Multi-center clinical trials: Randomization and ancillary statistics

The purpose of this paper is to investigate and develop methods for analysis of multi-center randomized clinical trials which only rely on the randomization process as a basis of inference. Our motivation is prompted by the fact that most current statistical procedures used in the analysis of randomized multi-center studies are model based. The randomization feature of the trials is usually ignored. An important characteristic of model based analysis is that it is straightforward to model covariates. Nevertheless, in nearly all model based analyses, the effects due to different centers and, in general, the design of the clinical trials are ignored. An alternative to a model based analysis is to have analyses guided by the design of the trial. Our development of design based methods allows the incorporation of centers as well as other features of the trial design. The methods make use of conditioning on the ancillary statistics in the sample space generated by the randomization process. We have investigated the power of the methods and have found that, in the presence of center variation, there is a significant increase in power. The methods have been extended to group sequential trials with similar increases in power.Comment: Published in at http://dx.doi.org/10.1214/07-AOAS151 the Annals of Applied Statistics (http://www.imstat.org/aoas/) by the Institute of Mathematical Statistics (http://www.imstat.org

Utility of the QT interval in predicting outcomes in patients presenting to the emergency department with chest pain.

OBJECTIVES: The aim of this study was to investigate whether prolongation of the heart rate-corrected QT interval (QTc) is an independent risk factor for predicting future acute coronary syndrome (ACS) occurrence or mortality in patients with at least one cardiac risk factor presenting with chest pain to the emergency department (ED). METHODS: This is a single-center, retrospective study of patients presenting with chest pain to the ED of Einstein Medical Center, Philadelphia, between 2011 and 2012. Proportional hazards models were used to calculate hazard ratios (HRs) for occurrence of ACS or death within 1 year. Kaplan-Meier curves were used to determine the time to event for QTc low (\u3c460 \u3ems) versus QTc high (≥460 ms) groups. RESULTS: A total of 595 patients met the inclusion criteria. Older age, hypertension, diabetes mellitus, and hyperlipidemia were more common in the QTc high group. Patients in the QTc high group were more likely to experience subsequent ACS or death (HR 8.12, 95% confidence interval 4.00-16.72), even after adjusting for traditional cardiac risk factors (HR 7.68, 95% confidence interval 3.57-16.61). CONCLUSION: QTc prolongation at ED presentation with chest pain and at least one cardiac risk factor predicts subsequent ACS and death

Insights into the molecular control of cross‑incompatibility in Zea mays

Gametophytic cross-incompatibility systems in corn have been the subject of genetic studies for more than a century. They have tremendous economic potential as a genetic mechanism for controlling fertilization without controlling pollination. Three major genetically distinct and functionally equivalent cross-incompatibility systems exist in Zea mays: Ga1, Tcb1, and Ga2. All three confer reproductive isolation between maize or teosinte varieties with different haplotypes at any one locus. These loci confer genetically separable functions to the silk and pollen: a female function that allows the silk to block fertilization by non-self-type pollen and a male function that overcomes the block of the female function from the same locus. Identification of some of these genes has shed light on the reproductive isolation they confer. The identification of both male and female factors as pectin methylesterases reveals the importance of pectin methylesterase activity in controlling the decision between pollen acceptance versus rejection, possibly by regulating the degree of methylesterification of the pollen tube cell wall. The appropriate level and spatial distribution of pectin methylesterification is critical for pollen tube growth and is affected by both pectin methylesterases and pectin methylesterase inhibitors. We present a molecular model that explains how cross-incompatibility systems may function that can be tested in Zea and uncharacterized cross-incompatibility systems. Molecular characterization of these loci in conjunction with further refinement of the underlying molecular and cellular mechanisms will allow researchers to bring new and powerful tools to bear on understanding reproductive isolation in Zea mays and related species

Senile Cardiac Amyloidosis: An Undervalued Cause of Heart Failure.

Despite recurrent hospitalizations for heart failure exacerbations, the underlying cause can be missed. Senile amyloidosis is a disease prevalent in the elderly African American population. Senile amyloidosis is underdiagnosed as a cause of heart failure because of its occurrence with more common comorbidities, such as long-standing systemic hypertension. It is important to maintain a high index of suspicion for senile amyloidosis in patients such as this case, who presented with multiple exacerbations of heart failure combined with characteristic electrocardiographic and echocardiographic findings

Inhibition of Bacterial Conjugation by Phage M13 and Its Protein g3p: Quantitative Analysis and Model

Conjugation is the main mode of horizontal gene transfer that spreads antibiotic resistance among bacteria. Strategies for inhibiting conjugation may be useful for preserving the effectiveness of antibiotics and preventing the emergence of bacterial strains with multiple resistances. Filamentous bacteriophages were first observed to inhibit conjugation several decades ago. Here we investigate the mechanism of inhibition and find that the primary effect on conjugation is occlusion of the conjugative pilus by phage particles. This interaction is mediated primarily by phage coat protein g3p, and exogenous addition of the soluble fragment of g3p inhibited conjugation at low nanomolar concentrations. Our data are quantitatively consistent with a simple model in which association between the pili and phage particles or g3p prevents transmission of an F plasmid encoding tetracycline resistance. We also observe a decrease in the donor ability of infected cells, which is quantitatively consistent with a reduction in pili elaboration. Since many antibiotic-resistance factors confer susceptibility to phage infection through expression of conjugative pili (the receptor for filamentous phage), these results suggest that phage may be a source of soluble proteins that slow the spread of antibiotic resistance genes

Tolerability of NGX-4010, a capsaicin 8% dermal patch, following pretreatment with lidocaine 2.5%/prilocaine 2.5% cream in patients with post-herpetic neuralgia

<p>Abstract</p> <p>Background</p> <p>Post-herpetic neuralgia (PHN) is a common type of neuropathic pain that can severely affect quality of life. NGX-4010, a capsaicin 8% dermal patch, is a localized treatment that can provide patients with significant pain relief for up to 3 months following a single 60-minute application. The NGX-4010 application can be associated with application-site pain and in previous clinical trials pretreatment with a topical 4% lidocaine anesthetic was used to enhance tolerability. The aim of the current investigation was to evaluate tolerability of NGX-4010 after pretreatment with lidocaine 2.5%/prilocaine 2.5% anesthetic cream.</p> <p>Methods</p> <p>Twenty-four patients with PHN were pretreated with lidocaine 2.5%/prilocaine 2.5% cream for 60 minutes before receiving a single 60-minute application of NGX-4010. Tolerability was assessed by measuring patch application duration, the proportion of patients completing over 90% of the intended treatment duration, application site-related pain using the Numeric Pain Rating Scale (NPRS), and analgesic medication use to relieve such pain. Safety was assessed by monitoring adverse events (AEs) and dermal irritation using dermal assessment scores.</p> <p>Results</p> <p>The mean treatment duration of NGX-4010 was 60.2 minutes and all patients completed over 90% of the intended patch application duration. Pain during application was transient. A maximum mean change in NPRS score of +3.0 was observed at 55 minutes post-patch application; pain scores gradually declined to near pre-anesthetic levels (+0.71) within 85 minutes of patch removal. Half of the patients received analgesic medication on the day of treatment; by Day 7, no patients required medication. The most common AEs were application site-related pain, erythema, edema, and pruritus. All patients experienced mild dermal irritation 5 minutes after patch removal, which subsequently decreased; at Day 7, no irritation was evident. The maximum recorded dermal assessment score was 2.</p> <p>Conclusion</p> <p>NGX-4010 was well tolerated following pretreatment with lidocaine 2.5%/prilocaine 2.5% cream in patients with PHN. The tolerability of the patch application appeared comparable with that seen in other studies that used 4% lidocaine cream as the pretreatment anesthetic. This study is registered at <url>http://www.clinicaltrials.gov</url> as number <a href="http://www.clinicaltrials.gov/ct2/show/NCT00916942">NCT00916942</a>.</p

Regulation of the Transglutaminase I gene

The transglutaminase I (TGase I) gene encodes an enzyme that catalyzes the cross-linking of structural proteins involved in the formation of the cornified envelope during squamous cell differentiation. To identify DNA elements important for the transcriptional control of the TGase I gene, we analyzed the ability of a 2.9-kilobase pair (kb) upstream regulatory region to control the expression of a reporter gene in vivo and in vitro. Transgenic mice bearing the pTG(-2.9kb)CAT construct exhibited the same pattern of tissue-specific expression of CAT as reported for TGase I. Deletion analysis in transiently transfected rabbit tracheal epithelial cells indicated that two sequences from bp -490 to -470 and from -54 to -37 are involved in the activation of TGase I transcription. Point mutation analysis and mobility shift assays showed that the sequence located between -54 and -37 is a functional Sp1-like transcription element. Sp1 and Sp3, but not Sp2, are part of nuclear protein complexes from differentiated RbTE cells binding to this site. The element TGATGTCA between bp -490 and -470 is contained in a larger 22-bp palindrome and resembles the consensus cAMP response element-binding protein (CREB)/AP-1 element recognized by dimeric complexes of members of the CREB, ATF, Fos, and Jun families. Mutations in this sequence greatly reduced promoter activity. Supershift analysis identified CREB1, JunB, c-Fos, Fra-1, and c-Jun in protein complexes isolated from differentiated rabbit tracheal epithelial cells binding to this site. Our study shows that the Sp1- and CREB/AP-1-like sites act in concert to stimulate transcription of the TGase I gene. The 2.9-kb promoter region could guide expression of specific genes in the granular layer of the epidermis and could be useful in gene therapy

The MicroRNA and MessengerRNA Profile of the RNA-Induced Silencing Complex in Human Primary Astrocyte and Astrocytoma Cells

GW/P bodies are cytoplasmic ribonucleoprotein-rich foci involved in microRNA (miRNA)-mediated messenger RNA (mRNA) silencing and degradation. The mRNA regulatory functions within GW/P bodies are mediated by GW182 and its binding partner hAgo2 that bind miRNA in the RNA-induced silencing complex (RISC). To date there are no published reports of the profile of miRNA and mRNA targeted to the RISC or a comparison of the RISC-specific miRNA/mRNA profile differences in malignant and non-malignant cells.RISC mRNA and miRNA components were profiled by microarray analysis of malignant human U-87 astrocytoma cells and its non-malignant counterpart, primary human astrocytes. Total cell RNA as well as RNA from immunoprecipitated RISC was analyzed. The novel findings were fourfold: (1) miRNAs were highly enriched in astrocyte RISC compared to U-87 astrocytoma RISC, (2) astrocytoma and primary astrocyte cells each contained unique RISC miRNA profiles as compared to their respective cellular miRNA profiles, (3) miR-195, 10b, 29b, 19b, 34a and 455-3p levels were increased and the miR-181b level was decreased in U-87 astrocytoma RISC as compared to astrocyte RISC, and (4) the RISC contained decreased levels of mRNAs in primary astrocyte and U-87 astrocytoma cells.The observation that miR-34a and miR-195 levels were increased in the RISC of U-87 astrocytoma cells suggests an oncogenic role for these miRNAs. Differential regulation of mRNAs by specific miRNAs is evidenced by the observation that three miR34a-targeted mRNAs and two miR-195-targeted mRNAs were downregulated while one miR-195-targeted mRNA was upregulated. Biological pathway analysis of RISC mRNA components suggests that the RISC plays a pivotal role in malignancy and other conditions. This study points to the importance of the RISC and ultimately GW/P body composition and function in miRNA and mRNA deregulation in astrocytoma cells and possibly in other malignancies

Introducing v0.5 of the AI Safety Benchmark from MLCommons

This paper introduces v0.5 of the AI Safety Benchmark, which has been created by the MLCommons AI Safety Working Group. The AI Safety Benchmark has been designed to assess the safety risks of AI systems that use chat-tuned language models. We introduce a principled approach to specifying and constructing the benchmark, which for v0.5 covers only a single use case (an adult chatting to a general-purpose assistant in English), and a limited set of personas (i.e., typical users, malicious users, and vulnerable users). We created a new taxonomy of 13 hazard categories, of which 7 have tests in the v0.5 benchmark. We plan to release version 1.0 of the AI Safety Benchmark by the end of 2024. The v1.0 benchmark will provide meaningful insights into the safety of AI systems. However, the v0.5 benchmark should not be used to assess the safety of AI systems. We have sought to fully document the limitations, flaws, and challenges of v0.5. This release of v0.5 of the AI Safety Benchmark includes (1) a principled approach to specifying and constructing the benchmark, which comprises use cases, types of systems under test (SUTs), language and context, personas, tests, and test items; (2) a taxonomy of 13 hazard categories with definitions and subcategories; (3) tests for seven of the hazard categories, each comprising a unique set of test items, i.e., prompts. There are 43,090 test items in total, which we created with templates; (4) a grading system for AI systems against the benchmark; (5) an openly available platform, and downloadable tool, called ModelBench that can be used to evaluate the safety of AI systems on the benchmark; (6) an example evaluation report which benchmarks the performance of over a dozen openly available chat-tuned language models; (7) a test specification for the benchmark

Architectures and biogenesis of non-flagellar protein appendages in Gram-negative bacteria

Bacteria commonly expose non-flagellar proteinaceous appendages on their outer surfaces. These extracellular structures, called pili or fimbriae, are employed in attachment and invasion, biofilm formation, cell motility or protein and DNA transport across membranes. Over the past 15 years, the power of molecular and structural techniques has revolutionalized our understanding of the biogenesis, structure, function and mode of action of these bacterial organelles. Here, we review the five known classes of Gram-negative non-flagellar appendages from a biosynthetic and structural point of view