patients with NSCLC, where inclusion of patients with treated CNS metastases was allowed. Incidence of CH in patients with brain metastases was quantified in each dataset. Results: A.) In 13 RCTs, with a total of 8443 patients with locally advanced, unresectable, or metastatic breast, renal, pancreatic, colorectal cancer, or NSCLC, brain metastases were identified in 187 patients (91 in BV-arms and 96 in control arm). Three of 91 (3.29%) BV-treated patients developed grade 4 CH, and one in 96 patients in the control arm (1.04%) developed grade 5 CH; B.) In open-label studies no CH was reported in 68 patients with CNS metastases, out of 3,252 patients enrolled. C.) In two studies in patients with treated CNS metastases, one subject in 83 (1.2%) BV treated patients developed a grade 2 CH. Conclusions: In this retrospective review, the rates of CH in BV-treated patients with CNS metastases is low, and appears consistent with historical rates of CH in these patient populations. Ongoing trials are expected to provide additional data regarding the risk of CH in patients with primary and metastatic CNS tumors.

[Table: see text]

Association of chromosome 2q36.1-36.3 and autosomal dominant transmission in ankylosing spondylitis: results of genetic studies across generations of Han Chinese families

Background:

Ankylosing spondylitis (AS) is a chronic, potentially crippling, spondyloarthropathy with strong genetic components affecting approximately 0.3% of the population. Its exact genetic mechanism and mode of transmission, however, remains obscure.

Methods and results:

The authors conducted a genome wide scan on 75 individuals across multiple generations of three Han Chinese families affected with AS. Segregation analysis and pedigree investigation suggested an autosomal dominant inheritance. Pairwise logarithm of odds (LOD) scores were calculated using LINKAGE package for the obtained genotypes. High resolution mapping was then performed based on markers with significant LOD scores. To minimise the number of crossovers in each family, haplotype were constructed and assigned. Two of the pedigrees shared one candidate region for AS on 2q36.1–2q36.3 spanning 6-cM (maximum heterogeneity LOD score of 12.41 at marker D2S2228), while the other showed strong linkage to the HLA-B region.

Conclusions:

This is the first report which proposes one of the new genetic models of autosomal dominant transmission in AS. The breakthrough in the identification of linkage to chromosome 2q36.1–2q36.3 and the HLA-B region highlights the future potential of more comprehensive genetic studies of determinants of disease risk.

Clinics in diagnostic imaging (126). Right atrial myxoma

A 47-year-old woman presented with dyspnoea on exertion for several weeks. Echocardiogram and multidetector computed tomography of the heart showed a right atrial mass typical of an atrial myxoma. This was confirmed on histology. The imaging features of atrial myxoma and other conditions presenting as a right-sided cardiac mass are discussed.

Induction of myocarditis lesions in Lewis rats by formalin-killed cells of group A Streptococcus

The feasibility of inducing rheumatic myocarditis lesions in Lewis rats by immunization with formalin-killed group A Streptococcus was evaluated. The rats were divided into three groups. Group A was immunized by injecting formalin-killed group A Streptococcus suspended in complete Freund's adjuvant (CFA) into the hind-foot pads and repeat immunization was given 1 week later by subcutaneous injection into the belly. The rats were then sacrificed 3 weeks after the initial immunization. In group B, the rats received the same initial immunization as group A, but the repeat immunization was carried out at 1, 2 and 3 weeks after the initial immunization and the rats were sacrificed 6 weeks after the initial immunization. Group C was a control group with the rats injected with saline/CFA and sacrificed on the same schedule as group A. Heart pathology sections showed that myocarditis lesions, focal inflammatory cell infiltration in interstitial near small vessels and valvulitis were induced in Lewis rats following immunization with formalin-killed group A Streptococcus.

Magnetic Resonance Scanning of the Upper Airway following Difficult Intubation Reveals an Unexpected Lingual Tonsil

We present a case of a 40-year-old woman requiring elective surgery who had an unexpected Grade 4 Cormack and Lehane laryngoscopy view. Both curved and straight laryngoscope blades in the sniffing and hyperextended head and neck positions were used. Endotracheal intubation was accomplished with some difficulty using a No. 3 Macintosh blade and Frova intubating catheter in the sniffing position. The cause of the difficult laryngoscopy was a lingual tonsil as shown in postoperative magnetic resonance scans.

We feel that a comprehensive postoperative evaluation should be conducted after every difficult laryngoscopy (Cormack and Lehane Grade 3b and 4). The use of magnetic resonance imaging may provide important objective information for both the anaesthetist and the patient, allowing a better understanding of causes and possible solutions for future airway management.

The frequency of the TRPC4AP haplotype in Alzheimer's patients

A haplotype in the gene for transient receptor potential cation channel, subfamily C, member 4 associated protein (TRPC4AP), has been identified in two extended pedigrees with late-onset Alzheimer's disease. Nine of the SNPs in the haplotype were analyzed in our unrelated Alzheimer's patients and controls. The H1 haplotype was found in 36% of the patients (199 patients) and in 26% of the controls (85 controls) (P=0.0282; OR=1.56; 95%CI=1.05-2.32). The latent classification method of analysis showed that the H1 haplotype was characteristic of Alzheimer's patients, with ages-of-onset between 66 and 80 years. When clinical phenotypes were analyzed, there was a suggestion that the patients with this haplotype may have more behavioral changes and hallucinations. Moreover, both the latent classification analysis and logistic regression analysis indicated that there was no association of the haplotype with either APOE status or gender. The gene is part of a superfamily of cation channels that are involved with calcium entry into cells.

Correlation of coronary angiography with "tombstoning" electrocardiographic pattern in patients after acute myocardial infarction

BACKGROUND

It has been suggested that a specific pattern of electrocardiographic (ECG) changes following acute myocardial infarction (AMI), the so-called "tombstoning," predicts a poorer outcome, although the cause and associations of such changes are not known. To address the possible cause and implications, we correlated angiographic findings with tombstoning in patients following AMI.

METHODS

The study investigated 124 patients with AMI, whose ECGs were taken within 24 h of onset of symptoms and who subsequently underwent angiography. In this population, 24 (19%) patients had a definite tombstoning pattern on their admission ECG.

RESULTS

Compared with non-tombstoning ECGs, the significant differences in the tombstoning group are as follows: (1) All patients, including those with inferior infarction, had either total or partial occlusion of the left anterior descending (LAD) artery (100 vs. 44%, p < 0.0001); (2) LAD occlusions were significantly more severe and mostly proximal (100% occlusion: 50 vs. 20.5%, p = 0.02; <50% occlusion: 0 vs. 15.9% p = 0.039; proximal occlusion: 92 vs. 65%, p = 0.017); (3) patients with tombstoning ECGs had a significantly greater incidence of occlusion of all three coronary arteries (54.1 vs. 22%, p = 0.001); (4) tombstoning ECGs were more strongly associated with anterior than with inferior infarction (83.3 vs. 33%, p < 0.0001).

CONCLUSIONS

The patients with a tombstoning pattern on the admission ECG, who underwent angiography, were associated with occlusion of a high-grade stenosis of the proximal LAD artery (usually with involvement of more than one artery) and were predominantly seen in association with anterior infarction.

Tunability of mobility and conductivity over large ranges in poly(3,3'''-didodecylquaterthiophene)/insulating polymer composites

Semiconducting polymers are currently being considered as active layers in field-effect transistors, in which high charge carrier mobility and low off conductivity are important. For other applications, such as certain spintronic mechanisms, the opposite characteristics are desirable. Blending such polymers with insulating polymers would be expected to lower the mobility. In this paper, we report that the use of hydrocarbon polymers such as polystyrene as insulators generally raises the mobility when the semiconducting polymer is poly(bisdodecylquaterthiophene). A high mobility value of nearly 0.1 cm(2)/V.s was obtained for an optimal blend. While this is counterintuitive, it is consistent with a few other recent reports. In order to lower the mobility significantly, a much more polar and irregular blending agent is needed. The further addition of tetrafluorotetracyanoquinodimethane as a dopant gave a rare low mobility/high conductivity combination of properties, with a charge carrier density on the order of 10(19) cm(-3). Thus, mobility and conductivity were tuned somewhat independently over 3 and 4 orders of magnitude, respectively.