CEE-ing is believing

Bioscience ventures in Central and Eastern Europe are becoming a presence in world healthcare markets despite a perennially short supply of venture funding and other support mechanisms relative to other world economic regions. Here are three up-and-coming CEE stories worth keeping an eye on.     

Sharing Research Data and Intellectual Property Law: A Primer

Sharing research data by depositing it in connection with a published article or otherwise making data publicly available sometimes raises intellectual property questions in the minds of depositing researchers, their employers, their funders, and other researchers who seek to reuse research data. In this context or in the drafting of data management plans, common questions are (1) what are the legal rights in data; (2) who has these rights; and (3) how does one with these rights use them to share data in a way that permits or encourages productive downstream uses? Leaving to the side privacy and national security laws that regulate sharing certain types of data, this Perspective explains how to work through the general intellectual property and contractual issues for all research data.For the researcher seeking to use another’s data, this Perspective offers some good news and some not as good news. The good news is that if a source of data—the researcher or repository—gives permission to reuse the data and one’s intended use fits within the scope of the permission, one need not be overly concerned with the details of the discussion that follows because the permission provides the legal basis for data reuse. For example, if one seeks data from the European Bioinformatics Institute, one will find that the terms of use state that “[t]he public databases of EMBL-EBI [The European Molecular Biology Laboratory-The European Bioinformatics Institute] are freely available by any individual and for any purpose” [1]. This would appear to give any individual academic researcher permission to copy and reuse the data at will. It leaves open a question about whether an employee acting on behalf of his or her employer (is s/he acting as “an individual”?) is equally granted this permission.There is, however, a catch. The EBI’s terms also warn the user that some third parties may claim intellectual property or other legal rights on the original data, and it is up to the researcher not to infringe these rights. This kind of legal uncertainty interferes with the productive reuse of research data. It can be avoided if the repository requires depositors to grant permission to downstream users or to give up any intellectual property rights they may have in the data. Alternatively, the final section of this Perspective describes means by which repositories can make it easy for depositors to signal the scope of the permission they grant to downstream users.In the absence of clear permission, mapping how intellectual property law does—and does not—apply to research data may be of use. In my view, the law makes all of this far more complicated than it need be. For those seeking to pick and choose which reuses of another’s data may be permitted by law, regrettably, the answers to the above questions are more context dependent than many would like.This is so for two reasons. First, the source of all intellectual property rights is national law. Certain international treaties harmonize intellectual property owners’ rights but leave the users’ rights to vary by country. Second, certain countries have added protection beyond what the treaties require. Specifically, the members of the European Union, candidate countries in Eastern Europe, Mexico [2], and South Korea have created a specialized database right that applies to certain databases created or maintained within their borders. These laws regulate uses of these databases only within their borders.     

Two-dimensional imaging detectors for structural biology with X-ray lasers

Our ability to harness the advances in microelectronics over the past decade(s) for X-ray detection has resulted in significant improvements in the state of the art. Biology with X-ray free-electron lasers present daunting detector challenges: all of the photons arrive at the same time, and individual high peak power pulses must be read out shot-by-shot. Direct X-ray detection in silicon pixel detectors—monolithic or hybrid—are the standard for XFELs today. For structural biology, improvements are needed for today''s 10–100 Hz XFELs, and further improvements are required for tomorrow''s 10+ kHz XFELs. This article will discuss detector challenges, why they arise and ways to overcome them, along with the current state of the art.     

Patients as Partners: A Qualitative Study of Patients’ Engagement in Their Health Care

To advocate for patients to be more actively involved with the healthcare services they receive, particularly patients living with chronic illness, the Faculty of Medicine of the University of Montreal and its affiliated hospitals developed the Patients as Partners concept where the patient is considered a full-fledged partner of the health care delivery team and the patient’s experiential knowledge is recognized. This study aims to show how patients view their engagement with healthcare professionals regarding their direct care. Using theoretical sampling, 16 semi-structured interviews were conducted with patients with chronic illness who were familiar with the concept of Patients as Partners. Data analysis followed a constructivist grounded theory approach. Patients describe themselves as proactively engaging in three types of practice, regardless of health professionals’ openness to their role as partners. The first is a process of continuous learning that allows them to acquire experiential knowledge about their health, as well as scientific information and technical know-how. The second involves their assessment of the healthcare they receive, in terms of its quality and how it aligns with their personal preferences. It includes their assessment of the quality of their relationship with the health professional and of the latter’s scientific knowledge and technical know-how. The third type, adaptation practices, builds on patients’ learning and assessments to compensate for and adapt to what has been perceived as optimal or non-optimal health or healthcare circumstances. Patients appear to play a more active and less docile role in their own direct care than suggested so far in the literature, regardless of the degree of reciprocity of the partnership or the degree to which the health professional seeks to encourage patient engagement.     

Evolvement of uniformity and volatility in the stressed global financial village

Background

In the current era of strong worldwide market couplings the global financial village became highly prone to systemic collapses, events that can rapidly sweep throughout the entire village.

Methodology/Principal Findings

We present a new methodology to assess and quantify inter-market relations. The approach is based on the correlations between the market index, the index volatility, the market Index Cohesive Force and the meta-correlations (correlations between the intra-correlations.) We investigated the relations between six important world markets—U.S., U.K., Germany, Japan, China and India—from January 2000 until December 2010. We found that while the developed “western” markets (U.S., U.K., Germany) are highly correlated, the interdependencies between these markets and the developing “eastern” markets (India and China) are volatile and with noticeable maxima at times of global world events. The Japanese market switches “identity”—it switches between periods of high meta-correlations with the “western” markets and periods when it behaves more similarly to the “eastern” markets.

Conclusions/Significance

The methodological framework presented here provides a way to quantify the evolvement of interdependencies in the global market, evaluate a world financial network and quantify changes in the world inter market relations. Such changes can be used as precursors to the agitation of the global financial village. Hence, the new approach can help to develop a sensitive “financial seismograph” to detect early signs of global financial crises so they can be treated before they develop into worldwide events.     

Inference or Enaction? The Impact of Genre on the Narrative Processing of Other Minds

Do narratives shape how humans process other minds or do they presuppose an existing theory of mind? This study experimentally investigated this problem by assessing subject responses to systematic alterations in the genre, levels of intentionality, and linguistic complexity of narratives. It showed that the interaction of genre and intentionality level are crucial in determining how narratives are cognitively processed. Specifically, genres that deployed evolutionarily familiar scenarios (relationship stories) were rated as being higher in quality when levels of intentionality were increased; conversely, stories that lacked evolutionary familiarity (espionage stories) were rated as being lower in quality with increases in intentionality level. Overall, the study showed that narrative is not solely either the origin or the product of our intuitions about other minds; instead, different genres will have different—even opposite—effects on how we understand the mind states of others.     

1(st) Central and Eastern European Proteomic Conference & 3(rd) Czech Proteomic Conference 29 - 31 October 2007, Prague, Czech Republic

More than 130 delegates from all over the world attended the 1(st) Central and Eastern European Proteomic Conference organized together with the 3(rd) Czech Proteomic Conference in the TOP Hotel, Prague in the Czech Republic from 29(th) to 31(st) October, 2007. The autumn nostalgia of the historical city of Prague provided the stage for a fascinating meeting that reviewed rapidly emerging proteomic research in the countries of Central and Eastern Europe, and focused on proteomics driven discovery and applications.     

Biological trade and markets

Cooperation between organisms can often be understood, like trade between merchants, as a mutually beneficial exchange of services, resources or other ‘commodities’. Mutual benefits alone, however, are not sufficient to explain the evolution of trade-based cooperation. First, organisms may reject a particular trade if another partner offers a better deal. Second, while human trade often entails binding contracts, non-human trade requires unwritten ‘terms of contract’ that ‘self-stabilize’ trade and prevent cheating even if all traders strive to maximize fitness. Whenever trading partners can be chosen, market-like situations arise in nature that biologists studying cooperation need to account for. The mere possibility of exerting partner choice stabilizes many forms of otherwise cheatable trade, induces competition, facilitates the evolution of specialization and often leads to intricate forms of cooperation. We discuss selected examples to illustrate these general points and review basic conceptual approaches that are important in the theory of biological trade and markets. Comparing these approaches with theory in economics, it turns out that conventional models—often called ‘Walrasian’ markets—are of limited relevance to biology. In contrast, early approaches to trade and markets, as found in the works of Ricardo and Cournot, contain elements of thought that have inspired useful models in biology. For example, the concept of comparative advantage has biological applications in trade, signalling and ecological competition. We also see convergence between post-Walrasian economics and biological markets. For example, both economists and biologists are studying ‘principal–agent’ problems with principals offering jobs to agents without being sure that the agents will do a proper job. Finally, we show that mating markets have many peculiarities not shared with conventional economic markets. Ideas from economics are useful for biologists studying cooperation but need to be taken with caution.     

Science vs Conspiracy: Collective Narratives in the Age of Misinformation

The large availability of user provided contents on online social media facilitates people aggregation around shared beliefs, interests, worldviews and narratives. In spite of the enthusiastic rhetoric about the so called collective intelligence unsubstantiated rumors and conspiracy theories—e.g., chemtrails, reptilians or the Illuminati—are pervasive in online social networks (OSN). In this work we study, on a sample of 1.2 million of individuals, how information related to very distinct narratives—i.e. main stream scientific and conspiracy news—are consumed and shape communities on Facebook. Our results show that polarized communities emerge around distinct types of contents and usual consumers of conspiracy news result to be more focused and self-contained on their specific contents. To test potential biases induced by the continued exposure to unsubstantiated rumors on users’ content selection, we conclude our analysis measuring how users respond to 4,709 troll information—i.e. parodistic and sarcastic imitation of conspiracy theories. We find that 77.92% of likes and 80.86% of comments are from users usually interacting with conspiracy stories.     

Taking Perspective: Personal Pronouns Affect Experiential Aspects of Literary Reading

Personal pronouns have been shown to influence cognitive perspective taking during comprehension. Studies using single sentences found that 3^rd person pronouns facilitate the construction of a mental model from an observer’s perspective, whereas 2^nd person pronouns support an actor’s perspective. The direction of the effect for 1^st person pronouns seems to depend on the situational context. In the present study, we investigated how personal pronouns influence discourse comprehension when people read fiction stories and if this has consequences for affective components like emotion during reading or appreciation of the story. We wanted to find out if personal pronouns affect immersion and arousal, as well as appreciation of fiction. In a natural reading paradigm, we measured electrodermal activity and story immersion, while participants read literary stories with 1^st and 3^rd person pronouns referring to the protagonist. In addition, participants rated and ranked the stories for appreciation. Our results show that stories with 1^st person pronouns lead to higher immersion. Two factors—transportation into the story world and mental imagery during reading—in particular showed higher scores for 1^st person as compared to 3^rd person pronoun stories. In contrast, arousal as measured by electrodermal activity seemed tentatively higher for 3^rd person pronoun stories. The two measures of appreciation were not affected by the pronoun manipulation. Our findings underscore the importance of perspective for language processing, and additionally show which aspects of the narrative experience are influenced by a change in perspective.     

Diversity through equity and inclusion: The responsibility belongs to all of us

Despite the recognized benefits of diversity and the decades of programs targeted at increasing diversity in science, technology, engineering, mathematics, and medicine, the underrepresentation of historically excluded groups continues due to persisting systemic inequalities. It is imperative that we reassess our current recruitment strategies and reimagine our campus and workplace environments to provide an inclusive and equitable culture that is free of institutional barriers, affording equal opportunities for each individual to succeed, thrive, and be their whole self. For too long this vision has been the fight of a heroic few, but it must become the fight of all in order to achieve true change. I am working toward, and look forward to, a future where contributing to diversity, equity, and inclusion is fully integrated into the core mission of our institutions and is an expectation for all of us.

James A. Olzmann

“It is not our differences that divide us. It is our inability to recognize, accept, and celebrate those differences.” —Audre Lorde

I am honored and grateful to receive the Günter Blobel Early Career Award from the American Society for Cell Biology (ASCB). As a graduate student, I was fortunate enough to receive a travel award through the ASCB Minorities Affairs Committee that allowed me to attend the 2005 ASCB annual meeting. I recall my first meeting as both a daunting and exhilarating experience, and I excitedly attended talks from my science heroes. Over the years, the excitement of the annual meeting has never faded for me, and it now feels much like a reunion of friends and colleagues. I have also come to appreciate that ASCB is much more than just the annual meeting—it is a community of amazing cell biologists and it is our community! Everything has come full circle and I am privileged to be a member of the ASCB Minorities Affairs Committee, striving to pay it forward to students from diverse backgrounds and to cultivate an inclusive community where we all feel that we belong and are welcomed.During a typical year, I would take this opportunity to discuss my path to become a cell biologist and how I became fascinated by lipid droplets, offer some tips for success in science and research, and perhaps wax poetic about the power of collaboration and mentorship. However, I think we can all agree that 2020 is not a typical year. Our world continues to reel from the impact of the COVID-19 pandemic and we are in the midst of the Black Lives Matter movement, the fire for this an anti-racism revolution rekindled by the needless and heartbreaking deaths of George Floyd, Breonna Taylor, and so many others. These events, which are just the most recent examples of all too common racially motivated violence, shine a light on our reality born out of a legacy of racism that permeates all aspects of our society. It is an understatement to say that our scientific community is not exempt from these systemic injustices, biases, and inequalities. To gain some small insight into the scope of the problem, we only need to look towards the #blackintheivory and #blackinivory hashtags on Twitter and recently published stories (Simmons, 2020) that chronicle the lived experiences of our black colleagues—the microaggressions, implicit and explicit bias, tokenism, etc. It is with these current events as the backdrop that I focus this essay on the need for systemic change and the importance of achieving diversity through equity and inclusion in science, technology, engineering, mathematics, and medicine (STEMM).     

“Positive” Results Increase Down the Hierarchy of the Sciences

The hypothesis of a Hierarchy of the Sciences with physical sciences at the top, social sciences at the bottom, and biological sciences in-between is nearly 200 years old. This order is intuitive and reflected in many features of academic life, but whether it reflects the “hardness” of scientific research—i.e., the extent to which research questions and results are determined by data and theories as opposed to non-cognitive factors—is controversial. This study analysed 2434 papers published in all disciplines and that declared to have tested a hypothesis. It was determined how many papers reported a “positive” (full or partial) or “negative” support for the tested hypothesis. If the hierarchy hypothesis is correct, then researchers in “softer” sciences should have fewer constraints to their conscious and unconscious biases, and therefore report more positive outcomes. Results confirmed the predictions at all levels considered: discipline, domain and methodology broadly defined. Controlling for observed differences between pure and applied disciplines, and between papers testing one or several hypotheses, the odds of reporting a positive result were around 5 times higher among papers in the disciplines of Psychology and Psychiatry and Economics and Business compared to Space Science, 2.3 times higher in the domain of social sciences compared to the physical sciences, and 3.4 times higher in studies applying behavioural and social methodologies on people compared to physical and chemical studies on non-biological material. In all comparisons, biological studies had intermediate values. These results suggest that the nature of hypotheses tested and the logical and methodological rigour employed to test them vary systematically across disciplines and fields, depending on the complexity of the subject matter and possibly other factors (e.g., a field''s level of historical and/or intellectual development). On the other hand, these results support the scientific status of the social sciences against claims that they are completely subjective, by showing that, when they adopt a scientific approach to discovery, they differ from the natural sciences only by a matter of degree.     

Adaptive Introgression Facilitates Adaptation to High Latitudes in European Aspen (Populus tremula L.)

Understanding local adaptation has become a key research area given the ongoing climate challenge and the concomitant requirement to conserve genetic resources. Perennial plants, such as forest trees, are good models to study local adaptation given their wide geographic distribution, largely outcrossing mating systems, and demographic histories. We evaluated signatures of local adaptation in European aspen (Populus tremula) across Europe by means of whole-genome resequencing of a collection of 411 individual trees. We dissected admixture patterns between aspen lineages and observed a strong genomic mosaicism in Scandinavian trees, evidencing different colonization trajectories into the peninsula from Russia, Central and Western Europe. As a consequence of the secondary contacts between populations after the last glacial maximum, we detected an adaptive introgression event in a genome region of ∼500 kb in chromosome 10, harboring a large-effect locus that has previously been shown to contribute to adaptation to the short growing seasons characteristic of Northern Scandinavia. Demographic simulations and ancestry inference suggest an Eastern origin—probably Russian—of the adaptive Nordic allele which nowadays is present in a homozygous state at the north of Scandinavia. The strength of introgression and positive selection signatures in this region is a unique feature in the genome. Furthermore, we detected signals of balancing selection, shared across regional populations, that highlight the importance of standing variation as a primary source of alleles that facilitate local adaptation. Our results, therefore, emphasize the importance of migration–selection balance underlying the genetic architecture of key adaptive quantitative traits.     

Factors Affecting Regional Per-Capita Carbon Emissions in China Based on an LMDI Factor Decomposition Model

China is considered to be the main carbon producer in the world. The per-capita carbon emissions indicator is an important measure of the regional carbon emissions situation. This study used the LMDI factor decomposition model–panel co-integration test two-step method to analyze the factors that affect per-capita carbon emissions. The main results are as follows. (1) During 1997, Eastern China, Central China, and Western China ranked first, second, and third in the per-capita carbon emissions, while in 2009 the pecking order changed to Eastern China, Western China, and Central China. (2) According to the LMDI decomposition results, the key driver boosting the per-capita carbon emissions in the three economic regions of China between 1997 and 2009 was economic development, and the energy efficiency was much greater than the energy structure after considering their effect on restraining increased per-capita carbon emissions. (3) Based on the decomposition, the factors that affected per-capita carbon emissions in the panel co-integration test showed that Central China had the best energy structure elasticity in its regional per-capita carbon emissions. Thus, Central China was ranked first for energy efficiency elasticity, while Western China was ranked first for economic development elasticity.     

Admixture in Africanized honey bees (Apis mellifera) from Panamá to San Diego,California (U.S.A.)

The Africanized honey bee (AHB) is a New World amalgamation of several subspecies of the western honey bee (Apis mellifera), a diverse taxon historically grouped into four major biogeographic lineages: A (African), M (Western European), C (Eastern European), and O (Middle Eastern). In 1956, accidental release of experimentally bred “Africanized” hybrids from a research apiary in Sao Paulo, Brazil initiated a hybrid species expansion that now extends from northern Argentina to northern California (U.S.A.). Here, we assess nuclear admixture and mitochondrial ancestry in 60 bees from four countries (Panamá; Costa Rica, Mexico; U.S.A) across this expansive range to assess ancestry of AHB several decades following initial introduction and test the prediction that African ancestry decreases with increasing latitude. We find that AHB nuclear genomes from Central America and Mexico have predominately African genomes (76%–89%) with smaller contributions from Western and Eastern European lineages. Similarly, nearly all honey bees from Central America and Mexico possess mitochondrial ancestry from the African lineage with few individuals having European mitochondria. In contrast, AHB from San Diego (CA) shows markedly lower African ancestry (38%) with substantial genomic contributions from all four major honey bee lineages and mitochondrial ancestry from all four clades as well. Genetic diversity measures from all New World populations equal or exceed those of ancestral populations. Interestingly, the feral honey bee population of San Diego emerges as a reservoir of diverse admixture and high genetic diversity, making it a potentially rich source of genetic material for honey bee breeding.     

The Risk of Nosocomial Transmission of Rift Valley Fever

In 2000, we investigated the Rift Valley fever (RVF) outbreak on the Arabian Peninsula—the first outside Africa—and the risk of nosocomial transmission. In a cross-sectional design, during the peak of the epidemic at its epicenter, we found four (0.6%) of 703 healthcare workers (HCWs) IgM seropositive but all with only community-associated exposures. Standard precautions are sufficient for HCWs exposed to known RVF patients, in contrast to other viral hemorrhagic fevers (VHF) such as Ebola virus disease (EVD) in which the route of transmission differs. Suspected VHF in which the etiology is uncertain should be initially managed with the most cautious infection control measures.     

Placebo Trends across the Border: US versus Canada

Background

Physicians around the world report to using placebos in a variety of situations and with varying degrees of frequency. Inconsistent methodologies, however, complicate interpretation and prevent direct comparisons across studies. While US- and Canada-based physicians share similar professional standards, Canada harbours a less-litigious universal healthcare model with no formal placebo-related policy—factors that may impact how physicians view and use placebos.

Methods

To compare American and Canadian data, we circulated an online survey to academic physicians practicing in Canada, collected anonymous responses, and extracted those of internists and rheumatologists for comparison to US data obtained through parallel methodologies.

Results

Whereas our data show overall concordance across the border—from definitions to ethical limitations and therapeutic potential—differences between American- and Canadian-based placebo practices merit acknowledgement. For example, compared to 45%-80% among US-based respondents, only 23±7% of Canada-based respondents reported using placebos in clinical practice. However, 79±7% of Canada-respondents—a figure comparable to US data—professed to prescribing at least one form of treatment without proven or expected efficacy. Placebo interventions including unwarranted vitamins and herbal supplements (impure placebos) as well as sugar pills and saline injections (pure placebos) appear more common in Canada, where more doctors described placebos as “placebos” (rather than “medications”) and used them as a “diagnostic” tool (rather than a means of placating patient demands for treatment).

Interpretation

Cross-border variation in the use of clinical placebos appears minor despite substantial differences in health care delivery system, malpractice climate, and placebo-related policy. The prevalence of impure placebos in both Canadian and US clinics raises ethical and practical questions currently unaddressed by policy and warranting investigation.     

Components and Public Health Impact of Population Growth in the Arab World

The Arab world, which consists of the 22 member states of the Arab League, is undergoing a rapid transition in demographics, including fertility, mortality, and migration. Comprising a distinctive geographic region spread across West Asia and North East Africa and unified by the Arabic language, these states share common values and characteristics despite having diverse economic and political conditions. The demographic lag (high fertility and low mortality) that characterizes the Arab world is unique, but the present trend of declining fertility, combined with the relatively low mortality, brings about significant changes in its population size. This research aimed to: (i) assess the population growth in the Arab world over 3 time periods, (ii) explore its components, and (iii) understand its public health impact. Data from the International Data Base (IDB) of the U.S. Census Bureau for 3 time periods (1992, 2002, and 2012) in 21 countries of the Arab world were analyzed by dividing them into four geographic sectors, namely, the Gulf Cooperation Council (GCC), West Asia, Maghreb, and the Nile Valley African Horn. The population of the Arab world has grown considerably due to both natural growth and migration. The immigration is pronounced, especially into resource-intensive GCC nations, not only from East Asian and Central African countries but also from resource-thrifty (limited-resource) Arab nations. The migrations within, as well as outside, the Arab world reveal an interesting demographic phenomenon that requires further research: migration flows and trends. However, the transformations in public health statistics related to mortality—the impact of demographic changes—depict a new era in the Arab world.     

BASE: A novel workflow to integrate nonubiquitous genes in comparative genomics analyses for selection

Inferring the selective forces that orthologous genes underwent across different lineages can help us understand the evolutionary processes that have shaped their extant diversity and the phenotypes they underlie. The most widespread metric to estimate the selection regimes of coding genes—across sites and phylogenies—is the ratio of nonsynonymous to synonymous substitutions (dN/dS, also known as ω). Nowadays, modern sequencing technologies and the large amount of already available sequence data allow the retrieval of thousands of orthologous genes across large numbers of species. Nonetheless, the tools available to explore selection regimes are not designed to automatically process all genes, and their practical usage is often restricted to the single‐copy ones which are found across all species considered (i.e., ubiquitous genes). This approach limits the scale of the analysis to a fraction of single‐copy genes, which can be as low as an order of magnitude in respect to those which are not consistently found in all species considered (i.e., nonubiquitous genes). Here, we present a workflow named BASE that—leveraging the CodeML framework—eases the inference and interpretation of gene selection regimes in the context of comparative genomics. Although a number of bioinformatics tools have already been developed to facilitate this kind of analyses, BASE is the first to be specifically designed to allow the integration of nonubiquitous genes in a straightforward and reproducible manner. The workflow—along with all relevant documentation—is available at github.com/for‐giobbe/BASE.