Functional analysis: evaluation of response intensities--tailoring ANOVA for lists of expression subsets.

Background: Microarray data is frequently used to characterize the expression profile of a whole genome and to compare the characteristics of that genome under several conditions. Geneset analysis methods have been described previously to analyze the expression values of several genes related by known biological criteria (metabolic pathway, pathology signature, co-regulation by a common factor, etc.) at the same time and the cost of these methods allows for the use of more values to help discover the underlying biological mechanisms. Results: As several methods assume different null hypotheses, we propose to reformulate the main question that biologists seek to answer. To determine which genesets are associated with expression values that differ between two experiments, we focused on three ad hoc criteria: expression levels, the direction of individual gene expression changes (up or down regulation), and correlations between genes. We introduce the FAERI methodology, tailored from a two-way ANOVA to examine these criteria. The significance of the results was evaluated according to the self-contained null hypothesis, using label sampling or by inferring the null distribution from normally distributed random data. Evaluations performed on simulated data revealed that FAERI outperforms currently available methods for each type of set tested. We then applied the FAERI method to analyze three real-world datasets on hypoxia response. FAERI was able to detect more genesets than other methodologies, and the genesets selected were coherent with current knowledge of cellular response to hypoxia. Moreover, the genesets selected by FAERI were confirmed when the analysis was repeated on two additional related datasets. Conclusions: The expression values of genesets are associated with several biological effects. The underlying mathematical structure of the genesets allows for analysis of data from several genes at the same time. Focusing on expression levels, the direction of the expression changes, and correlations, we showed that two-step data reduction allowed us to significantly improve the performance of geneset analysis using a modified two-way ANOVA procedure, and to detect genesets that current methods fail to detect.

Use of new biochemical plasmatic markers, plasma free and total metanephrines, for the diagnosis and follow-up of neuroblastoma in children with clinical correlation

Background: Neuroblastoma is a paediatrictumour derived from the neural crest. Biochemical diagnosis and follow up rely on quantitation of urinary catecholamines (dopamine and noradrenaline) and their metabolites vanillylmandelic acid (VMA) and homovanillic acid (HVA) (gold-standard). When combined, these analyses have a sensitivity of 95%. However, they are clearly limited by inaccuracy of urine collection in young children and normalisation of catecholamine concentrations by creatininuria. Recent development in biochemical diagnosis of pheochromocytoma, another neural crest tumour found in adults, shows that plasmatic measurement of methoxylated catecholamines called metanephrines are more sensitive and specific than other biomarkers. Moreover, a study to determine the reference intervals for metanephrines in a pediatric population has recently been completed. The aim of this work is to describe the role of metanephrines monitoring in the follow up of neuroblastoma. Method: This retrospective study included patients with neuroblastoma in whom the following parameters were determined: plasma free and total metanephrines, plasma catecholamines, 24h urinary catecholamines and metanephrines in absolute value and corrected by creatinine, VMA and HVA at the diagnosis and during treatment at the University Hospital of Lausanne (Switzerland). Eleven patients aged between the first day of life and 7 years old were followed between 2005 and 2012. Clinical outcome and biochemical concentrations of the analytes were correlated. Results: At diagnosis, plasma free and total normetanephrines and methoxytyramine have a sensitivity of 100% compared to 85% for the actual gold standard. Metanephrine remain below the upper reference limit as expected since these tumours do not produce adrenaline. The relationship between biochemical markers and clinical outcome is illustrated graphically. Plasma or urinary normetanephrine and methoxytyramine correlate better with the history of the patient than VMA and HVA, as evaluated by ordinal logistic regression. Concentrations of analytes in urine show a better correlation with clinical events when the results are corrected by creatininuria. Conclusion: Normetanephrine and methoxytyramine reflect disease history in neuroblastoma patients and could play a significant role in the follow up of this type of tumour. Formal studies in a sufficient number of patients are needed to confirm this preliminary observation.

Dépistage et prévention chez les aînés: quelles interventions proposer, à qui, et jusqu'à quel âge [Screening and prevention in the elderly: which interventions should be proposed, to whom, and up to what age?].

Recommendations on preventive services rarely mention how to apply them to older people. Even though general criteria (prevalence of disease, quality of screening tests) that influence screening's efficacy remain important, appropriateness of screening in older persons depends much more on individual criteria, such as comorbidity, functional status, and life expectancy. More than with any other age group, patients preferences regarding future investigation and treatment guide the clinical decision. This article focuses on primary and secondary prevention, and discusses specific criteria to consider in each patient. A table summarizes the appropriate recommendations.

Select-divide-and-conquer method for large-scale configuration interaction

A select-divide-and-conquer variational method to approximate configuration interaction (CI) is presented. Given an orthonormal set made up of occupied orbitals (Hartree-Fock or similar) and suitable correlation orbitals (natural or localized orbitals), a large N-electron target space S is split into subspaces S0,S1,S2,...,SR. S0, of dimension d0, contains all configurations K with attributes (energy contributions, etc.) above thresholds T0={T0egy, T0etc.}; the CI coefficients in S0 remain always free to vary. S1 accommodates KS with attributes above T1≤T0. An eigenproblem of dimension d0+d1 for S0+S 1 is solved first, after which the last d1 rows and columns are contracted into a single row and column, thus freezing the last d1 CI coefficients hereinafter. The process is repeated with successive Sj(j≥2) chosen so that corresponding CI matrices fit random access memory (RAM). Davidson's eigensolver is used R times. The final energy eigenvalue (lowest or excited one) is always above the corresponding exact eigenvalue in S. Threshold values {Tj;j=0, 1, 2,...,R} regulate accuracy; for large-dimensional S, high accuracy requires S 0+S1 to be solved outside RAM. From there on, however, usually a few Davidson iterations in RAM are needed for each step, so that Hamiltonian matrix-element evaluation becomes rate determining. One μhartree accuracy is achieved for an eigenproblem of order 24 × 106, involving 1.2 × 1012 nonzero matrix elements, and 8.4×109 Slater determinants

Monitoring compliance in resistant hypertension: an important step in patient management.

Poor compliance with antihypertensive drug regimens is one recognized cause of inadequate blood pressure control. Compliance is difficult to measure, so poor adherence to treatment remains largely undiagnosed in clinical practice. When the therapeutic response to a drug is not the one expected, it is a major challenge for many physicians to decide whether the patient is a non-responder or a non-complier. Poor compliance is therefore often incorrectly interpreted as a lack of response to treatment. Not detecting non-compliance can lead to the wrong measures being taken. Electronic monitoring of compliance provides important longitudinal information about drug-intake behaviour that cannot be obtained in the clinic. Such monitoring can improve both compliance and blood pressure control, and help physicians to make more rational therapeutic decisions. A reliable assessment of compliance could have a great impact on medical costs by preventing unnecessary investigations or dose adaptations in patients who are not taking their drugs adequately, or potentially reducing the number of hospitalizations. Side-effects and lack of effectiveness are two frequent causes of poor compliance. The right choice of antihypertensive drug can therefore contribute to compliance. In this respect, it is important to find a drug regimen that is effective, long-acting and well tolerated. Long-acting antihypertensive drugs that provide good blood pressure control beyond the 24-h dosing period should perhaps be considered as drugs of choice in non-compliant patients with hypertension because they help to prevent the consequences of occasional drug omissions.

Relation soignant-soigné quand les blogs s'en mêlent [Patient-caregiver relationship: when illness blogs step in].

The use of social media as a communication tool is rapidly growing in the community, and more specifically in patients, through illness blogs. This has been true for several years in North America, but is becoming a reality in Europe as well. We report here the first results of studies on the putative psychological benefits and risks of illness blogs for their authors. We also explore the possible impact of blogging on the patient-caregiver relationship. Social media are expected to have a growing influence in certain areas of health care. Physicians should therefore stay informed about them, take advantage of their benefits, and anticipate their risks.

Youthful Offender Program Follow Up Report, 2001

In 1996, the Iowa Division of Criminal and Juvenile Justice Planning was asked by the Governor’s Alliance on Substance Abuse (GASA) to examine the five Youthful Offender Programs (YOPs) that were in operation at that time. The focus of the original study was to describe the programs, their clientele, and two outcome measures (program completion and recidivism). One section of the report provided a detailed description of each of the five programs in operation at the time of the original study and the findings for each. Another section of the report highlighted program completion rates and recidivism rates. The Youthful Offender Programs were designed to operate as part of a partnership with a number of different agencies (county attorneys, the district departments of correctional services, and a variety of different treatment agencies) to provide a holistic approach in the rehabilitation of youthful offenders. These programs were designed specifically for offenders between the ages of 16 and 21 who had committed first time felonies or aggravated misdemeanors as an alternative to incarceration or in response to non-compliant probationer behaviors. Offenders who were 16 and 17 years of age had to have been waived to the adult court to be eligible for entry to the program.

Surgical treatment of lumbar spinal stenosis. Five-year follow-up.

We carried out a retrospective review of 155 patients with lumbar spinal stenosis who had been treated surgically and followed up regularly: 77 were evaluated at a mean of 6.5 years (5 to 8) after surgery by two independent observers. The outcome was assessed using the scoring system of Roland and Morris, and the rating system of Prolo, Oklund and Butcher. Instability was determined according to the criteria described by White and Panjabi. A significant decrease in low back pain and disability was seen. An excellent or good outcome was noted in 79% of patients; 9% showed secondary radiological instability. Surgical decompression is a safe and efficient procedure. In the absence of preoperative radiological evidence of instability, fusion is not required.

Extended bottom-up proteomics with secreted aspartic protease Sap9.

We investigate the benefits and experimental feasibility of approaches enabling the shift from short (1.7kDa on average) peptides in bottom-up proteomics to about twice longer (~3.2kDa on average) peptides in the so-called extended bottom-up proteomics. Candida albicans secreted aspartic protease Sap9 has been selected for evaluation as an extended bottom-up proteomic-grade enzyme due to its suggested dibasic cleavage specificity and ease of production. We report the extensive characterization of Sap9 specificity and selectivity revealing that protein cleavage by Sap9 most often occurs in the vicinity of proximal basic amino acids, and in select cases also at basic and hydrophobic residues. Sap9 is found to cleave a large variety of proteins in a relatively short, ~1h, period of time and it is efficient in a broad pH range, including slightly acidic, e. g., pH5.5, conditions. Importantly, the resulting peptide mixtures contain representative peptides primarily in the target 3-7kDa range. The utility and advantages of this enzyme in routine analysis of protein mixtures are demonstrated and the limitations are discussed. Overall, Sap9 has a potential to become an enzyme of choice in an extended bottom-up proteomics, which is technically ready to complement the traditional bottom-up proteomics for improved targeted protein structural analysis and expanded proteome coverage. BIOLOGICAL SIGNIFICANCE: Advances in biological applications of mass spectrometry-based bottom-up proteomics are oftentimes limited by the extreme complexity of biological samples, e.g., proteomes or protein complexes. One of the reasons for it is in the complexity of the mixtures of enzymatically (most often using trypsin) produced short (<3kDa) peptides, which may exceed the analytical capabilities of liquid chromatography and mass spectrometry. Information on localization of protein modifications may also be affected by the small size of typically produced peptides. On the other hand, advances in high-resolution mass spectrometry and liquid chromatography have created an intriguing opportunity of improving proteome analysis by gradually increasing the size of enzymatically-derived peptides in MS-based bottom-up proteomics. Bioinformatics has already confirmed the envisioned advantages of such approach. The remaining bottle-neck is an enzyme that could produce longer peptides. Here, we report on the characterization of a possible candidate enzyme, Sap9, which may be considered for producing longer, e.g., 3-7kDa, peptides and lead to a development of extended bottom-up proteomics.

Fas-associated death domain protein (FADD) and caspase-8 mediate up-regulation of c-Fos by Fas ligand and tumor necrosis factor-related apoptosis-inducing ligand (TRAIL) via a FLICE inhibitory protein (FLIP)-regulated pathway.

Fas, a death domain-containing member of the tumor necrosis factor receptor family and its ligand FasL have been predominantly studied with respect to their capability to induce cell death. However, a few studies indicate a proliferation-inducing signaling activity of these molecules too. We describe here a novel signaling pathway of FasL and the tumor necrosis factor-related apoptosis-inducing ligand (TRAIL) that triggers transcriptional activation of the proto-oncogene c-fos, a typical target gene of mitogenic pathways. FasL- and TRAIL-mediated up-regulation of c-Fos was completely dependent on the presence of Fas-associated death domain protein (FADD) and caspase-8, but caspase activity seemed to be dispensable as a pan inhibitor of caspases had no inhibitory effect. Upon overexpression of the long splice form of cellular FADD-like interleukin-1-converting enzyme (FLICE) inhibitory protein (cFLIP) in Jurkat cells, FasL- and TRAIL-induced up-regulation of c-Fos was almost completely blocked. The short splice form of FLIP, however, showed a rather stimulatory effect on c-Fos induction. Together these data demonstrate the existence of a death receptor-induced, FADD- and caspase-8-dependent pathway leading to c-Fos induction that is inhibited by the long splice form FLIP-L.

The Smartcanula: a new tool for remote access perfusion in limited access cardiac surgery.

Devices for venous cannulation have seen significant progress over time: the original, rigid steel cannulas have evolved toward flexible plastic cannulas with wire support that prevents kinking, very thin walled wire wound cannulas allowing for percutaneous application, and all sorts of combinations. In contrast to all these rectilinear venous cannula designs, which present the same cross-sectional area over their entire intravascular path, the smartcanula concept of "collapsed insertion and expansion in situ" is the logical next step for venous access. Automatically adjusting cross-sectional area up to a pre-determined diameter or the vessel lumen provides optimal flow and ease of use for both, insertion and removal. Smartcanula performance was assessed in a small series of patients (76 +/- 17 kg) undergoing redo procedures. The calculated target pump flow (2.4 L/min/m2) was 4.42 +/- 61 L/ min. Mean pump flow achieved during cardiopulmonary bypass was 4.84 +/- 87 L/min or 110% of the target. Reduced atrial chatter, kink resistance in situ, and improved blood drainage despite smaller access orifice size, are the most striking advantages of this new device. The benefits of smart cannulation are obvious in remote cannulation for limited access cardiac surgery, but there are many other cannula applications where space is an issue, and that is where smart cannulation is most effective.

Sudden death among young people with first-episode psychosis: an 8-10 year follow-up study.

Individuals with first episode psychosis (FEP) experience high rates of premature mortality, in particular due to suicide. The study aims were to: a) Estimate the rate of sudden death among young people with FEP during an 8-10 year period following commencement of treatment; b) Examine and describe the socio-demographic and clinical characteristics associated with sudden death; and c) Examine the timing of death in relation to psychiatric treatment.This was a cohort study. The sample comprised 661 patients accepted into treatment at the Early Psychosis Prevention and Intervention Centre between 1/1/1998 and 31/12/2000. Demographic and clinical data were collected by examination of the medical files. Mortality data were collected via a search of the National Coroners Information System; the Victorian State Coroner's office and clinical files. Nineteen patients died and just over two thirds of deaths were classified as intentional self-harm or suicide. Death was associated with male gender, previous suicide attempt and greater symptom severity at last contact. People with FEP are at increased risk of premature death, in particular suicide. A previous suicide attempt was very common amongst those who died, suggesting that future research could focus upon the development of interventions for young people with FEP who engage in suicidal behaviour.

Production of human secretory component with dimeric IgA binding capacity using viral expression systems.

The cDNA encoding the NH2-terminal 589 amino acids of the extracellular domain of the human polymeric immunoglobulin receptor was inserted into transfer vectors to generate recombinant baculo- and vaccinia viruses. Following infection of insect and mammalian cells, respectively, the resulting truncated protein corresponding to human secretory component (hSC) was secreted with high efficiency into serum-free culture medium. The Sf9 insect cell/baculovirus system yielded as much as 50 mg of hSC/liter of culture, while the mammalian cells/vaccinia virus system produced up to 10 mg of protein/liter. The M(r) of recombinant hSC varied depending on the cell line in which it was expressed (70,000 in Sf9 cells and 85-95,000 in CV-1, TK- 143B and HeLa). These variations in M(r) resulted from different glycosylation patterns, as evidenced by endoglycosidase digestion. Efficient single-step purification of the recombinant protein was achieved either by concanavalin A affinity chromatography or by Ni(2+)-chelate affinity chromatography, when a 6xHis tag was engineered to the carboxyl terminus of hSC. Recombinant hSC retained the capacity to specifically reassociate with dimeric IgA purified from hybridoma cells.

Opportunity for catch-up HPV vaccination in young women after first delivery.

Background Early age at first delivery has been identified as a risk factor for high-risk HPV-type infection and cervical cancer development. Methods A cross-sectional study was carried out in a large public maternity hospital in Sao Paulo, Brazil. During June 2006 to February 2007, 301 women aged 15-24 years who gave birth to their first child were recruited between 43 and 60 days after delivery. Detection of HPV DNA in cervical specimens was performed using a standardised PCR protocol with PGMY09/11 primers. The association of selected factors with HPV infection was assessed by using a Generalised Linear Model. Results HPV DNA was detected in 58.5% (95% CI 52.7% to 64.0%) of the enrolled young women. The most common types of HPV found were: HPV16, HPV51, HPV52, HPV58 and HPV71. The overall prevalence of HPV types targeted by the HPV prophylactic vaccines was: HPV 16-12.0%, HPV 18-2.3% and HPV 6 and 11 4.3%. In the multivariate analysis, only age (inversely, p for trend=0.02) and smoking habits were independently associated with HPV infection. Conclusions The findings show that these young primiparous women had high cervical HPV prevalence, suggesting that this is a high-risk group for cervical cancer development. Nevertheless, 17.3% were positive for any of the four HPV types included in HPV vaccines (HPV6, 11, 16 or 18), with 13.3% positive for HPV 16 or 18 and only 1.0% having both vaccine related-oncogenic HPV types. Thus, young primiparous women could benefit from catch-up HPV vaccination programmes.