The impact of comorbidities and their stacking on short- and long-term prognosis of patients over 50 with community-acquired pneumonia

BACKGROUND

The prognosis of patients hospitalized with community-acquired pneumonia (CAP) with regards to intensive care unit (ICU) admission, short- and long-term mortality is correlated with patient's comorbidities. For patients hospitalized for CAP, including P-CAP, we assessed the prognostic impact of comorbidities known as at-risk (AR) or high-risk (HR) of pneumococcal CAP (P-CAP), and of the number of combined comorbidities.

METHODS

Data on hospitalizations for CAP among the French 50+ population were extracted from the 2014 French Information Systems Medicalization Program (PMSI), an exhaustive national hospital discharge database maintained by the French Technical Agency of Information on Hospitalization (ATIH). Their admission diagnosis, comorbidities (nature, risk type and number), other characteristics, and their subsequent hospital stays within the year following their hospitalization for CAP were analyzed. Logistic regression models were used to assess the associations between ICU transfer, short- and 1-year in-hospital mortality and all covariates.

RESULTS

From 182,858 patients, 149,555 patients aged ≥ 50 years (nonagenarians 17.8%) were hospitalized for CAP in 2014, including 8270 with P-CAP. Overall, 33.8% and 90.5% had ≥ 1 HR and ≥ 1 AR comorbidity, respectively. Cardiac diseases were the most frequent AR comorbidity (all CAP: 77.4%). Transfer in ICU occurred for 5.4% of CAP patients and 19.4% for P-CAP. Short-term and 1-year in-hospital mortality rates were 10.9% and 23% of CAP patients, respectively, significantly lower for P-CAP patients: 9.2% and 19.8% (HR 0.88 [95% CI 0.84-0.93], p < .0001). Both terms of mortality increased mostly with age, and with the number of comorbidities and combination of AR and HR comorbidities, in addition of specific comorbidities.

CONCLUSIONS

Not only specific comorbidities, but also the number of combined comorbidities and the combination of AR and HR comorbidities may impact the outcome of hospitalized CAP and P-CAP patients.

Reasons for intravesical instillation postponement during adjuvant treatment of non-muscle-invasive bladder cancer: A prospective study

INTRODUCTION

Intravesical instillations for adjuvant treatment of non-muscle-invasive bladder cancer (NMIBC) may be postponed of necessity. However, the frequency and reasons for postponement are unclear.

MATERIALS

We carried out a prospective, epidemiological study in an Urology department of the Île-de-France, between August 2016 and March 2017, to determine the frequency and reasons for postponement of intravesical instillations during adjuvant treatment of NMIBC. One-hundred consecutive patients treated by intravesical instillations of mitomycin C (MMC) or Bacillus Calmette-Guérin (BCG) were included. At each session and in case of instillation postponement, the medical team completed a specially designed questionnaire.

RESULTS

A total of 541 instillations were performed in the 100 patients. Twenty-four instillations (4.4%) were postponed in 19 patients. The major cause of postponement was an untreated positive urine analysis and culture (UAC) in 13/24 (54%) cases. The causes of cancellation did not differ significantly between MMC and BCG. The most frequently cancelled instillations were the first in the therapeutic protocol in 26% of cases. The number of instillations preceding those cancelled did not differ significantly between MMC and BCG (2.1±2.0 instillations for MMC vs. 1.5±1.6 for BCG; P=0.64).

CONCLUSIONS

There was a low rate of postponed instillations (4.4%). The main reasons, namely an untreated UAC and a positive dipstick test, based on the jurisprudence, are not included in the latest CC-AFU guidelines.

LEVEL OF EVIDENCE

3.

French adaptation of the "Frenchay Dysarthria Assessment 2" speech intelligibility test

OBJECTIVES

Speech intelligibility can be defined as "the degree to which a speaker's intended message is recovered by a listener". Loss of intelligibility is one of the most frequent complaints in patients suffering from speech disorder, impairing communication. Measurement of intelligibility is therefore an important parameter in follow-up. We developed a French version of the "Frenchay Dysarthria Assessment, 2nd edition" (FDA-2), an intelligibility test recognized internationally in its English version. The present study details the construction of the test and its preliminary validation.

MATERIALS AND METHODS

We first compiled a set of words and phrases in French, based on the criteria defined in FDA-2. In a second step, we validated the test in healthy subjects in normal and noisy conditions, to check sensitivity to speech signal degradation.

RESULTS

The test proved valid and sensitive, as scores were significantly lower for noise-degraded stimuli.

CONCLUSION

This French-language intelligibility test can be used to evaluate speech disorder: for example, in dysarthria, head and neck cancer or after cochlear implantation.

Relevance of TSH evaluation in elderly in-patients with non-thyroidal illness

BACKGROUND

Non-thyroidal illness (NTI) is frequent in hospitalized patients. Its recovery is characterized by a raise in TSH levels. However, the clinical significance of high TSH levels at admission in hospitalized elderly patients with NTI remains uncertain.

AIM

To explore the relevance of baseline TSH evaluation in hospitalized elderly patients with NTI.

METHODS

We examined the participants with NTI (n = 123) from our previous study (Sforza, 2017). NTI was defined as: low T3 (< 80 ng/dL) and normal or low total T4 in the presence of TSH values between 0.1 and 6.0 mU/L. Thyroid function tests were performed on day 1 and day 8 of the hospital stay. Positive TSH changes (+ ΔTSH) were considered when the day-8 TSH value increased more than the reference change value for TSH (+ 78%). Multiple logistic regression was used to evaluate the independent association of baseline TSH, sex, clinical comorbidities (by ACE-27) and medications with + ΔTSH.

RESULTS

Out of 123 patients (77 ± 8 years, 52% female), 34 showed a + ΔTSH. These patients had a lower TSH at admission (p < 0.001) and intra-hospital mortality (p = 0.003) than the others. In multiple logistic regression, TSH > 2.11 mU/L at baseline was associated with reduced odds to show + ΔTSH [odds ratio (95 CI) 0.29 (0.11-0.75); p = 0.011] in a model adjusted by age, sex and ACE-27.

DISCUSSION

Inappropriately higher TSH levels at admission in hospitalized elderly patients were associated with a reduced ability to raise their TSH levels later on. The present results confront the idea that TSH levels at admission are irrelevant in this clinical context.

Hypothyroidism in hospitalized elderly patients: a sign of worse prognosis

PURPOSE

Overt hypothyroidism has adverse clinical consequences and might worsen prognosis in critically ill elderly patients. However, the difficult interpretation of thyroid function tests (TFT) due to non-thyroidal illness (NTI) has led to discouragement of screening for thyroid dysfunction. Our aim was to determine the prevalence of TFT compatible with hypothyroidism and to study its influence on mortality among hospitalized elderly patients.

METHODS

In this prospective study we consecutively included all patients ≥60 years admitted by the Internal Medicine Department to the hospital ward (n = 451) of the Cesar Milstein Hospital in Buenos Aires, Argentina. TFT were done on day 1 and 8. Thyroid function categories were defined as overt and subclinical hypothyroidism, overt and subclinical hyperthyroidism, euthyroidism and NTI. Stage of chronic kidney disease (CKD), Adult Comorbidity Evaluation (ACE)-27, and intra-hospital mortality were recorded. The association between mortality and TFT categories was studied by Cox regression.

RESULTS

Out of 451 patients (77.0 ± 7.9 years, 54% females) 76% were categorized as NTI, 4% as overt hypothyroid, 10% as subclinical hypothyroid, 1% as subclinical hyperthyroid and 9% as euthyroid. Overt hypothyroid patients showed significantly higher mortality than the rest of the groups (25%, p < 0.05) while ACE-27 was similar among all of them (p = 0.658). In addition, patients within the overt hypothyroid category showed a higher mortality rate than NTI in a model adjusted by Stage 5-CKD, ACE-27, sex and age [HR 3.1 (1.14-8.41), p < 0.026].

CONCLUSION

Overt hypothyroidism during hospitalization was associated with elevated mortality. Further studies would reveal if TFT alterations compatible with hypothyroidism should be diagnosed/treated in hospitalized elderly patients.

Abstract P1-08-06: SToRM: A prospective clinical trial of 1502 metastatic breast cancer (mBC) patients with detail of clinical presentation, molecular subtype, treatment modalities, prognosis and GWAS genotyping

Background: Due to better molecular classification and new treatment options, epidemiology and prognosis of mBC is rapidly changing. Clinical data extracted from randomized studies are only relevant to specific subpopulations and retrospective studies are prone to selection bias. SToRM is a prospective clinical trial that aims to create a cohort of 1500 mBC patients, with the ultimate goal of identifying germ line polymorphisms associated with prognosis of breast cancer (BC) and response to treatment in the metastatic phase.

Material and methods: Any newly (within 1 year) diagnosed mBC patients were eligible. Whole blood samples were drawn and germline DNA extracted for genetic analysis. Extensive epidemiologic data, disease history from primary diagnosis to metastatic spread, pathological characteristics and ER, PR and HER2 status were collected. Patients are prospectively followed until death. Genotyping using the HumanCoreExome chipset from Illumina is currently underway and will be completed in early summer 2015.

Results: 1502 patients were included from March 2012 to May 2014 from 71 French institutions. Median age at metastatic relapse was 60 years (range 26-93). Median time from primary diagnosis to metastatic relapse was 30 months (range 0-473) with 24% of patients already metastatic at initial diagnosis. 78% of patients were ER+, 18% were HER2+ and only 16% were triple negative. Molecular subtype classification derived from pathological data following St Gallen consensus recommendations is presented below:

 n (%)Luminal A like261 (22.2%)Luminal B like HER2 negative476 (40.5%)Luminal B like HER2 positive134 (11.4%)HER2 positive non Luminal (ER-)111 (9.5%)Triple negative193 (16.4%)Missing data327

64% of the patients had received previous adjuvant treatment, among which 81% received adjuvant chemotherapy and 9% trastuzumab.

At metastatic relapse, loco-regional progression, liver, lung and bone metastasis were documented in 301 (20%), 494 (33%), 410 (27%) and 1017 (68%) patients respectively. 313 patients (21%) had bone only metastatic disease. First line treatment included: chemotherapy (71%), endocrine therapy (50%) and anti-HER2 treatments (17%). Survival data will be presented at the meeting.

Conclusion: Despite a theoretically better prognosis and widespread use of adjuvant hormonal treatment, ER+/HER2- breast cancer still account for more than 60% of mBC. The proportion of patients with HER2+ disease (18%) and triple negative disease (16%) is consistent with percentages observed in early BC populations. In comparison with a cohort of "cured", localized cancer, such as the SIGNAL/PHARE study, GWAS analysis will allow for the identification of genetic polymorphisms correlated with treatment resistance. Fundamentally, such variants will provide insight into the molecular mechanisms responsible for host-genetic influence on BC progression. From a clinical perspective, genetic variants that predispose to metastatic disease can serve as stratification variables in future clinical trials, particularly as the development of new treatment options for resistant BC is needed.

Citation Format: Bachelot T, Lavergne E, Romieu G, Rios M, Heudel P-E, Roemer-Becuwe C, Jouannaud C, Tredan O, Chaigneau L, Arnedos M, Orfeuvre H, Petit T, Quenel-Tueux N, Jacquin J-P, Ferrero J-M, Moullet I, Abadie-Lacourtoisie S, Penault-Llorca F, Blanc E, Cox D. SToRM: A prospective clinical trial of 1502 metastatic breast cancer (mBC) patients with detail of clinical presentation, molecular subtype, treatment modalities, prognosis and GWAS genotyping. [abstract]. In: Proceedings of the Thirty-Eighth Annual CTRC-AACR San Antonio Breast Cancer Symposium: 2015 Dec 8-12; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2016;76(4 Suppl):Abstract nr P1-08-06.

TORAVA trial: Lessons from this trial in the two control arms, sunitinib and bevacizumab in combination with interferon

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Background: The TORAVA trial, reported at ASCO 2010, was a randomized phase II study aimed to determine the efficacy and safety of temsirolimus and bevacizumab combination. Both efficacy and safety were demonstrated as insufficient. Interestingly, 2 control arms were used in this study, sunitinib (arm B) or bevacizumab and a-interferon (arm C). Both PFS and RR were higher in arm C than arm B (16.8 mths and 39% vs. 8.6 mths and 23.8%). Post-hoc analysis were thus performed to determine the predictive factors for better efficacy.

Methods: Overall, 171 pts were randomized in this study, 42 in arm B and 41 in arm C. The study was stratified on PS only, 0–1 vs 2. These 83 pts were analyzed regarding baseline characteristics, and dose reduction.

Results: Some important differences were detected in the 2 arms, in favor of arm C: DFI>12mths (29 vs. 39%), good MSKCC risk (31 vs. 39%), Fuhrman grade 1–2 (32 vs. 38%), liver metastases (19 vs. 14.6%), high LDH (17.1 vs. 7.9%). Interestingly, pts who had dose reduction of interferon (27/41 pts) had a longer PFS than those who did not reduced the dose. Updated analyses will be presented.

Conclusions: Small randomized trials such as randomized phase II trials are not guaranteed to balance predictive/ prognostic factors across treatment arms. Before interpreting RR and PFS in mRCC, careful analysis of pt characteristics should be performed. However, this study will probably help to determine a population more likely to benefit from bevacizumab-interferon combination.

[Table: see text]

The translation of recombinant proteins in E. coli can be improved by in silico generating and screening random libraries of a -70/+96 mRNA region with respect to the translation initiation codon

Recombinant protein translation in Escherichia coli may be limited by stable (i.e. low free energy) secondary structures in the mRNA translation initiation region. To circumvent this issue, we have set-up a computer tool called ‘ExEnSo’ (Expression Enhancer Software) that generates a random library of 8192 sequences, calculates the free energy of secondary structures of each sequence in the −70/+96 region (base 1 is the translation initiation codon), and then selects the sequence having the highest free energy. The software uses this ‘optimized’ sequence to create a 5′ primer that can be used in PCR experiments to amplify the coding sequence of interest prior to sub-cloning into a prokaryotic expression vector. In this article, we report how ExEnSo was set-up and the results obtained with nine coding sequences with low expression levels in E. coli. The free energy of the −70/+96 region of all these coding sequences was increased compared to the non-optimized sequences. Moreover, the protein expression of eight out of nine of these coding sequences was increased in E. coli, indicating a good correlation between in silico and in vivo results. ExEnSo is available as a free online tool.

[Ultrasound and CT study of duodenal pathology]

The radiological evaluation of the duodenum has traditionally been based on barium transit studies; however, ultrasound (US) and computed tomography (CT) are becoming more important in the assessment of this portion of the intestine and the structures that surround it. This report describes and illustrates the CT and US findings for different entities that affect the duodenum, including diseases of the duodenum itself and those of neighboring organs that affect this portion of the small intestine. We classify the pathologies by etiology into congenital, traumatic, iatrogenic and foreign bodies, bezoars, hematologic, inflammatory and neoplastic. Moreover, we present the incidental duodenal and periduodenal findings in US and CT that radiologists should be familiar with given the widespread use of these techniques.

Dysregulation of IL-2/IL-2R system alters proliferation of early activated CD4+ T cell subset in patients with end-stage renal failure

BACKGROUND/AIM

Although CD4+ T cells are preactivated in patients with end-stage renal failure (ESRF), these patients present an impairment of T cell immune response, which is partly responsible for the higher incidence of infection in this population. The aim of the present study was to analyze the mechanisms underlying the altered function of activated CD4+ T cells in patients with ESRF.

METHODS

Thirty patients undergoing chronic hemodialysis (HD) and 20 patients with ESRF were compared with 15 sex- and age-matched controls. CD4+ T cell early activation (CD69, CD25), interleukin-2 (IL-2)/IL-2 receptor (IL-2R) system, and proliferation capacity of CD69+/CD4+ T cells were assessed ex vivo after blood draw sampling, in culture conditions and after phytohemagglutinin (PHA) stimulation.

RESULTS

Although the CD4+ T cell count was lower in chronic HD patients than in predialysis patients and controls (p = 0.007), CD4+ T cells showed a pre-activation state as demonstrated by higher percentage of CD69+/CD4+ T cells and CD25+/CD4+ T cells in chronic HD patients compared with the other groups ex vivo. Furthermore, CD69+/CD4+ T cells from chronic HD patients spontaneously released more IL-2 (22 +/- 6 pg/ml) than those from pre-dialysis patients (12 +/- 4 pg/ml, p = 0.005) and controls (5 +/- 3 pg/ml, p = 0.001). However, after PHA stimulation, CD69+/CD4+ T cells from chronic HD patients expressed lower cell surface CD25 density, and were unable to show further activation. Indeed, these cells produced less IL-2 and released more soluble IL-2R, and correlatively with IL-2 production, they showed lower proliferation capacity compared with predialysis patients (p = 0.001) and controls (p < 0.001). They also displayed decreased responsiveness to exogenous human recombinant IL-2. The restoration of the PHA stimulation index of CD69+/CD4+ T cells from chronic HD patients in the presence of normal human serum as well as the decreased stimulation index of CD69+/CD4+ T cells from control subjects incubated with HD serum, strongly suggest that uremic toxins and mediators induced by HD affect the IL-2/IL-2R pathway.

CONCLUSION

These findings demonstrate the presence, in chronic HD patients, and to lesser extent, in predialysis patients, of abnormally high proportion of spontaneously preactivated CD4+ T cells whose proliferation and further activation are blunted due to dysregulation of the IL-2/IL-2R system.

Potential use of real-space refinement in protein structure determination

Through testing refinement protocols using free R-factor estimates of model quality, it is shown that real-space refinement can be a useful addition to conventional reciprocal-space refinement, even for protein structures with poor electron-density maps derived from multiple isomorphous replacement. By alternating real- and reciprocal-space refinements, starting with an experimental map, then calculating 2F(o) - F(c) maps, it is demonstrated with the structure of HMG-CoA reductase, that quick automatic refinement can yield a model with a free R factor 1.5% better than exhaustive reciprocal-space refinement, and within 1% of a model that was interactively rebuilt and refined repeatedly.

Refinement of severely incomplete structures with maximum likelihood in BUSTER-TNT

BUSTER-TNT is a maximum-likelihood macromolecular refinement package. BUSTER assembles the structural model, scales observed and calculated structure-factor amplitudes and computes the model likelihood, whilst TNT handles the stereochemistry and NCS restraints/constraints and shifts the atomic coordinates, B factors and occupancies. In real space, in addition to the traditional atomic and bulk-solvent models, BUSTER models the parts of the structure for which an atomic model is not yet available ('missing structure') as low-resolution probability distributions for the random positions of the missing atoms. In reciprocal space, the BUSTER structure-factor distribution in the complex plane is a two-dimensional Gaussian centred around the structure factor calculated from the atomic, bulk-solvent and missing-structure models. The errors associated with these three structural components are added to compute the overall spread of the Gaussian. When the atomic model is very incomplete, modelling of the missing structure and the consistency of the BUSTER statistical model help structure building and completion because (i) the accuracy of the overall scale factors is increased, (ii) the bias affecting atomic model refinement is reduced by accounting for some of the scattering from the missing structure, (iii) the addition of a spatial definition to the source of incompleteness improves on traditional Luzzati and sigmaA-based error models and (iv) the program can perform selective density modification in the regions of unbuilt structure alone.

[Retroperitoneal fibrosis, an unrecognized inflammatory disease. Clinical observations and review of the literature]

Retroperitoneal fibrosis (RF) is a rare disease, typically with an insidious clinical course. The peak incidence is seen in patients 40 to 60 years of age and mostly in man. The characteristic finding in this disease is a periaortic fibrous mass that often surrounds the ureters. Although usually regarded as an obstructive uropathy, there has been growing recognition of the condition as a generalized disease. It may have a wide variety of manifestations including mediastinitis, thyroiditis and sclerosing cholangitis. The most common mode of presentation remains abdominal or flank pain with uremia, anemia and a high sedimentation rate. Although ultrasound and renal scintigraphy may contribute to the general evaluation of patients with RF, CT-scanner is the preferred imaging method. The multiplanar imaging capability of magnetic resonance may facilitate assessment of disease extent. The pathogenesis of the disease remains unknown. Steroids and, more recently tamoxifen, appear to be effective in the treatment of the RF. In most instances, RF does not lead to long-term morbidity or affect survival. The three cases of RF reported herein illustrate the varied mode of presentation and the response to the treatment.

High-resolution experimental phases for tryptophanyl-tRNA synthetase (TrpRS) complexed with tryptophanyl-5'AMP

Native data, anomalous data at three wavelengths and an independent peak-wavelength data set for SeMet-substituted protein have been collected from cryoprotected crystals of the TrpRS-adenylate product (TAM) complex to a resolution limit of 1.7 A. Independent phase sets were developed using SHARP and improved by solvent flipping with SOLOMON using molecular envelopes derived from experimental densities for, respectively, peak-wavelength SAD data from four different crystals, MAD data and their M(S)IRAS combinations with native data. Hendrickson-Lattman phase-probability coefficients from each phase set were used in BUSTER to drive maximum-likelihood refinements of well defined parts of the previously refined room-temperature 2.9 A structure. Maximum-entropy completion followed by manual rebuilding was then used to generate a model for the missing segments, bound ligand and solvent molecules. Surprisingly, peak-wavelength SAD experiments produced the smallest phase errors relative to the refined structures. Selenomethionylated models deviate from one another by 0.25 A and from the native model by 0.38 A, but all have r.m.s. deviations of approximately 1.0 A from the 2.9 A model. Difference Fourier calculations between amplitudes from the 300 K experiment and the new amplitudes at 100 K using 1.7 A model phases show no significant structural changes arising from temperature variation or addition of cryoprotectant. The main differences between low- and high-resolution structures arise from correcting side-chain rotamers in the core of the protein as well as on the surface. These changes improve various structure-validation criteria.

[A functional gene map is required to adapt therapy of metastatic neuroblastoma]

Neuroblastoma is a very common solid tumor which arises in childhood and shows an extreme heterogeneity at the clinical, histological and genetic levels. Besides age and stage, N-myc amplification and 1p deletion are prognostic factors of the disease: in Europe, these genetic markers are used to conduct therapy. In France, N-myc amplification is a factor of bad prognosis which leads, in all forms of the disease including localised forms and metastatic forms of children aged of less than 1 year, to a myeloablative treatment with autologous hematopoietic stem cells transplantation. By contrast, N-myc amplification has no impact on the survival of children aged of more than 1 year with a poor prognosis (30% overall survival, 5 years) but this genetic abnormality is taken into account to treat primary tumor of these patients. In an attempt to find out prognostic factors of these aggressive forms of the disease, various pathways (apoptosis, differentiation angiogenesis, detoxication, immune response) have been recently surveyed, but studies have been carried out on a limited number of genes. Moreover, experimental models of human metastatic neuroblastoma have been obtained in which variations of genes transcript levels involved in these pathways, are observed. The current break-through of cDNA microarrays allows to develop a dynamic transcriptomic scanning of these models as well as of tumors and bone marrows from patients upon conventional chemotherapy. This technology will enable: i) to define molecular entities of the metastatic disease; ii) to apply adapted treatment; iii) to develop new therapeutic strategies.

Real space refinement of acto-myosin structures from sectioned muscle

We have adapted a real space refinement protocol originally developed for high-resolution crystallographic analysis for use in fitting atomic models of actin filaments and myosin subfragment 1 (S1) to 3-D images of thin-sectioned, plastic-embedded whole muscle. The rationale for this effort is to obtain a refinement protocol that will optimize the fit of the model to the density obtained by electron microscopy and correct for poor geometry introduced during the manual fitting of a high-resolution atomic model into a lower resolution 3-D image. The starting atomic model consisted of a rigor acto-S1 model obtained by X-ray crystallography and helical reconstruction of electron micrographs. This model was rebuilt to fit 3-D images of rigor insect flight muscle at a resolution of 7 nm obtained by electron tomography and image averaging. Our highly constrained real space refinement resulted in modest improvements in the agreement of model and reconstruction but reduced the number of conflicting atomic contacts by 70% without loss of fit to the 3-D density. The methodology seems to be well suited to the derivation of stereochemically reasonable atomic models that are consistent with experimentally determined 3-D reconstructions computed from electron micrographs.

Modelling prior distributions of atoms for macromolecular refinement and completion

Until modelling is complete, macromolecular structures are refined in the absence of a model for some of the atoms in the crystal. Techniques for defining positional probability distributions of atoms, and using them to model the missing part of a macromolecular crystal structure and the bulk solvent, are described. The starting information may consist of either a tentative structural model for the missing atoms or an electron-density map. During structure completion and refinement, the use of probability distributions enables the retention of low-resolution phase information while avoiding premature commitment to uncertain higher resolution features. Homographic exponential modelling is proposed as a flexible, compact and robust parametrization that proves to be superior to a traditional Fourier expansion in approximating a model protein envelope. The homographic exponential model also has potential applications to ab initio phasing of Fourier amplitudes associated with macromolecular envelopes.

A new fold in the scorpion toxin family, associated with an activity on a ryanodine-sensitive calcium channel

We determined the structure in solution by (1)H two-dimensional NMR of Maurocalcine from the venom of Scorpio maurus. This toxin has been demonstrated to be a potent effector of ryanodyne-sensitive calcium channel from skeletal muscles. This is the first description of a scorpion toxin which folds following the Inhibitor Cystine Knot fold (ICK) already described for numerous toxic and inhibitory peptides, as well as for various protease inhibitors. Its three dimensional structure consists of a compact disulfide-bonded core from which emerge loops and the N-terminus. A double-stranded antiparallel beta-sheet comprises residues 20-23 and 30-33. A third extended strand (residues 9-11) is perpendicular to the beta-sheet. Maurocalcine structure mimics the activating segment of the dihydropyridine receptor II-III loop and is therefore potentially useful for dihydropyridine receptor/ryanodine receptor interaction studies. Proteins 2000;40:436-442.

Extensive biopsy protocol improves the detection rate of prostate cancer

PURPOSE

We evaluated improvement in the rate of prostate cancer detection when using an extensive biopsy protocol involving peripheral cores.

MATERIALS AND METHODS

We prospectively evaluated 303 consecutive men who underwent transrectal ultrasound guided biopsy due to elevated prostate specific antigen (PSA) and/or abnormal digital rectal examination. Ten biopsies were performed, including at least 5 at the base and middle of each lobe. In addition to standard biopsy at a 45-degree angle, a more peripheral 30-degree angle biopsy was obtained. At the apex only 1 standard biopsy was done. However, when prostate volume was greater than 50 cm.3, an additional peripheral biopsy was obtained at the apex.

RESULTS

The complication rate in this biopsy protocol was 1% (3 patients). Prostate cancer was detected in 118 of the 303 men (38. 9%). Overall this extensive protocol resulted in 6.6% improvement in the detection rate. Improvement was 6.5% in men with PSA 10 ng./ml. or less and 7% in those with PSA greater than 10 (not significant).

CONCLUSIONS

Increasing the number of biopsy cores and improving prostate peripheral zone sampling resulted in a significant improvement in the detection of prostate cancer.

Developmental study of rat vestibular neuronal circuits during a spaceflight of 17 days

The aim of this study was to investigate the potential plasticity of the vestibular system, in structural and biochemical terms, at the level of the gravity receptors (the sensory hair cells), the primary neurons relaying the sensory signals (the vestibular ganglion neurons) and their projections into the vestibular nuclei. We studied the biochemical differentiation of the sensory cells and of the vestibular ganglion by investigating which calcium-binding proteins were present. We studied the development of peripheral synaptic connections of the efferent system by investigating the distribution of CGRP (calcitonin-gene related-peptide) and we also studied the cerebellar synaptic connections in the vestibular nuclei, as identified by the presence of calbindin. Putative changes were studied after a 17-day episode of microgravity (Neurolab STS-90), in developing rats between postnatal days 8 and 25. The extent to which these changes could be caused by alterations in gravity was determined by examining sensory and nervous structures not involved in gravity detection, the cochlea and the cochlear nuclei.

Solution structure of BmKTX, a K+ blocker toxin from the Chinese scorpion Buthus Martensi

BmKTX is a toxin recently purified from the venom of Buthus Martensi, which belongs to the kaliotoxin family. We have determined its solution structure by use of conventional two-dimensional NMR techniques followed by distance-geometry and energy minimization. The calculated structure is composed of a short alpha-helix (residues 14 to 20) connected by a tight turn to a two-stranded antiparallel beta-sheet (sequences 25-27 and 32-34). The beta-turn connecting these strands belongs to type I. The N-terminal segment (sequence 1 to 8) runs parallel to the beta-sheet although it cannot be considered as a third strand. Comparison of the conformation of BmKTX and toxins of the kaliotoxin family clearly demonstrates that they are highly related. Therefore, analysis of the residues belonging to the interacting surface of those toxins allows us to propose a functional map of BmKTX slightly different from the one of KTX and AgTX2, which may explain the variations in affinities of these toxins towards the Kv1.3 channels.

Critical initial real-space refinement in the structure determination of arginine kinase

Arginine kinase (AK), a homologue of creatine kinase, catalyses the reversible transfer of a phosphoryl group between a guanidino phosphate and ADP. The family of phosphagen kinases eluded structure determination for over 25 years until an inactive form creatine kinase (CK) structure was determined [Fritz-Wolf et al. (1996). Nature (London), 381, 341-345]. The structure determination of the active-form transition-state complex was non-trivial, owing to the distant relatedness and domain reorientation of AK compared with CK. Phases from a molecular-replacement solution of the large domain, supplemented by single isomorphous replacement and inter-crystal averaging, did not reveal interpretable electron density for the small domain. Reciprocal-space refinement of the initial model (Rfree = 0.54) by any of the commonly used methods, including post facto application of maximum-likelihood methods, led to overfitting without significant improvement of the partial initial model. By contrast, in the local real-space refinements which proved successful, the interdependence of atoms is limited to immediate neighbors, and atomic positions are not influenced by errors or omissions in remote parts of the structure. Modest improvement was possible without overfitting, and this was critical to the calculation of improved phases. Phases were refined and extended from 4.0 to 2.5 A resolution by Fourier inversion of omit maps, combination with isomorphous replacement phases and averaging between crystal forms, after several batches of real- and reciprocal-space atomic refinement. The final structure refinement, against a 1.86 A cryo data set yielded a high-quality model with R = 0.196 and Rfree = 0.224.

Diagnostic value of ten systematic TRUS-guided prostate biopsies

OBJECTIVE

To evaluate the improvement in the rate of detection of prostate cancer using an extensive protocol involving ten transrectal biopsies.

METHODS

A total of 162 patients submitted to transrectal ultrasound-guided biopsy for elevated prostate-specific antigen (PSA) and/or abnormality on digital rectal examination were studied consecutively and prospectively. Five biopsies were performed in each lobe: between the three standard biopsies on each side, two additional biopsy specimens were taken in the same plane and at the same 45 degrees angle.

RESULTS

The complication rate with the ten-biopsy protocol was 1.85%. Prostate cancer was detected in 40.1% of the patients. In the overall series, the percentage of diagnostic improvement brought about by this ten-biopsy protocol was +3.1%. The percentage improvement was greatest (+4.9%) in patients with PSA </=10 ng/ml.

CONCLUSION

Increasing the number of biopsy cores without altering the angle of biopsy and/or the zone sampled does not lead to a significant improvement in the detection of prostate cancer.

Solution structure of potassium channel-inhibiting scorpion toxin Lq2

Lq2 is a unique scorpion toxin. Acting from the extracellular side, Lq2 blocks the ion conduction pore in not only the voltage- and Ca2+ -activated channels, but also the inward-rectifier K+ channels. This finding argues that the three-dimensional structures of the pores in these K+ channels are similar. However, the amino acid sequences that form the external part of the pore are minimally conserved among the various classes of K+ channels. Because Lq2 can bind to all the three classes of K+ channels, we can use Lq2 as a structural probe to examine how the non-conserved pore-forming sequences are arranged in space to form similar pore structures. In the present study, we determined the three-dimensional structure of Lq2 using nuclear magnetic resonance (NMR) techniques. Lq2 consists of an alpha-helix (residues S10 to L20) and a beta-sheet, connected by an alphabeta3 loop (residues N22 to N24). The beta-sheet has two well-defined anti-parallel strands (residues G26 to M29 and residues K32 to C35), which are connected by a type I' beta-turn centered between residues N30 and K31. The N-terminal segment (residues Z1 to T8) appears to form a quasi-third strand of the beta-sheet.

Real-space molecular-dynamics structure refinement

Real-space targets and molecular-dynamics search protocols have been combined to improve the convergence of macromolecular atomic refinement. This was accomplished by providing a local real-space target function for the molecular-dynamics program X-PLOR. With poor isomorphous replacement experimental phases, molecular dynamics does not improve real-space refinement. However, with high-quality anomalous diffraction phases convergence is improved at the start of refinement, and torsion-angle real-space molecular dynamics performs better than other available least-squares or maximum-likelihood methods in real or reciprocal space. It is shown that the improvements result from an optimization method that can escape local minima and from a reduction of overfitting through the implicit use of phases and through use of a local refinement in which errors in remote parts of the structure cannot be mutually compensating.

[Value of the use of a questionnaire in the evaluation of incontinence surgery]

OBJECTIVE

To assess the contribution of a questionnaire in the evaluation of patients operated for urinary stress incontinence.

PATIENTS AND METHODS

From 1988 to 1996, 42 patients underwent bladder neck suspension for urinary stress incontinence. Only 7 patients had no history of pelvic surgery, 24 patients presented pure urinary stress incontinence and 19 presented mixed incontinence, 37 patients were evaluable with a mean follow-up of 2 years. The evaluation consisted of two aspects: clinical assessment, based on review of the case files, showing that 77% of patients were continent, and a questionnaire (non-validated translation of "Q7" and "UD16"). This questionnaire evaluated quality of life (7 items) and symptoms. Each item was scored from 0 to 3.

RESULTS

To interpret the results we divided the three main scores into three intervals, the first third corresponding to good results. The percentage of good results for the overall score, quality of life score and symptom score was 62%, 73% and 46% respectively. The most discriminative questions of the questionnaire can be used to analyse urine leaks related to effort, urgency episodes of incontinence. A score of 0 or 1 was considered to be a good result. The percentage of good results for these three questions was therefore 72%, 60% and 64%, respectively.

CONCLUSION

The cure rate therefore varies as a function of the criteria selected: the questionnaire allows the urologist to more accurately assess the patient's postoperative state.

Improved free R factors for cross-validation of macromolecular structure - importance for real-space refinement

Improvements in free R cross-validation are based on changed scaling procedures and the use, in map calculation, of estimates of the validation amplitudes which are independent of the actual observed values. The deleterious effects of the omitted test data are mitigated by reduction of the test-set size, which is made possible by constraining test and working sets to share the same scaling coefficients, thereby reducing the degrees of freedom and the dependence of free R on data selection. Further improvements come with use of a modified free R factor, R freeTA. Instead of omitting the validation reflections from map calculation, their amplitudes are replaced by the average of resolution peers that is (nearly) independent of the actual cross-validation amplitudes. The improvements are relevant to model building, phase refinement by density modification and especially to real-space refinement. Although for real data at about 3 A resolution, free R factors of about 0.25 are affected little, the precision of the structure is improved by about 0.1 A. Tests with simulated data show that with good agreement between observed and calculated amplitudes (as in very high resolution studies or simulated refinement tests), free R factors can be improved by factors greater than two.