bluuebunny/crossref_metadata_2025 huggingface dataset:
Metrological aspects of the safety and quality of meat products
Authors: Oganyan N G , Semenova A A , Dobrovolskiy V I
Published: March 2022

The meat industry is one of the most important sectors of the economy closely related to animal husbandry. In the human diet, meat is the main source of animal protein. Therefore, quality of a final product is extremely important and depends on many factors at all stages of the production. Requirements for parameters of food safety and quality are established in the most countries and are revised permanently depending on the new scientific data.

In the Russian Federation and the Customs Union, the controlled parameters are normalized on the basis of scientific data and approved for use in the relevant Technical Regulations. In order to avoid actions misleading consumers, special requirements for product labeling have been developed. In particular, the labeling of slaughter products and meat products must be conformed in accordance to the Technical Regulation of the Customs Union "Food products in terms of their labeling " - TR CU 022/2011, as well as to the some clauses of the Technical Regulation TR CU 034/2013 On the Safety of Meat and Meat Products.

According to the working regulation, the manufacturers must indicate nutritional parameters (protein, fat, carbohydrates) of meat products on the product label as the parameter true values. At the same time, each standard for analytical methods includes a permissible relative error of the measured value at the confidence level of 0.95, which had not to be exceeded under the conditions described in the standard. In that way target measurement uncertainty is established.

This paper shows the possible risks of false decisions when assessing meat products for its compliance with the labeling, depending on the measurement uncertainty, as well as methods for minimizing these risks.
Metrological problems of measurements of environmental objects in terms of spectrometry and radiometry of alpha, beta, gamma-emitting radionuclides
Authors: Berlyand T P , Tonkikh N G
Published: March 2022

This article deals with methods for measuring the characteristics of ionizing radiation in solving problems of radiation monitoring of the environment, industrial premises, sanitary protection zones, human pollution control using measurement techniques certified in the prescribed manner. The types of measuring instruments involved in the measurement of various quantities are listed. The main objects of measurements used in radiation monitoring of the environment, control of surface contamination and human contamination are named. The metrological characteristics (measured quantities) of measuring instruments are compared with the metrological characteristics of real measurement objects. A number of necessary established metrological characteristics for radiometric and spectrometric measuring instruments for the successful use of a measuring instrument in solving one or another problem of radiation measurements is indicated. An example from a real work is considered, in which the method of mathematical modeling when calculating additional metrological characteristics showed a significant discrepancy with the real data obtained during the experiment.
Development of a lunar soil simulator for Earth-based experiments
Authors: Alexandrov P A , Vasiliev A L , Kalechits V I , Kapustin Yu V , Klyuev V V , Makaveev P Yu , Patsaev T D , Shakhov M N
Published: March 2022

A simulator of lunar soil and lunar dust has been developed, designed for modeling various engineering processes in terrestrial conditions. The elemental and granulometric compositions of the simulator were studied using X-ray fluorescence analysis, scanning electron microscopy and laser light scattering. The resulting material will be used in the future to simulate thermophysical processes when creating lunar power generating plants. The finely dispersed component of the simulator based on basalt wool will be used to study the filtration of lunar dust.
A moving platform photometric observation based attitude and angular velocity estimation method for space target
Authors: Chen Shengyi , Fan Chaoran , Zhang Feng , Shi Liu
Published: March 2022

Based on the photometric information, a method is proposed for estimating space target attitude and angular velocity under the condition of moving observation platform. Firstly, according to the dynamically changing relative pose relationship among the target, the observation platform and the sun, photometric measurement model is established. Then, in the framework of Unscented Kalman Filter, the joint estimation of target attitude and angular velocity is realized by combining use of quaternion and Modified Rodriguez Parameters. Finally, the feasibility and estimation accuracy of the method are verified by numerical simulation experiments. The results show that the proposed method achieves high accuracy and has certain value in practical application.
Molecular mechanism study of Astragalus adsurgens Pall synergistically induced by plasma and plasma-activated water
Authors: LI Yibing , ZHANG Tao , SONG Zhiqing , DING Changjiang , CHEN Hao
Published: March 2022

The mutagenic effects of discharge plasma and plasma+PAW (plasma and its activated water combined) on Astragalus adsurgens Pall seeds were explored. Needle array-plate dielectric-barrier discharge plasma was used to treat A. adsurgens Pall seeds and PAW was prepared at the same time. The deionized water and the obtained PAW were used to cultivate plasma-treated seeds in groups and the survival rate of each group was counted. Results showed that the survival rate of the treated seeds of A. adsurgens Pall when cultured with deionized water was not significantly different from that of the control check (CK). The culture with PAW had an obvious lethal effect and each group reached the half-lethal dose. Reactive oxygen species (ROS) and RNA-Seq analysis of seedlings in the 3 h treatment group showed that the content of ROS in the 3 d post-treatment group was significantly higher than that of the CK. Because expression of the gene with the function of scavenging superoxide free radicals was upregulated, the ROS content of seedlings on the sixth day was significantly lower than that on the third day. Plasma and plasma+PAW treatments changed a large number of gene expressions; particularly, the plasma+PAW group caused plant-growth genes to be significantly upregulated. After treatment, the seedlings of A. adsurgens Pall may grow faster and have higher nutritional value. This research is of great significance to the wider application of isoelectronic bodies and their activated water physicochemical mutagens in biological effects and breeding research.
Effect of short carbon fiber/SiC on tribological properties of aluminium matrix hybrid composites
Authors: Joshi Tanmay Vivek , Mohanty Akash
Published: March 2022

This research study was carried out to combine the benefits of Silicon Carbide (SiC) and short carbon fiber (CF) as reinforcements in the aluminum matrix to develop the composites for automotive applications. The powder metallurgy (PM) technique was used to fabricate five samples with different compositions. Linear wear, coefficient of friction, density, and Vickers hardness of the samples were determined and compared. The sample with 6 wt.% CF and 10 wt.% SiC was found to have the optimal properties. It was observed that the linear wear was 52.32% less and the hardness was 14.58% more than the base metal.
Qualitative Research: Foundations, Approaches, and Practices
Authors: Greckhamer Thomas , Cilesiz Sebnem
Published: March 2022

Qualitative research is an umbrella term that is typically used in contrast to quantitative research and captures research approaches that predominantly rely on collecting and analyzing qualitative data (i.e., data in the form of words, still or moving images, and artifacts). Qualitative research encompasses a wide range of research approaches with different philosophical and theoretical foundations and empirical procedures. Different assumptions about reality and knowledge underlying these diverse approaches guide researchers with respect to epistemological and methodological questions and inform their choices regarding research questions, data collection, data analysis, and the writing of research accounts. While at present a few dominant approaches are commonly used by researchers, a rich repertoire of qualitative approaches is available to management researchers that has the potential to facilitate deeper and broader insights into management phenomena.
Employee Voice: Meanings, Approaches, and Research Directions
Authors: Della Torre Edoardo , Gritti Alessia , Wilkinson Adrian
Published: March 2022

Employee voice (EV) refers to all the ways and means through which employees have a say in the decisions that affect their work and the overall running of their organization. It involves different domains and topics and occurs through a variety of channels (direct and indirect, formal and informal, individual and collective). The main distinction is between direct voice channels, through which employees have the opportunity to express their ideas and opinions directly to managers without the mediation of representatives, and indirect voice channels, through which EV is expressed by representatives, usually elected from the wider group of employees.

Since the last decades of the 20th century, EV has become a central topic in human resource management (HRM), industrial relations, (IR) and organizational behavior (OB) literature, providing researchers and practitioners with an extensive and ever-increasing amount of knowledge. However, each discipline has created its own conceptualization of the meanings of and purposes for EV, leading EV to become a contested terrain, characterized by research silos and competing literatures. While the OB perspective concentrates on the informal and prosocial nature of individual EV, the IR approach is mainly focused on formal structures for collective EV and the contrasting interests of management and workers, and the HRM approach tends to emphasize the role of direct EV as a component of the wider HRM systems that may generate higher organizational outcomes.

Integrative approaches that can bring together different disciplinary perspectives are therefore required for a more comprehensive understanding of how EV takes shape in organizations and affects individual and organizational outcomes. Greater attention should also be paid to the multidimensionality of EV, investigating further how it relates to employee silence and to other phenomena, such as ethical employee voice and whistle-blowing. Finally, little is known about the emerging forms of EV related to workplace digitalization and working remotely.
An Identity Lens to Understand Teams in International Business
Authors: Raghav Sonia , Gibson Cristina
Published: March 2022

In international business, teams can take on a variety of forms, including domestic collocated teams, multinational collocated teams, global virtual teams, and multicultural teams. All of these types of teams offer the potential for developing innovative products and services, but they also may face substantial challenges with respect to collaboration and coordination. Team members are likely to identify with a variety of affiliations, based on dimensions such as gender, family roles, ethnicity, culture, nation, profession, organization, and team. Identification with each of these social groups brings with it the opportunity for diverse insights and perspectives, skill breadth, and broad social connections. However, this can lead to both benefits and challenges for teams. As a result, the ability to negotiate identities has become critical in international business. Drawing upon concepts of social identity, an identity lens can be used to document the promise and problems of teams in international business. An understanding of how multiple identity interactions within an individual can affect processes and outcomes for the team has the potential to create a more nuanced comprehension of international teams.
Effective Strategies and Psychological Mechanisms for Cooperation Induction in Social Dilemmas: A Review and Future Research
Authors: Chen Xiao-Ping
Published: March 2022

A social dilemma is a situation in which people face a conflict between maximizing personal interest (noncooperation) and maximizing collective interest (cooperation). Although a noncooperative choice leads to a better individual outcome, when all people do the same, all will be worse off than if all choose to cooperate. Climate “Code Red,” overpopulation, funding for public television, and the depletion of scarce and valuable resources such as forests and fisheries are all typical examples of social dilemmas. A long-lasting theme in the research into social dilemmas is the identification of effective approaches to induce voluntary cooperation. In the past five decades, many strategies have been discovered, with communication, sanction, emotion, and norm formation being the most effective ones. Meanwhile, a personality trait called social value orientation (SVO) demonstrated its stable predictive power of human cooperation in social dilemmas. A close examination of the effects of the strategies and SVO reveals several distinct and common underlying psychological mechanisms, namely, group identity, cooperative norm, expectation of others’ cooperation, and interpersonal trust. These strategies and mechanisms have important implications for future research into social dilemmas because in the age of digitization and social distancing, new forms of social dilemmas that pose enormous challenge to human existence such as online teamwork and organization, global warming, and COVID-19, are emerging and calling for solutions.
Micro-Foundations of Institutional Logic Shifts: Entrepreneurial Action in Response to Crises
Authors: Williams Trenton Alma
Published: March 2022

Institutional logics shape how actors interpret and organize their environment. Institutional logics include society’s structural, normative, and symbolic influences that provide organizations and individuals with norms, values, assumptions, and rules that guide decision-making and action. While institutional logics influence individuals and organizations, they do not exist/form in a vacuum, but rather are instantiated in the practices and patterned behaviors of actors who act as carriers of logics in specific contexts. Given the dynamic interaction between institutional logics and individual/organizational actors, research has begun to explore the micro-level processes that influence institutional logic changes to help explain how and why those who are shaped by an institution enact changes in the very context in which they are embedded. Thus, the formation and changing of institutional logics involve precipitating action—which can include entrepreneurial action. Entrepreneurial action—especially in moments of crisis (e.g., when there is a disruptive event, natural disaster, or external feature that disturbs the status quo), can function as a micro-foundation for institutional logic shifts. An entrepreneurship model of dominant logic shifts therefore reveals how crises induce sensemaking activities that can influence shifts in how actor’s see the world, which in turn motivates the pursuit of entrepreneurial opportunities. Significant disruptions, such as environmental jolts, have a triggering effect in enabling individuals to problematize previously held beliefs and logics, allowing them to temporarily “step out of” status quo institutional logics. With prior beliefs and logics problematized, individual decision-makers become open to seeing new interpretations of their surroundings as it is and as it could be. Therefore, actors shift their dominant way of seeing the world (e.g., dominant logic) and then enact this new logic through ventures that, ultimately, can shift and alter institutional-level logics. Therefore, an entrepreneurship model of dominant logic shifts serves as an explanation for how broader institutional logics may shift as a result of the interaction between entrepreneurial action and the environment following a major disruption.
Confidence in Decision-Making
Authors: Peters Megan A.K.
Published: March 2022

The human brain processes noisy information to help make adaptive choices under uncertainty. Accompanying these decisions about incoming evidence is a sense of confidence: a feeling about whether a decision is correct. Confidence typically covaries with the accuracy of decisions, in that higher confidence is associated with higher decisional accuracy. In the laboratory, decision confidence is typically measured by asking participants to make judgments about stimuli or information (type 1 judgments) and then to rate their confidence on a rating scale or by engaging in wagering (type 2 judgments). The correspondence between confidence and accuracy can be quantified in a number of ways, some based on probability theory and signal detection theory. But decision confidence does not always reflect only the probability that a decision is correct; confidence can also reflect many other factors, including other estimates of noise, evidence magnitude, nearby decisions, decision time, and motor movements. Confidence is thought to be computed by a number of brain regions, most notably areas in the prefrontal cortex. And, once computed, confidence can be used to drive other behaviors, such as learning rates or social interaction.
The Planets in Alchemy and Astrology (Medieval and Renaissance)
Authors: Campion Nicholas
Published: March 2022

In the Middle Ages and Renaissance, alchemy and astrology shared a common language in the meanings and characters attributed to the celestial bodies, which provided a cosmic framework for understanding all terrestrial affairs. Astrology is the name given to a series of diverse practices based in the idea that the stars, planets, and other celestial phenomena possess significance and meaning for events on the Earth. In practical terms, astrology’s function was to predict the future, manage the present, and understand the past. In the Middle Ages and Renaissance, these three functions were not seen as separate, because time existed as a single entity—past, present, and future coexisted in the mind of God. Astrology assumed a link between Earth and sky in which all existence, spiritual, psychological, and physical, is interconnected. Time and space existed in a mutually dependent continuum, in which both were infused with the same qualities, represented in terms of astrological language by zodiac signs and planets. The practice of alchemy applied such assumptions to the material world, attempting to convert one metal into another, typically lead into gold. As all things were interconnected, including soul and body, the physical practice of alchemy was intimately connected with spiritual practice intended to purify the soul in preparation for its meeting with the divine.

The planets had roles in both astrology and alchemy. A planet, from the Greek planētai, meaning wanderer, is a star, a point, or source of light in the sky that constantly alters its position. This is in contrast to the so-called fixed stars, which appear to keep exactly the same position relative to each other, at least over historic periods of time.

Technical astrology largely developed in the Hellenistic, Greek-speaking world from the early third century BCE onward. With the collapse of the Roman Empire and classical learning in most of Western Europe from the 5th century, the complex astrology of the Classical world largely disappeared. It returned to Western Europe in two phases. The first phase, mainly in the 12th century, included the translation into Latin of major texts from Arabic, including those originally composed in Greek, and was accompanied by Aristotelian works that justified the use of astrology in naturalistic terms, thereby negating Christian disapproval. Alchemy was introduced into Western Europe at the same time. The second phase began mainly in the 15th century, during the Renaissance, as part of a wider revival of Classical thought encouraged by the translation of Platonic, neo-Platonic, and Hermetic works from Greek directly into Latin. By the end of the 17th century, the practice of both astrology and alchemy had largely disappeared. Astrology was confined to popular almanacs and alchemy was replaced by modern chemistry.
Lunar Exploration Missions and Environmental Discovery: Status and Progress
Authors: Kim Kyeong J.
Published: March 2022

Exploration of the Moon is currently one of the most important and interesting subjects. The Moon is considered not only a place to explore but also a place to live in preparation to explore planets beyond it. This opportunity has arisen due to a series of discoveries associated with water on the Moon during the past half century. Lunar exploration of the moon began with the flyby mission by the United States in 1959. Since then, scientific investigations of the Moon have increased understanding of the lunar geology and surface environment. Based on more than 70 lunar missions to date, a major goal is to explore how humans can live on the Moon for a long period of time to examine sustainability on the Moon. Consequently, the area of lunar science and technology is being employed to discover how in situ resources can be utilized for humans to live on the Moon and, eventually, Mars and beyond.
Archaeological Adhesives
Authors: Langejans Geeske , Aleo Alessandro , Fajardo Sebastian , Kozowyk Paul
Published: March 2022

An adhesive is any substance that bonds different materials together. This broad definition includes materials used in everything from hafted stone tools to monumental architecture. In addition, the combination of bonding, plasticity, and insolubility meant that some adhesives were exploited for waterproofing and sealing of materials, as self-adhering inlays and putties, and as paints, varnishes, and inks. Adhesives have a history of at least 200,000 years. Throughout (pre)history and around the world, people used materials, including bitumen/asphalt, carbohydrate polymers such as starches and gums, natural rubbers, mortars, proteins (from casein, soy, blood, and animal connective tissue), insect and plant resins, and tars made from various barks and woods. Adhesives thus are very diverse and have widely varying properties: they can be tacky, pliable, elastic, brittle, water-resistant, fluid, viscous, clear, dark, and much more. They are a plastic avant la lettre. These properties can and were tweaked by mixing ingredients or by further processing. In the study of archaeological adhesives, their characterization is essential and this is best done with chemical and spectroscopic methods. When larger coherent samples as opposed to single finds are analyzed, adhesive studies can provide data on past technologies, socioeconomic organizations, and environments and raw material availability. Through sourcing and mapping of ingredients and adhesive end products, travel and transfer of materials and knowledge can be illuminated. Additionally, experimental reproductions provide data on technological aspects that otherwise are lost in the archaeological record. An archaeology of adhesives can reveal the transport networks, subsistence, mobility strategies, division of labor, and technological know-how that held societies together.
Jews in the US Armed Forces
Authors: Cooperman Jessica
Published: March 2022

Jewish service in the American military parallels that of many other Americans. Jews have served in colonial militias, in the American Revolution, and in all American military conflicts since the establishment of the country. In the United States’ early years, the total number of Jewish military personnel, like the Jewish population of the country as a whole, was very small. As the size of the American Jewish population grew during the late 19th and early 20th centuries, however, so did the number of Jews who served in the American Armed Forces. Jews responded to the country’s calls to arms alongside other Americans, even as they faced challenges that differentiated them from their compatriots. Like other racial, ethnic, and religious minority groups, Jews had to struggle against prejudices in the military, and like other immigrant communities, they have sometimes had to balance patriotism against transnational ties. Jews in the United States, however, always understood military service as part of the bargain of modern citizenship. They volunteered for service and responded to calls for conscription in order to fulfill their responsibilities as citizens, and they used military service both to express their commitment to the United States and to assert their rights as equal members of American society.
A Likely False Travel Account to Northeastern Brazil in the 16th Century
Authors: de Souza Filho José Alexandrino
Published: March 2022

It is known that the French cosmographer André Thevet (1516–1592) used to appropriate materials produced by third parties to enrich his own writings and travel narratives. He firmly claims to have made two expeditions to Brazil, but only one of them is proven (the foundation of a French colony in Guanabara Bay, in 1555). The other expedition includes a trip to Northeastern Brazil in the text, but this claim is probably false. There is no way to positively affirm or deny the hypothesis of the two expeditions, because there is no evidence. However, the analysis of the documents of the “northeastern chapters” strongly suggests that they were written based on the portolan prepared by the French cartographer Jacques de Vau de Claye, at the request of Philippe Strozzi, within the scope of the crisis of succession to the Portuguese throne, that is, between 1578 and 1582. The motive for rewriting the same experience some thirty years later (1588), as History of the two travels made by André Thevet to the Southern and Western Indies, seems to come from the theft of a manuscript written by René de Laudonnière, chief of a French former colony in Florida, lent by Thevet himself to the English compiler Richard Hakluyt, who published it without authorization, on behalf of a French friend, Martin Basanier. Regardless of whether or not the cosmographer’s trip to Northeastern Brazil is true, one can read Thevet’s latest travel account as a kind of literary memorial of the (unsuccessful) experiences of French colonization on the American continent, whether in Canada, Florida, or Brazil.
Statin Medications and Amyotrophic Lateral Sclerosis Incidence and Mortality
Authors: Weisskopf Marc G , Levy Joseph , Dickerson Aisha S , Paganoni Sabrina , Leventer-Roberts Maya
Published: March 2022

Studies of statins and amyotrophic lateral sclerosis (ALS) incidence and survival have had conflicting findings possibly related to difficulties with confounding by indication. We considered potency of statins used and duration of use to explore confounding by indication. Within the Clalit Health Services in Israel, we identified 948 ALS case patients from 2004 through 2017 and matched them with 1,000 control subjects each. Any statin use up to 3 years before ALS onset was not associated with ALS incidence but was associated with a reduced hazard ratio (HR) for death. Odds of ALS did not vary by statin potency, but use of only lower-potency statins was associated with longer survival (HR = 0.82, 95% CI: 0.68, 0.98), whereas the association with higher-potency statins was null compared with those case patients who did not use statins. However, duration of statin use appeared to account for these findings. Those who used statins only up to 3 years had longer survival (HR = 0.77, 95% CI: 0.61, 0.96) than did case patients who did not use statins, but those who used statins for >3 years did not. Although other explanations are possible, these findings could suggest a protective effect of statins on ALS survival that is partially masked by a worse prognosis from underlying reasons for taking statins that deserves further exploration.
LIQUORICE: detection of epigenetic signatures in liquid biopsies based on whole-genome sequencing data
Authors: Peneder Peter , Bock Christoph , Tomazou Eleni M
Published: March 2022

Fragmentation patterns of cell-free DNA reflect the chromatin structure of the cells from which these fragments are derived. Nucleosomes protect the DNA from fragmentation, resulting in decreased sequencing coverage in regions of open chromatin. LIQUORICE is a user-friendly software tool that takes aligned whole-genome sequencing data as input and calculates bias-corrected coverage signatures for predefined, application-specific sets of genomic regions. The tool thereby enables a blood-based analysis of cell death in the body, and it provides a minimally invasive assessment of tumor chromatin states and cell-of-origin. With user-defined sets of regions that exhibit tissue-specific or disease-specific open chromatin, LIQUORICE can be applied to a wide range of detection, classification and quantification tasks in the analysis of liquid biopsies.

Availability and implementation

LIQUORICE is freely and openly available as a Python package and command-line tool for UNIX-based systems from bioconda. Documentation, examples and usage instructions are provided at http://liquorice.computational-epigenetics.org.

Supplementary information

Supplementary data are available at Bioinformatics Advances online.
A comprehensive evaluation of regression-based drug responsiveness prediction models, using cell viability inhibitory concentrations (IC50 values)
Authors: Park Aron , Joo Minjae , Kim Kyungdoc , Son Won-Joon , Lim GyuTae , Lee Jinhyuk , Kim Jung Ho , Lee Dae Ho , Nam Seungyoon
Published: March 2022

Motivation

Predicting drug response is critical for precision medicine. Diverse methods have predicted drug responsiveness, as measured by the half-maximal drug inhibitory concentration (IC50), in cultured cells. Although IC50s are continuous, traditional prediction models have dealt mainly with binary classification of responsiveness. However, since there are few regression-based IC50 predictions, comprehensive evaluations of regression-based IC50 prediction models, including machine learning (ML) and deep learning (DL), for diverse data types and dataset sizes, have not been addressed.

Results

Here, we constructed 11 input data settings, including multi-omics settings, with varying dataset sizes, then evaluated the performance of regression-based ML and DL models to predict IC50s. DL models considered two convolutional neural network architectures: CDRScan and residual neural network (ResNet). ResNet was introduced in regression-based DL models for predicting drug response for the first time. As a result, DL models performed better than ML models in all the settings. Also, ResNet performed better than or comparable to CDRScan and ML models in all settings.

Availability and implementation

The data underlying this article are available in GitHub at https://github.com/labnams/IC50evaluation.

Supplementary information

Supplementary data are available at Bioinformatics online.
Fast and accurate inference of gene regulatory networks through robust precision matrix estimation
Authors: Passemiers Antoine , Moreau Yves , Raimondi Daniele
Published: March 2022

Motivation

Transcriptional regulation mechanisms allow cells to adapt and respond to external stimuli by altering gene expression. The possible cell transcriptional states are determined by the underlying gene regulatory network (GRN), and reliably inferring such network would be invaluable to understand biological processes and disease progression.

Results

In this article, we present a novel method for the inference of GRNs, called PORTIA, which is based on robust precision matrix estimation, and we show that it positively compares with state-of-the-art methods while being orders of magnitude faster. We extensively validated PORTIA using the DREAM and MERLIN+P datasets as benchmarks. In addition, we propose a novel scoring metric that builds on graph-theoretical concepts.

Availability and implementation

The code and instructions for data acquisition and full reproduction of our results are available at https://github.com/AntoinePassemiers/PORTIA-Manuscript. PORTIA is available on PyPI as a Python package (portia-grn).

Supplementary information

Supplementary data are available at Bioinformatics online.
Extending prediction models for use in a new target population with failure time outcomes
Authors: Steingrimsson Jon A
Published: March 2022

Prediction models are often built and evaluated using data from a population that differs from the target population where model-derived predictions are intended to be used in. In this article, we present methods for evaluating model performance in the target population when some observations are right censored. The methods assume that outcome and covariate data are available from a source population used for model development and covariates, but no outcome data, are available from the target population. We evaluate the finite sample performance of the proposed estimators using simulations and apply the methods to transport a prediction model built using data from a lung cancer screening trial to a nationally representative population of participants eligible for lung cancer screening.
Cumulative Antibiotic Exposure in the First 5 Years of Life: Estimates for 45 Low- and Middle-Income Countries From Demographic and Health Survey Data
Authors: Levine Gillian A , Bielicki Julia , Fink Günther
Published: March 2022

Background

Estimates of the total cumulative exposure to antibiotics of children in low-resource settings, and the source of these treatments, are limited.

Methods

We estimated the average number of antibiotic treatments children received in the first 5 years of life in 45 low- and middle-income countries (LMICs) using Demographic and Health Survey data. The 2-week point prevalence of fever, diarrhea, or cough and antibiotic treatment for these illnesses were estimated for ages 0–59 months and aggregated to estimate cumulative illness and antibiotic treatment for each country. We estimated treatment rates and contribution to total antibiotic use attributable to medical care, informal care, and self-medication.

Results

Forty-five countries contributed 438 140 child-observations. The proportion of illness episodes treated with antibiotics ranged from 10% (95% confidence interval [CI], 9%–12%]) in Niger to 72% (95% CI, 69%–75%) in Jordan. A mean of 42.7% (95% CI, 42.1%–43.3%) of febrile and 32.9% of nonfebrile (95% CI, 32.4%–33.5%) illness episodes received antibiotics. In their first 5 years, we estimate children received 18.5 antibiotic treatments on average (interquartile range [IQR], 11.6–24.6) in LMICs. Cumulative antibiotic exposure ranged from 3.7 treatments in Niger (95% CI, 2.8%–4.6%) to 38.6 treatments in the Democratic Republic of Congo (95% CI, 34.7%–42.4%). A median of 9.0% of antibiotic treatments was attributable to informal care (IQR, 5.9%–21.2%), and 16.9% to self-medication (IQR, 9.5%–26.2%).

Conclusions

Childhood antibiotic exposure is high in some LMICs, with considerable variability. While access to antibiotics for children is still not universal, important opportunities for reducing excess use also exist, particularly with respect to the informal care sector and self-medication.
Impact of the COVID-19 pandemic on contact tracing of patients with pulmonary tuberculosis
Authors: Godoy Pere , Parrón Ignasi , Barrabeig Irene , Caylà Joan A , Clotet Laura , Follia Núria , Carol Monica , Orcau Angels , Alsedà Miquel , Ferrús Gloria , Plans Pere , Jane Mireia , Millet Joan-Pau , Domínguez Angela ,   the Transmission of Tuberculosis in Catalonia (Spain) Working Group, Alsedà Miquel , Barrabeig Irene , Carol Monica , Caylà Joan , Clotet Laura , Domínguez Angela , Ferrús Gloria , Follia Núria , Godoy Pere , Jané Mireia , Minguell Sofia , Millet Joan Pau , Orcau Angels , Parrón Ignasi , Plans Pere , Ros Miriam , Sabater Maria , Sala Maria-Rosa , Toledo Diana
Published: March 2022

Background

The COVID-19 pandemic could have negative effects on tuberculosis (TB) control. The objective was to assess the impact of the pandemic in contact tracing, TB and latent tuberculosis infection (LTBI) in contacts of patients with pulmonary TB in Catalonia (Spain).

Methods

Contact tracing was carried out in cases of pulmonary TB detected during 14 months in the pre-pandemic period (1 January 2019 to 28 February 2020) and 14 months in the pandemic period (1 March 2020 to 30 April 2021). Contacts received the tuberculin skin test and/or interferon gamma release assay and it was determined whether they had TB or LTBI. Variables associated with TB or LTBI in contacts (study period and sociodemographic variables) were analyzed using adjusted odds ratio (aOR) and the 95% confidence intervals (95% CI).

Results

The pre-pandemic and pandemic periods showed, respectively: 503 and 255 pulmonary TB reported cases (reduction of 50.7%); and 4676 and 1687 contacts studied (reduction of 36.1%). In these periods, the proportion of TB cases among the contacts was 1.9% (84/4307) and 2.2% (30/1381) (P = 0.608); and the proportion of LTBI was 25.3% (1090/4307) and 29.2% (403/1381) (P < 0.001). The pandemic period was associated to higher LTBI proportion (aOR = 1.3; 95% CI 1.1–1.5), taking into account the effect on LTBI of the other variables studied as sex, age, household contact and migrant status.

Conclusions

COVID-19 is affecting TB control due to less exhaustive TB and LTBI case detection. An increase in LTBI was observed during the pandemic period. Efforts should be made to improve detection of TB and LTBI among contacts of TB cases.
Response to leucine in Schizosaccharomyces pombe (fission yeast)
Authors: Ohtsuka Hokuto , Shimasaki Takafumi , Aiba Hirofumi
Published: March 2022

Leucine (Leu) is a branched-chain, essential amino acid in animals, including humans. Fungi, including the fission yeast Schizosaccharomyces pombe, can biosynthesize Leu, but deletion of any of the genes in this biosynthesis leads to Leu auxotrophy. In this yeast, although a mutation in the Leu biosynthetic pathway, leu1-32, is clearly inconvenient for this species, it has increased its usefulness as a model organism in laboratories worldwide. Leu auxotrophy produces intracellular responses and phenotypes different from those of the prototrophic strains, depending on the growing environment, which necessitates a certain degree of caution in the analysis and interpretation of the experimental results. Under amino acid starvation, the amino acid-auxotrophic yeast induces cellular responses, which are conserved in higher organisms without the ability of synthesizing amino acids. This mini-review focuses on the roles of Leu in S. pombe and discusses biosynthetic pathways, contribution to experimental convenience using a plasmid specific for Leu auxotrophic yeast, signaling pathways, and phenotypes caused by Leu starvation. An accurate understanding of the intracellular responses brought about by Leu auxotrophy can contribute to research in various fields using this model organism and to the understanding of intracellular responses in higher organisms that cannot synthesize Leu.
Patent protection and foreign R&D investment location choices: inventor mobility and policy convergence
Authors: Park Jinhyuck (Joseph) , Belderbos René
Published: March 2022

We suggest two boundary conditions for the positive role of patent protection in attracting inward foreign R&D investments. Patent protection is less effective in limiting the leakage of nonpatented knowledge through interfirm mobility of employees, and a gradual strengthening of patent protection worldwide diminishes its effect as countries get closer to the intellectual property rights (IPR) frontier. We provide evidence in an empirical analysis of 3393 multinational firms’ R&D location choices for 8015 greenfield R&D investments in 105 (potential) host countries, during 2003–2014. The relationship between R&D investment location choices and IPR protection is subject to declining marginal effects and negatively moderated by inventor mobility.
Adaptive regularization minimization algorithms with nonsmooth norms
Authors: Gratton S , Toint Ph L
Published: March 2022

An adaptive regularization algorithm (AR$1p$GN) for unconstrained nonlinear minimization is considered, which uses a model consisting of a Taylor expansion of arbitrary degree and regularization term involving a possibly nonsmooth norm. It is shown that the nonsmoothness of the norm does not affect the ${\mathcal {O}}(\epsilon _1^{-(p+1)/p})$ upper bound on evaluation complexity for finding first-order $\epsilon _1$-approximate minimizers using $p$ derivatives, and that this result does not hinge on the equivalence of norms in $\mathbb {R}^n$. It is also shown that, if $p=2$, the bound of ${\mathcal {O}}(\epsilon _2^{-3})$ evaluations for finding second-order $\epsilon _2$-approximate minimizers still holds for a variant of AR$1p$GN named AR2GN, despite the possibly nonsmooth nature of the regularization term. Moreover, the adaptation of the existing theory for handling the nonsmoothness results is an interesting modification of the subproblem termination rules, leading to an even more compact complexity analysis. In particular, it is shown when the Newton’s step is acceptable for an adaptive regularization method. The approximate minimization of quadratic polynomials regularized with nonsmooth norms is then discussed, and a new approximate second-order necessary optimality condition is derived for this case. A specialized algorithm is then proposed to enforce first- and second-order conditions that are strong enough to ensure the existence of a suitable step in AR$1p$GN (when $p=2$) and in AR2GN, and its iteration complexity is analyzed. A final section discusses how practical approximate curvature measures may lead to weaker second-order optimality guarantees.
“The Empire that Shaka Zulu was Unable to Bring About”: Ethnicizing Sovereignty in Apartheid South Africa, 1959–1970
Authors: Parcells Ashley
Published: March 2022

Arrangements of sovereignty in Africa fundamentally shifted during the era of decolonization, temporarily bringing about political possibilities beyond empire or nation-state. The apartheid state drew on this “federal moment” and attempted to save white minority rule by creating ethnically defined self-governing “homelands,” or bantustans, that could be fashioned as “independent” nation-states within a Southern African confederation. This article examines the ethnicization of sovereignty in the planning of KwaZulu, a bantustan for Zulu people. Rather than solely focusing on the central state, it explores how bureaucrats, royal family members, and other African leaders made claims to the boundaries of ethnicity and the proper arrangements of power. Initially, the government assumed that the Zulu homeland could be built atop the former Zulu kingdom. The planned bantustan, however, included both territory and populations that never recognized the Zulu monarchy before colonialism. As Zulu royal allies advocated for an expansive bantustan under a re-empowered monarchy, ethnologists and other bureaucrats clashed over the geographic limits of Zuluness and the relationship between the Zulu king and Africans across the Natal province. As the government retreated from its plan to empower the monarchy, Mangosuthu Buthelezi, an influential royal cousin, used competing historical claims to marginalize the royal house and position himself as the rightful hereditary leader of both the future bantustan and the Zulu kingdom. Ideas of a Zulu ethnic sovereignty that would shape the late apartheid period and democratic transition, I argue, initially emerged through these contingent struggles in the 1960s over territory, populations, and authority.
On the high-energy proton regular acceleration in the Fermi bubbles
Authors: Istomin Ya N , Gunya A A
Published: March 2022

We propose a model of the global structure of the electromagnetic fields in the Fermi bubbles (FBs), which makes possible the proton regular acceleration up to ultrahigh energies. The poloidal and the toroidal magnetic fields, as well as the radial electric field, are found to have a structure similar to fields that exist in jets ejected out from active galactic nuclei. A powerful source of relativistic particles observed in the centre of the Galaxy and associated with the rotating supermassive black hole Sgr A* can energize the FB and keep it active for a long time. The absence of accretion on to a black hole (BH) and thus the absence of a relativistic jet does not mean that there is no loss of rotational energy of BH. In the case of FB, the energy lost by a BH can keep the FB activity going. The regular FB structure could be formed by inheritance from a relativistic jet that presumably existed in the active past of the Galaxy 107 yr ago, or by processes near the Galactic Centre existing during the entire life cycle of the Galaxy. The acceleration of protons in electromagnetic fields of FB is found up to energies Emax ≃ 1017 eV, which explains the observed radiation of FB in the gamma range, as well as the emission of high-energy neutrinos.
Legacy Survey of Space and Time cadence strategy evaluations for active galactic nucleus time-series data in Wide-Fast-Deep field
Authors: Sheng Xinyue , Ross Nicholas , Nicholl Matt
Published: March 2022

Machine learning is a promising tool to reconstruct time-series phenomena, such as variability of active galactic nuclei (AGNs), from sparsely sampled data. Here, we use three Continuous Autoregressive Moving Average (CARMA) representations of AGN variability – the Damped Random Walk (DRW) and (over/under)Damped Harmonic Oscillator – to simulate 10-yr AGN light curves as they would appear in the upcoming Vera Rubin Observatory Legacy Survey of Space and Time (LSST), and provide a public tool to generate these for any survey cadence. We investigate the impact on AGN science of five proposed cadence strategies for LSST’s primary Wide-Fast-Deep (WFD) survey. We apply for the first time in astronomy a novel Stochastic Recurrent Neural Network (SRNN) algorithm to reconstruct input light curves from the simulated LSST data, and provide a metric to evaluate how well SRNN can help recover the underlying CARMA parameters. We find that the light-curve reconstruction is most sensitive to the duration of gaps between observing season, and that of the proposed cadences, those that change the balance between filters, or avoid having long gaps in the g band perform better. Overall, SRNN is a promising means to reconstruct densely sampled AGN light curves and recover the long-term structure function of the DRW process (SF∞) reasonably well. However, we find that for all cadences, CARMA/SRNN models struggle to recover the decorrelation time-scale (τ) due to the long gaps in survey observations. This may indicate a major limitation in using LSST WFD data for AGN variability science.