Net efficacy adjusted for risk (NEAR): a simple procedure for measuring risk:benefit balance

Background

Although several mathematical models have been proposed to assess the risk:benefit of drugs in one measure, their use in practice has been rather limited. Our objective was to design a simple, easily applicable model. In this respect, measuring the proportion of patients who respond favorably to treatment without being affected by adverse drug reactions (ADR) could be a suitable endpoint. However, remarkably few published clinical trials report the data required to calculate this proportion. As an approach to the problem, we calculated the expected proportion of this type of patients.

Methodology/Principal Findings

Theoretically, responders without ADR may be obtained by multiplying the total number of responders by the total number of subjects that did not suffer ADR, and dividing the product by the total number of subjects studied. When two drugs are studied, the same calculation may be repeated for the second drug. Then, by constructing a 2×2 table with the expected frequencies of responders with and without ADR, and non-responders with and without ADR, the odds ratio and relative risk with their confidence intervals may be easily calculated and graphically represented on a logarithmic scale. Such measures represent “net efficacy adjusted for risk” (NEAR).We assayed the model with results extracted from several published clinical trials or meta-analyses. On comparing our results with those originally reported by the authors, marked differences were found in some cases, with ADR arising as a relevant factor to balance the clinical benefit obtained. The particular features of the adverse reaction that must be weighed against benefit is discussed in the paper.

Conclusion

NEAR representing overall risk-benefit may contribute to improving knowledge of drug clinical usefulness. As most published clinical trials tend to overestimate benefits and underestimate toxicity, our measure represents an effort to change this trend.     

Interaction with PCNA is essential for yeast DNA polymerase eta function.

In both yeast and humans, DNA polymerase (Pol) eta functions in error-free replication of ultraviolet-damaged DNA, and Poleta promotes replication through many other DNA lesions as well. Here, we present evidence for the physical and functional interaction of yeast Poleta with proliferating cell nuclear antigen (PCNA) and show that the interaction with PCNA is essential for the in vivo function of Poleta. Poleta is highly inefficient at inserting a nucleotide opposite an abasic site, but interaction with PCNA greatly stimulates its ability for nucleotide incorporation opposite this lesion. Thus, in addition to having a pivotal role in the targeting of Poleta to the replication machinery stalled at DNA lesions, interaction with PCNA would promote the bypass of certain DNA lesions.     

Smooth ROC curves and surfaces for markers subject to a limit of detection using monotone natural cubic splines

The use of ROC curves in evaluating a continuous or ordinal biomarker for the discrimination of two populations is commonplace. However, in many settings, marker measurements above or below a certain value cannot be obtained. In this paper, we study the construction of a smooth ROC curve (or surface in the case of three populations) when there is a lower or upper limit of detection. We propose the use of spline models that incorporate monotonicity constraints for the cumulative hazard function of the marker distribution. The proposed technique is computationally stable and simulation results showed a satisfactory performance. Other observed covariates can be also accommodated by this spline‐based approach.     

Probable case of Binder syndrome in a skeleton from Quarai,New Mexico

Binder syndrome (maxillonasal dysplasia) is a not uncommon disorder reported in the clinical literature and is characterized by hypoplastic development of the midface. An extensive review of the paleopathology literature did not reveal any examples of Binder syndrome. In this paper, a probable case of Binder syndrome in a female skeleton, 16-17 years at age of death, from Quarai, New Mexico (ca. AD 1375-1450) is presented. This case was identified during standard documentation prior to repatriation at the National Museum of Natural History, Smithsonian Institution.The skull of this individual (381243) exhibits unusual facial features, including an underdeveloped midface, flattened glabella, absent nasal spine, and apparent alveolar prognathism, in addition to a vertebral anomaly. All of these characteristics are consistent with skeletal dysmorphologies associated with Binder syndrome. Measurements of the Quarai skull are compared with published data on Binder patients and normal control groups in order to quantify the nature of the observed morphology. Univariate analysis of craniometric/cephalometric data provides further support for a diagnosis of Binder syndrome, as critical measurements on the Quarai skull are consistent with those reported in Binder patients and significantly different from those reported for normal control groups. In addition to presenting a probable prehistoric case of Binder syndrome, this paper demonstrates the applicability of using direct comparisons of clinical data to help identify unusual conditions in skeletal remains.     

The DNA polymerase activity of Saccharomyces cerevisiae Rev1 is biologically significant

A cell's ability to tolerate DNA damage is directly connected to the human development of diseases and cancer. To better understand the processes underlying mutagenesis, we studied the cell's reliance on the potentially error-prone translesion synthesis (TLS), and an error-free, template-switching pathway in Saccharomyces cerevisiae. The primary proteins mediating S. cerevisiae TLS are three DNA polymerases (Pols): Rev1, Pol ζ (Rev3/7), and Pol η (Rad30), all with human homologs. Rev1's noncatalytic role in recruiting other DNA polymerases is known to be important for TLS. However, the biological significance of Rev1's unusual conserved DNA polymerase activity, which inserts dC, is much less well understood. Here, we demonstrate that inactivating Rev1's DNA polymerase function sensitizes cells to both chronic and acute exposure to 4-nitroquinoline-1-oxide (4-NQO) but not to UV or cisplatin. Full Rev1-dependent resistance to 4-NQO, however, also requires the additional Rev1 functions. When error-free tolerance is disrupted through deletion of MMS2, Rev1's catalytic activity is more vital for 4-NQO resistance, possibly explaining why the biological significance of Rev1's catalytic activity has been elusive. In the presence or absence of Mms2-dependent error-free tolerance, the catalytic dead strain of Rev1 exhibits a lower 4-NQO-induced mutation frequency than wild type. Furthermore, Pol ζ, but not Pol η, also contributes to 4-NQO resistance. These results show that Rev1's catalytic activity is important in vivo when the cell has to cope with specific DNA lesions, such as N(2)-dG.     

Analysing covariates with spike at zero: A modified FP procedure and conceptual issues

In epidemiology and in clinical research, risk factors often have special distributions. A common situation is that a proportion of individuals have exposure zero, and among those exposed, we have some continuous distribution. We call this a ‘spike at zero’. Examples for this are smoking, duration of breastfeeding, or alcohol consumption. Furthermore, the empirical distribution of laboratory values and other measurements may have a semi‐continuous distribution as a result of the lower detection limit of the measurement. To model the dose–response function, an extension of the fractional polynomial approach was recently proposed. In this paper, we suggest a modification of the previously suggested FP procedure. We first give the theoretical justification of this modified procedure by investigating relevant distribution classes. Here, we systematically derive the theoretical shapes of dose–response curves under given distributional assumptions (normal, log normal, gamma) in the framework of a logistic regression model. Further, we check the performance of the procedure in a simulation study and compare it to the previously suggested method, and finally we illustrate the procedures with data from a case–control study on breast cancer.     

Invariant Features of Memory Capacity

Our purpose in these experiments was to study short-term (immediate) and long-term memory in the memorization of the same subject matter. By memory capacity is meant the number of units a person is able to reproduce in one repetition, or on an average in one repetition. In short-term reception and full reproduction of the material to be memorized, short-term memory capacity is commensurate with the number of units reproduced. Long-term memory capacity reflects the ability to accumulate as well as to retain information. When the material to be remembered exceeds the short-term memory capacity, the first reproduction is incomplete, and multiple presentation and repetition of the information are necessary for error-free and complete reproduction. In this case the memory capacity is equal to the number of units contained in the presented material divided by the number of repetitions.     

Ubiquitin binding site of the ubiquitin E2 variant (UEV) protein Mms2 is required for DNA damage tolerance in the yeast RAD6 pathway

Different ubiquitin modifications to proliferating cell nuclear antigen (PCNA) signal distinct modes of lesion bypass in the RAD6 pathway of DNA damage tolerance. The modification of PCNA with monoubiquitin signals an error-prone bypass, whereas the extension of this modification into a Lys-63-linked polyubiquitin chain promotes error-free bypass. Chain formation is catalyzed by the Mms2/Ubc13 conjugating enzyme variant/conjugating enzyme (UEV.E2) complex together with the Rad5 ubiquitin ligase. In vitro studies of this UEV.E2 complex have identified a ubiquitin binding site that is mainly localized on Mms2. However, the role of this site in DNA damage tolerance and the molecular features of the ubiquitin/Mms2 interaction are poorly understood. Here we identify two molecular determinants, the side chains of Mms2-Ile-57 and ubiquitin-Ile-44, that are required for chain assembly in vitro and error-free lesion bypass in vivo. Mutating either of these side chains to alanine elicits a severe 10-20-fold inhibition of chain synthesis that is caused by compromised binding of the acceptor ubiquitin to Mms2. These results suggest that the ubiquitin binding site of Mms2 is necessary for error-free lesion bypass in the RAD6 pathway and provide new insights into ubiquitin recognition by UEV proteins.     

Amniotic membranes in ophthalmology: long term data on transplantation outcomes

The use of amniotic membrane (AM) is a widespread clinical practice for eye surgeries and the treatment of an increasing number of ocular surface pathologies. Here we describe the AM collection methods and donor selection criteria adopted by our tissue bank to distribute 5349 amniotic membrane patches over the last 12 years for the treatment of several ocular pathologies. Specific quality control measures are described and the long term results attained using the reported procedure are presented. A case of AM utilized to treat severe ocular ulceration is also described as an example of AM transplantation. Collective data for the total amniotic membrane patches deployed to treat various ocular diseases are discussed and success rates for AM transplantations are reported. An extensive follow-up is illustrated. The results suggest that the procedures and protocols used by the Treviso Tissue Bank Foundation and Veneto Eye Bank Foundation for collection, preservation, distribution and follow-up are of an optimal standard. Accordingly, the authors conclude that the safety and efficiency of the proposed procedure for the therapeutic use of AM to treat various ocular pathologies are reproducible, with additional evidence favoring the use of AM as an alternative to conventional medical treatment for certain ocular conditions.     

Nuclear morphometry as an intermediate endpoint biomarker in chemoprevention of cervical carcinoma using alpha-difluoromethylornithine.

The use of nuclear morphometry as an intermediate endpoint biomarker is described in a Phase I, dose-seeking trial of chemoprevention of cervical cancer, using the agent alpha-difluoromethylornithine (DFMO). Thirty patients with grade III cervical intraepithelial neoplasia (CIN III) were enrolled, and these received daily doses of DFMO at 0.06-1.0 mg/m(2) for a period of 1 month. Fifteen patients were observed to have a complete or partial regressive response to the agent, as assessed by histopathology. No significant differences in cell feature measurements were found between responders and nonresponders in specimens obtained before treatment, indicating that it may be difficult to predict response on the basis of these measurements. In specimens collected after treatment, large differences in morphometric features were observed between responders and nonresponders, indicating a differential effect of DFMO. Significantly modulated features were considered in terms of their correlations with CIN grade, which was determined from an independent set of measurements from archival tissue. Differences between features were consistent with a deletion of cells with high grade nuclei in the responders, and with the persistence of a more heterogeneous population of high grade cells in the nonresponders. Based on an independent set of measurements from archival material, a morphometric index of progression was derived, yielding a quantitative measure of the degree of nuclear atypia in these lesions. When applied to this trial, the morphometric index was seen to be specifically and consistently decreased in responsive lesions, and unchanged in nonresponders. The study indicates that morphometric features fulfill the requirements for an intermediate endpoint biomarker of cervical cancer chemoprevention.     

Checkpoint kinase 2 is required for efficient immunoglobulin diversification

Maintenance of genome integrity relies on multiple DNA repair pathways as well as on checkpoint regulation. Activation of the checkpoint kinases Chk1 and Chk2 by DNA damage triggers cell cycle arrest and improved DNA repair, or apoptosis in case of excessive damage. Chk1 and Chk2 have been reported to act in a complementary or redundant fashion, depending on the physiological context. During secondary immunoglobulin (Ig) diversification in B lymphocytes, DNA damage is abundantly introduced by activation-induced cytidine deaminase (AID) and processed to mutations in a locus-specific manner by several error-prone DNA repair pathways. We have previously shown that Chk1 negatively regulates Ig somatic hypermutation by promoting error-free homologous recombination and Ig gene conversion. We now report that Chk2 shows opposite effects to Chk1 in the regulation of these processes. Chk2 inactivation in B cells leads to decreased Ig hypermutation and Ig class switching, and increased Ig gene conversion activity. This is linked to defects in non-homologous end joining and increased Chk1 activation upon interference with Chk2 function. Intriguingly, in the context of physiological introduction of substantial DNA damage into the genome during Ig diversification, the 2 checkpoint kinases thus function in an opposing manner, rather than redundantly or cooperatively.     

An alternative approach to asymptotic results on genetic composition when the population size is varying

This paper is concerned with methodology for studying the long-term genetic composition of a population of haploid individuals in the case where the population size is varying. A general approach requiring a minimum of assumptions is described based on constructing martingales out of expressions for the means of the numbers of allelic types, conditional on the past. Earlier investigations were based on studying the asymptotic behaviour of the proportion of alleles of a certain type in the population. Several applications demonstrate that the approach suggested in the paper provides results which usefully complement ones obtained previously.     

Effect of cytoskeletal geometry on intracellular diffusion.

A method is presented for determining the retardation of diffusion of particles inside cells owing to cytoskeletal barriers. The cytoskeletal meshwork is treated as a repeating periodic two-dimensional or three-dimensional lattice composed of elements of given size, shape, and spacing. We derive an analytic expression for the diffusion coefficient relative to that of the cytosol. This expression is evaluated by solving numerically an appropriate boundary-value problem for the Laplace equation. For the two-dimensional case, e.g., diffusion in a membrane, the results are quantitatively similar to those obtained by Saxton (1987. Biophys. J. 52:989-997) using Monte Carlo methods. The three-dimensional results are quantitatively similar to experimental results reported by Luby-Phelps et al. (1987. Proc. Natl. Acad. Sci. USA. 84:4910-4913) for the diffusion of dextran and Ficoll particles in Swiss 3T3 cells. By accounting for geometrical factors, these results allow one to assess the relative contributions of geometrical hindrance and of binding to the cytoskeletal lattice from measurements of intracellular diffusion coefficients of proteins.     

The Rad5 helicase activity is dispensable for error-free DNA post-replication repair

DNA post-replication repair (PRR) functions to bypass replication-blocking lesions and is subdivided into two parallel pathways: error-prone translesion DNA synthesis and error-free PRR. While both pathways are dependent on the ubiquitination of PCNA, error-free PRR utilizes noncanonical K63-linked polyubiquitinated PCNA to signal lesion bypass through template switch, a process thought to be dependent on Mms2-Ubc13 and a RING finger motif of the Rad5 ubiquitin ligase. Previous in vitro studies demonstrated the ability of Rad5 to promote replication fork regression, a function dependent on its helicase activity. To investigate the genetic and mechanistic relationship between fork regression in vitro and template switch in vivo, we created and characterized site-specific mutations defective in the Rad5 RING or helicase activity. Our results indicate that both the Rad5 ubiquitin ligase and the helicase activities are exclusively involved in the same error-free PRR pathway. Surprisingly, the Rad5 helicase mutation abolishes its physical interaction with Ubc13 and the K63-linked PCNA polyubiquitin chain assembly. Indeed, physical fusions of Rad5 with Ubc13 bypass the requirement for either the helicase or the RING finger domain. Since the helicase domain overlaps with the SWI/SNF chromatin-remodelling domain, our findings suggest a structural role of this domain and that the Rad5 helicase activity is dispensable for error-free lesion bypass.     

VAD protocol for treatment of advanced refractory multiple myeloma

Twenty-three patients with advanced refractory multiple myeloma were treated with a combination chemotherapeutic regimen consisting of four-day continuous infusion of vincristine and doxorubicin plus intermittent high-dose dexamethasone (VAD). All patients included in the study were heavily pretreated with cytostatics and radiotherapeutic measures, and generally presented in poor general condition. In 3 of the 16 evaluable patients (18%) a response, and in 7 patients (44%) an improvement as defined by a reduction in tumor mass by more than 50% was achieved. Six patients had progressive disease. Evaluation of survival for responders (15 mos) versus non-responders (2 mos) by the landmark method seems to confirm the relative therapeutic efficacy of the VAD protocol in refractory multiple myeloma. The somewhat inferior response rate as well as the occurrence of considerable toxicity in several cases (when compared to the recent M. D. Anderson trial) may be related to differences in clinical features and pretreatment status of the two studies' population.     

Discrete-time nonlinear observer-based estimators for the on-line estimation of the kinetic rates in bioreactors

Simple discrete-time estimators which allow the on-line estimation of the kinetic rates from the measurements of components' concentrations inside a bioreactor are proposed. In fact, the proposed estimators are obtained by a direct forward Euler discretization of continuous-time estimators. The design of the estimators in the continuous as well as in the discrete-time does not require or assume any model for the kinetic rates. One of the main characteristics of these estimators lies in the easiness of their calibration. We here emphasize on the performances of the discrete version of these estimators, whose stability and convergence are proved under the same conditions as in the continuous case with an additional mild assumption on the sampling time. Simulation and real-life experiments results corresponding to the discrete estimation are given. The accuracy of the obtained estimates as well as the easiness of the estimators' implementation do constitute reliable and powerful arguments for their use, in particular in adaptive control schemes.     

Arm lengths and arm reaches: some interrelationships of structural and functional body dimensions

Structural measurements of the human body have for the most part been of little practical use as indicators of such functional body dimensions as arm reaches. These dimensions, which define the area around the body to which a person can reach given certain specified conditions and constraints are often critical for the design and layout of workspaces. However, they are relatively difficult and time-consuming to obtain, usually requiring specially constructed measuring systems for each differing design situation, as well as resurveys for each physically distinct population. An alternate approach, described here, investigates the interrelationships between these two classes of measurements with the aim of predicting functional reaches from structural body dimensions. In the present study traditional structural measurements and 117 functional arm reaches were obtained on 100 subjects. Correlations between the two types of measures are reported. Regression equations are presented which can predict functional arm reaches from two structural body dimensions on anthropometrically differing populations under a fixed set of workspace conditions.     

Optimal weight in estimating and comparing areas under the receiver operating characteristic curve using longitudinal data

In the setting of longitudinal study, subjects are followed for the occurrence of some dichotomous outcome. In many of these studies, some markers are also obtained repeatedly during the study period. Emir et al. introduced a non-parametric approach to the estimation of the area under the ROC curve of a repeated marker. Their non-parametric estimate involves assigning a weight to each subject. There are two weighting schemes suggested in their paper: one for the case when within-patient correlation is low, and the other for the case when within-subject correlation is high. However, it is not clear how to assign weights to marker measurements when within-patient correlation is modest. In this paper, we consider the optimal weights that minimize the variance of the estimate of the area under the ROC curve (AUC) of a repeated marker, as well as the optimal weights that minimize the variance of the AUC difference between two repeated markers. Our results in this paper show that the optimal weights depend not only on the within-patient control--case correlation in the longitudinal data, but also on the proportion of subjects that become cases. More importantly, we show that the loss of efficiency by using the two weighting schemes suggested by Emir et al. instead of our optimal weights can be severe when there is a large within-subject control--case correlation and the proportion of subjects that become cases is small, which is often the case in longitudinal study settings.     

Shock wave therapy for femoral head necrosis—Pressure measurements inside the femoral head

There is a persisting need for effective therapies of femoral head necrosis, a common bone disease. Promising clinical results have been stated for the treatment with extracorporeal shock waves (ESW). However, the effective remaining pressure in the target region inside the femoral head has never been determined. Aim of this study was to investigate whether ESW are able to propagate through bone without an excessive loss of pressure. The remaining ESW pressure generated by an electromagnetic device after passing a certain intraosseous distance within the femoral head was measured. Standardized holes were drilled in porcine femora and the absorption in relation to reference measurements in degassed water was determined. The results showed continuous attenuation of shock waves in bone. After a clinical relevant intraosseous distance of 10 mm an ESW pressure of ～50% remained.In conclusion, ESW have the potential to reach necrotic regions with therapeutic pressure levels and to effectively treat femoral head necrosis.     

Fucosylated haptoglobin is a novel marker for pancreatic cancer: detailed analyses of oligosaccharide structures

Changes in oligosaccharide structures have been reported in certain types of malignant transformation and thus can be used as tumor markers in certain types of cancer. In the case of pancreatic cancer (PC) cell lines, a variety of fucosylated proteins are secreted into the conditioned media. To identify fucosylated proteins in the sera of patients with PC, we performed Western blot analysis using Aleuria Aurantia Lectin (AAL), which is specific for fucosylated structures. An approximately 40 kD protein was found to be highly fucosylated in PC and N-terminal analysis revealed that it was the beta chain of haptoglobin. While the appearance of fucosylated haptoglobin has been reported in other diseases such as hepatocellular carcinoma, liver cirrhosis, gastric cancer, and colorectal cancer, the incidence was significantly higher in the case of PC. Fucosylated haptoglobin was observed more frequently at the advanced stage of PC and disappeared after operation. Haptoglobin has four sites of N-glycans and site-directed oligosaccharide analysis involving MS was performed. Site-specific increases in fucosylation of bi-antennary glycans of sites 2 and 4, and of tri-antennary glycans of all sites were observed in PC, compared to in normal volunteers and chronic pancreatitis. Therefore, increases in fucosylation seem to be not due to inflammation, but cancer itself. Coculturing of a human hepatoma cell line, Hep3B, with PC cells-induced production of fucosylated haptoglobin, suggesting that PC produces a factor that induces the production of fucosylated haptoglobin. On clinical investigation of 100 cases of colorectal cancer, cases in which it was located near the liver showed a higher positive rate of fucosylated haptoglobin, suggesting that the location of the cancer might also be an important factor for fucosylated haptoglobin if cancer tissues produce such inducible factors. Thus, fucosylated haptoglobin could become a novel tumor marker for PC and complicated mechanisms would be involved in its production.