Publications

The language and conceptual framework of "research reproducibility" are nonstandard and unsettled across the sciences.In this Perspective, we review an array of explicit and implicit definitions of reproducibility and related terminology, and discuss how to avoid potential misunderstandings when these terms are used as a surrogate for "truth.

John Ioannidis, Nikolaos Patsopoulos, and Evangelos Evangelou argue that, although meta-analyses often measure heterogeneity between studies, these estimates can have large uncertainty, which must be taken into account when interpreting evidence

Abstract Background HIV-1 remains the leading cause of death among adults in Sub-Saharan Africa, and over 1 million people are infected annually. Better identification of at-risk groups could benefit prevention and treatment programmes. We systematically identified factors related to HIV-1 infection in two nationally representative cohorts of women that participated in Zambia’s Demographic and Health Surveys (DHS). Methods We conducted a comprehensive analysis to identify and replicate the association of 1,415 social, economic, environmental, and behavioral indicators with HIV-1 status. We used the 2007 and 2013-2014 DHS surveys conducted among 5,715 and 15,433 Zambian women, respectively (727 indicators in 2007; 688 in 2013-2014; 688 in both). We used false discovery rate criteria to identify indicators that are strongly associated with HIV-1 in univariate and multivariate models in the entire population, as well as in subgroups stratified by wealth, residence, age, and history of HIV-1 testing. Findings In the univariate analysis we identified 102 and 182 variables that are associated with HIV-1 in the 2007 and 2013-2014 surveys, respectively, among which 79 were associated in both. Variables that were associated with HIV-1 status in all full-sample models (unadjusted and adjusted) as well as in at least 17 out of 18 subgroups include being formerly in a union (adjusted OR 2007 2.8, p<10 −16 ; 2013-2014 2.8, p<10 −29 ), widowhood (adjusted OR 2007 3.7, p<10 −12 ; 2013-2014 4.2, p<10 −30 ), history of genital ulcers in the last 12 months (adjusted 2007 OR 2.4, p<10 −5 ; 2013-2014 2.2, p<10 −6 ), and having a woman for the head of the household (2007 OR 1.7, p<10 −7 ; 2013-2014 OR 2.1, p<10 −26 ), while owning a bicycle (adjusted 2007 OR 0.6, p<10 −6 ; 2013-2014 0.6, p<10 −8 ) and currently breastfeeding (adjusted 2007 OR 0.5, p<10 −9 ; 2013-2014 0.4, p<10 −26 ) were associated with decreased risk. Using the identified variables, area under the curve for HIV-1 positivity ranged from 0.76 to 0.82. Interpretation Our X-wide association study in Zambian women identifies multiple under-recognized factors correlated with HIV-1 infection in 2007 and 2013-2014, including widowhood, breastfeeding, and being the head of the household. These variables could be used to improve HIV-1 testing and identification programs.

This paper has described the different trends in the digital circuit design and changes over the past two decades moving from chips that contained tens of thousands of devices to today' s chips that may contain over a billion transistors. The job of the digital circuit designer has grown with the chips, moving from optimizing and validating gates, to working on functional units, to now designing complete systems. While the progress in digital design has clearly been tremendous, power challenges are an important issue in future VLSI designing system. Designers used considerable ingenuity to make CMOS compatible with the older bipolar ECL/TTL families, concentrating on meeting all aspects of the without requiring external components.

Traditionally, operating systems have fulfilled the dual roles of enforcing security on computer systems, as well as managing and virtualizing resources for the various applications sharing the machine. However, more recently, there have been some promising proposals in creating systems where hardware, rather than software enforces security and protection. These proposals would require an operating system running on such hardware to manage resources on behalf of applications that do not trust it. Unfortunately, the implementation of such an operating system has not received much attention in the literature and it is not clear if a traditional services of an operating system could be provided on such hardware. This paper discusses the modifications that are necessary to make a modern operating system execute on such hardware. The modifications were modest, the most significant changes were in the areas that perform context switches, signal handling, and virtual memory management.

Pre-registration is a research practice where a protocol is deposited in a repository before a scientific project is performed. The protocol may be publicly visible immediately upon deposition or it may remain hidden until the work is completed/published. It may include the analysis plan, outcomes, and/or information about how evaluation of performance (e.g. forecasting ability) will be made, Pre-registration aims to enhance the trust one can put on scientific work. Deviations from the original plan, may still often be desirable, but pre-registration makes them transparent. While pre-registration has been advocated and used to variable extent in diverse types of research, there has been relatively little attention given to the possibility of pre-registration for mathematical modeling studies. Feasibility of pre-registration depends on the type of modeling and the ability to pre-specify processes and outcomes. In some types of modeling, in particular those that involve forecasting or other outcomes that can be appraised in the future, trust in model performance would be enhanced through pre-registration. Pre-registration can also be seen as a component of a larger suite of research practices that aim to improve documentation, transparency, and sharing-eventually allowing better reproducibility of the research work. The current commentary discusses the evolving landscape of the concept of pre-registration as it relates to different mathematical modeling activities, the potential advantages and disadvantages, feasibility issues, and realistic goals.

Cecile Janssens and colleagues present the GRIPS Statement, a checklist to help strengthen the reporting of genetic risk prediction studies.

Petitions and open letters signed by large numbers of scientists are not new, but they have proliferated in the covid-19 era. 1 2 They have a clear role when it comes to questions of ethics, social problems, and injustices.With monumental consequences from both the pandemic and the response to the pandemic, debating ethical and social matters is the right of every citizen, including scientists.A collateral damage, however, is when these documents are aimed to prove or disprove scientific positions.

Embedded wireless sensors, once deployed, may remain in active use for decades. At the same time, as motes come to dominate both the number of hosts and data traffic of the Internet, their security will become fundamental to general Internet security. This paper argues that the next generation of embedded networked sensor devices (motes) should consider this tension in their basic design and be designed to remain secure for 20 years in a rapidly changing and evolving security and cryptographic landscape. The key insight in this paper is that the economics of modern system-on-a-chip (SoC) designs provides ample space for hardware accelerators and cryptographic engines. A next generation mote can therefore include many such co-processors and features at almost no production cost. The paper describes an initial design for what hardware security support such a device should have, focusing on five hardware primitives: an atomic, unique counter, a random number generator based on physical entropy, additional instructions to accelerate symmetric ciphers, an elliptic curve accelerator, and support for modular polynomial multiplication used in post-quantum cryptographic signing algorithms. We call this architecture CESEL.

ABSTRACT We evaluated how the gender composition of top-cited authors within different subfields of research has evolved over time. We considered 9,071,122 authors with at least 5 full papers in Scopus as of September 1, 2022. Using a previously validated composite citation indicator, we identified the 2% top-cited authors for each of 174 science subfields (Science-Metrix classification) in 4 separate publication age cohorts (first publication pre-1992, 1992-2001, 2002-2011, post-2011). Using NamSor we assigned 3,784,507 authors as men, and 2,011,616 as women (for 36.1% gender assignment uncertain). Men outnumbered women 1.88-fold among all authors, decreasing from 3.93-fold to 1.36-fold over time. Men outnumbered women 3.21-fold among top-cited authors, decreasing from 6.41-fold to 2.28-fold over time. In the youngest (post-2011) cohort, 32/174 (18%) subfields had >=50% women, 97/174 (56%) subfields had >=30% women, and 3 subfields had =<10% women among the top-cited authors. Gender imbalances in author numbers decreased sharply over time in both high-income countries (including the USA) and other countries, but the latter had little improvement in gender imbalances for top-cited authors. In random samples of 100 women and 100 men from the youngest (post-2011) cohort, in-depth assessment showed that most were currently (April 2023) working in academic environments. 32 women and 44 men had some faculty appointment, but only 2 women and 2 men were full professors. Our analysis shows large heterogeneity across scientific disciplines in the amelioration of gender imbalances with more prominent imbalances persisting among top-cited authors and slow promotion pathways even for the most-cited young scientists.