Biology Literature Research Articles

Approximations of Piecewise Deterministic Markov Processes and their convergence properties

Piecewise deterministic Markov processes (PDMPs) are a class of stochastic processes with applications in several fields of applied mathematics spanning from mathematical modelling of physical phenomena to computational methods. A PDMP is specified by three characteristic quantities: the deterministic motion, the law of the random event times, and the jump kernels. The applicability of PDMPs to real world scenarios is currently limited by the fact that these processes can be simulated only when these three characteristics of the process can be simulated exactly. In order to overcome this problem, we introduce discretisation schemes for PDMPs which make their approximate simulation possible. In particular, we design both first order and higher order schemes that rely on approximations of one or more of the three characteristics. For the proposed approximation schemes we study both pathwise convergence to the continuous PDMP as the step size converges to zero and convergence in law to the invariant measure of the PDMP in the long time limit. Moreover, we apply our theoretical results to several PDMPs that arise from the computational statistics and mathematical biology literature.

Nonlinear multi-objective flux balance analysis of the Warburg Effect

Due to its implication in cancer treatment, the Warburg Effect has received extensive in silico investigation. Flux Balance Analysis (FBA), based on constrained optimization, was successfully applied in the Warburg Effect modelling. Yet, the assumption that cell types have one invariant cellular objective severely limits the applicability of the previous FBA models. Meanwhile, we note that cell types with different objectives show different extents of the Warburg Effect. To extend the applicability of the previous model and model the disparate cellular pathway preferences in different cell types, we built a Nonlinear Multi-Objective FBA (NLMOFBA) model by including three key objective terms (ATP production rate, lactate generation rate and ATP yield) into one objective function through linear scalarization. By constructing a cellular objective map and iteratively varying the objective weights, we showed disparate cellular pathway preferences manifested by different cell types driven by their unique cellular objectives, and we gained insights about the causal relationship between cellular objectives and the Warburg Effect. In addition, we obtained other biologically consistent results by using our NLMOFBA model. For example, augmented with the constraint associated with inefficient mitochondria function, low oxygen availability, or limited substrate, NLMOFBA predicts cellular pathways supported by the biology literature. Collectively, our NLMOFBA model can help build a complete understanding towards the Warburg Effect in different cell types. Finally, we investigated the impact of glutaminolysis, an important pathway related to glycolysis, on the occurrence of the Warburg Effect by using linear programming.

Discovering Content through Text Mining for a Synthetic Biology Knowledge System.

Scientific articles contain a wealth of information about experimental methods and results describing biological designs. Due to its unstructured nature and multiple sources of ambiguity and variability, extracting this information from text is a difficult task. In this paper, we describe the development of the synthetic biology knowledge system (SBKS) text processing pipeline. The pipeline uses natural language processing techniques to extract and correlate information from the literature for synthetic biology researchers. Specifically, we apply named entity recognition, relation extraction, concept grounding, and topic modeling to extract information from published literature to link articles to elements within our knowledge system. Our results show the efficacy of each of the components on synthetic biology literature and provide future directions for further advancement of the pipeline.

Words matter: a systematic review of communication in non-native aquatic species literature

How scientists communicate can influence public viewpoints on invasive species. In the scientific literature, some invasion biologists adopt neutral language, while others use more loaded language, for example by emphasizing the devastating impacts of invasive species and outlining consequences for policy and practice. An evaluation of the use of language in the invasion biology literature does not exist, preventing us from understanding which frames are used and whether there are correlations between message framing in scientific papers and local environmental impacts associated with invasive species. Thus, we conducted a systematic literature review of 278 peer-reviewed articles published from 2008–2018 to understand communication styles adopted by social and natural scientists while reporting on aquatic non-native species research. Species-centered frames (45%) and human-centered frames (55%) were adopted to nearly equal degrees. Negative valence was dominant in that 81.3% of articles highlighted the negative risks and impacts of invasive species. Additionally, the use of terminology was found to broadly align with the stage of invasion, in that “invasive” was most commonly used except when the research was conducted at early stages of invasion, when “non-native” was most commonly used. Terminology use therefore enables readers of scientific papers to infer the status and severity of ongoing invasions. Given that science communication within the peer-reviewed literature affects public understanding of research outcomes, these findings provide an important point of reflection for researchers.

An Invitation to Dance

An Invitation to Dance

Testing the reproducibility and robustness of the cancer biology literature by robot.

Scientific results should not just be ‘repeatable’ (replicable in the same laboratory under identical conditions), but also ‘reproducible’ (replicable in other laboratories under similar conditions). Results should also, if possible, be ‘robust’ (replicable under a wide range of conditions). The reproducibility and robustness of only a small fraction of published biomedical results has been tested; furthermore, when reproducibility is tested, it is often not found. This situation is termed ‘the reproducibility crisis', and it is one the most important issues facing biomedicine. This crisis would be solved if it were possible to automate reproducibility testing. Here, we describe the semi-automated testing for reproducibility and robustness of simple statements (propositions) about cancer cell biology automatically extracted from the literature. From 12 260 papers, we automatically extracted statements predicted to describe experimental results regarding a change of gene expression in response to drug treatment in breast cancer, from these we selected 74 statements of high biomedical interest. To test the reproducibility of these statements, two different teams used the laboratory automation system Eve and two breast cancer cell lines (MCF7 and MDA-MB-231). Statistically significant evidence for repeatability was found for 43 statements, and significant evidence for reproducibility/robustness in 22 statements. In two cases, the automation made serendipitous discoveries. The reproduced/robust knowledge provides significant insight into cancer. We conclude that semi-automated reproducibility testing is currently achievable, that it could be scaled up to generate a substantive source of reliable knowledge and that automation has the potential to mitigate the reproducibility crisis.

The coherence time of sunlight in the context of natural and artificial light-harvesting

The suggestion that quantum coherence might enhance biological processes such as photosynthesis is not only of fundamental importance but also leads to hopes of developing bio-inspired ‘green’ quantum technologies that mimic nature. A key question is how the timescale of coherent processes in molecular systems compare to that of the driving light source—the Sun. Across the quantum biology literature on light-harvesting, the coherence time quoted for sunlight spans about two orders of magnitude, ranging from 0.6 to ‘10s’ of femtoseconds. This difference can potentially be significant in deciding whether the induced light-matter coherence is long enough to affect dynamical processes following photoexcitation. Here we revisit the historic calculations of sunlight coherence starting with the black-body spectrum and then proceed to provide values for the more realistic case of atmospherically filtered light. We corroborate these values with interferometric measurements of the complex degree of temporal coherence from which we calculate the coherence time of atmospherically filtered sunlight as 1.12pm {0.04},{hbox { fs}}, as well as the coherence time in a chlorophyll analogous filtered case as 4.87pm {0.21},{hbox { fs}}.

Hierarchical Bayesian integrated model for estimating migratory bird harvest in Canada

AbstractThe Canadian Wildlife Service (CWS) requires reliable estimates of the harvest of migratory game birds, including waterfowl, to effectively manage populations of these hunted species. The National Harvest Survey is an annual survey of hunters who purchase Canada's mandatory migratory game bird hunting permit, integrating information from a survey of hunting activity with information from a separate survey of species composition in the harvest. We used these survey data to estimate the number of birds harvested for each species and hunting activity metrics (e.g., number of active hunters, days spent hunting). The analytical methods used to generate these estimates have not changed since the survey was first designed in the early 1970s. We describe a new hierarchical Bayesian integrated model, which replaces the series of ratio estimators that comprised the old model. We are using this new model to generate estimates for migratory bird harvests as of the 2019–2020 hunting season, and to generate updated estimates for all earlier years. The hierarchical Bayesian model uses over‐dispersed Poisson distributions to model mean hunter activity and harvest (zero‐inflated Poisson and zero‐truncated Poisson, respectively). It also includes multinomial distributions to model some key components (e.g., variation in harvest across periods of the hunting season, the species composition of the harvest within each of those periods, the age and sex composition in the harvests of a given species). We estimated the parameters of the Poisson and the multinomial distributions for each year as random effects using first‐difference time‐series. This time‐series component allows the model to share information across years and reduces the sensitivity of the estimates to annual sampling noise. The new model estimates are generally very similar to those from the old model, particularly for the species that occur most commonly in the harvest, so the results do not suggest any major changes to harvest management decisions and regulations. Estimates for all species from the new model are more precise and less susceptible to annual sampling error, particularly for species that occur less commonly in the harvest (e.g., sea ducks, other species of conservation concern). This new model, with its hierarchical Bayesian framework, will also facilitate future improvements and elaborations, allowing the incorporation of prior information from the rich literature and knowledge in game bird management and biology.

Student stress in focus: Short-term fixes and long-term pedagogical change in business school curriculum

This paper explores course design and curriculum decisions made to acknowledge the contextual and personal stressors experienced by business school students. Business school professors have an opportunity to promote an active orientation to stress management, teach stress management skills, and link these practices to students’ lives beyond academia. We use a lens of intersectionality to understand the human experience of stress and coping, connecting research from the management, psychology, biology, and sociology literatures to reveal a more complicated picture of stress for students in the 2020–2021 academic year. We then examine recent pedagogical changes in two business courses, Personal and Professional Development I for first-year students and Organizational Behaviour for second year students, as we discuss how many stressors can be addressed at the course-design level (through principles of simplicity, predictability, and consistency) as well as through module design (by creating community and connections to services, societies, and supports). Rather than viewing pandemic-induced course modifications as a temporary “fix” for the current situation, professors can use this time to re-imagine the importance of student stress in the learning process. We offer recommendations for long-term change to business school curriculum to accomplish this goal.

Opiine parasitoids (Hymenoptera: Braconidae) and biological control of fruit flies (Diptera: Tephritidae) in Australia: Past, present and future

AbstractOpiine braconids are parasitoids of the immature stages of frugivorous tephritids. The female wasp lays her eggs into the eggs or larvae of the fruit fly host, where the immature wasp develops before emerging as a next‐generation adult from the now dead host pupal case. In support of a new generation of Australian fruit fly parasitoid research, this paper comprehensively reviews what is known about the Australian fruit fly infesting opiines. Based on the most recent taxonomic revision 11 fruit fly infesting opiine species are documented to occur in Australia, but we consider as doubtful the record forDiachasmimorpha longicaudataand consider the record forFopius illusoriusto be tentative without further collections. We identify that the systematics and taxonomy of the Australian native fruit fly infesting opiines are in urgent need of further work. The history of fruit fly biological control in Australia is comprehensively reviewed, including the export of native Australian opiines for fruit fly control elsewhere in the world. Australia was actively involved in three major classical biological control programmes against fruit flies from the turn of the 1900s until the mid‐1960s. Despite the introduction of 11 opiine species, plus numerous other natural enemies, onlyFopius arisanusestablished in eastern Australia, where in South‐east Queensland it can now cause between 30 and 40% mean parasitism. In addition to the exoticF. arisanus, the native speciesDiachasmimorpha kraussiiandDiachasmimorpha tryonialso cause fruit fly parasitism in agriculturally important crops: both species have also been liberated widely outside of Australia for fruit fly control. Other Australian opiines have not been reared from flies infesting commercial crops and appear biologically restricted to the fruits and environs of Australian east‐coast rainforests. The biology literature forD. tryoniandD. kraussiiis comprehensively reviewed, while forF. arisanus, already reviewed elsewhere, key literature only is covered. Forward looking, we consider the potential for inoculative or inundative releases of opiines in areas where they do not currently occur to be good, while conservation biological control may help to increase the impacts of parasitoids in areas where they are already established.

Taxonomic Chauvinism in Pesticide Ecotoxicology.

Taxonomic Chauvinism in Pesticide Ecotoxicology.

Morphological Description of the Esophagus in the Mallard Duck (Anas platyrhynchos)

The esophageal morphology of Mallard Duck (Anas platyrhynchos) was investigated to fill the dearthof information on the morphology of esophagus from available literature and help in understandingits digestive tract biology. The esophagus is long and highly distensible, musculomembranous tubularshape, it began from oropharyngeal cavity and terminated on the proventriculus. The esophagus wasdivided into two regions are represented by cervical part and Thoracic part, the crop was absent.Internal lining of the esophagus consisted of un- branched straight longitudinal folds the mean lengthof esophagus was about 25 cm; it was wider in the anterior part than the posterior part.

Oxygen Deficient (OD) Combustion and Metabolism: Allometric Laws of Organs and Kleiber’s Law from OD Metabolism?

The biology literature presents allometric relations for the specific metabolic rate (SMRk) of an organ k of mass mk within the body of mass mB: SMRk ∝ mBfk (body mass allometry, BMA). Wang et al. used BMA, summed-up energy from all organs and validated Kleiber’s law of the whole body: SMRM ∝ mBb’, b’ = −0.25. The issues raised in biology are: (i) why fk and b’ < 0, (ii) how do the organs adjust fk to yield b’? The current paper presents a “system” approach involving the field of oxygen deficient combustion (ODC) of a cloud of carbon particles and oxygen deficient metabolism (ODM), and provides partial answers by treating each vital organ as a cell cloud. The methodology yields the following: (i) a dimensionless “group” number GOD to indicate extent of ODM, (ii) SMRk of an organ in terms of the effectiveness factor; (iii) curve fitting of the effectiveness factor to yield the allometric exponents for the organ mass-based allometric laws (OMA); (iv) validation of the results with data from 111 biological species (BS) with mB ranging from 0.0075 to 6500 kg. The “hypoxic” condition at organ level, particularly for COVID-19 patients, and the onset of cancer and virus multiplication are interpreted in terms of ODM and glycolysis.

Platform technologies for regenerative endodontics from multifunctional biomaterials to tooth-on-a-chip strategies.

The aim of this review is to highlight recent progress in the field of biomaterials-mediated dental pulp tissue engineering. Specifically, we aim to underscore the critical design criteria of biomaterial platforms that are advantageous for pulp tissue engineering, discuss models for preclinical evaluation, and present new and innovative multifunctional strategies that hold promise for clinical translation. The current article is a comprehensive overview of recent progress over the last 5 years. In detail, we surveyed the literature in regenerative pulp biology, including novel biologic and biomaterials approaches, and those that combined multiple strategies, towards more clinically relevant models. PubMed searches were performed using the keywords: "regenerative dentistry," "dental pulp regeneration," "regenerative endodontics," and "dental pulp therapy." Significant contributions to the field of regenerative dentistry have been made in the last 5 years, as evidenced by a significant body of publications. We chose exemplary studies that we believe are progressive towards clinically translatable solutions. We close this review with an outlook towards the future of pulp regeneration strategies and their clinical translation. Current clinical treatments lack functional and predictable pulp regeneration and are more focused on the treatment of the consequences of pulp exposure, rather than the restoration of healthy dental pulp. Clinically, there is great demand for bioinspired biomaterial strategies that are safe, efficacious, and easy to use, and clinicians are eager for their clinical translation. In particular, we place emphasis on strategies that combine favorable angiogenesis, mineralization, and functional tissue formation, while limiting immune reaction, risk of microbial infection, and pulp necrosis.

Isolating the Role of Corticosterone in the Hypothalamic-Pituitary-Gonadal Transcriptomic Stress Response

Investigation of the negative impacts of stress on reproduction has largely centered around the effects of the adrenal steroid hormone, corticosterone (CORT), and its influence on a system of tissues vital for reproduction—the hypothalamus of the brain, the pituitary gland, and the gonads (the HPG axis). Research on the action of CORT on the HPG axis has predominated the stress and reproductive biology literature, potentially overshadowing other influential mediators. To gain a more complete understanding of how elevated CORT affects transcriptomic activity of the HPG axis, we experimentally examined its role in male and female rock doves (Columba livia). We exogenously administrated CORT to mimic circulating levels during the stress response, specifically 30 min of restraint stress, an experimental paradigm known to increase circulating CORT in vertebrates. We examined all changes in transcription within each level of the HPG axis as compared to both restraint-stressed birds and vehicle-injected controls. We also investigated the differential transcriptomic response to CORT and restraint-stress in each sex. We report causal and sex-specific effects of CORT on the HPG transcriptomic stress response. Restraint stress caused 1567 genes to uniquely differentially express while elevated circulating CORT was responsible for the differential expression of 304 genes. Only 108 genes in females and 8 in males differentially expressed in subjects that underwent restraint stress and those who were given exogenous CORT. In response to elevated CORT and restraint-stress, both sexes shared the differential expression of 5 genes, KCNJ5, CISH, PTGER3, CEBPD, and ZBTB16, all located in the pituitary. The known functions of these genes suggest potential influence of elevated CORT on immune function and prolactin synthesis. Gene expression unique to each sex indicated that elevated CORT affected more gene transcription in females than males (78 genes versus 3 genes, respectively). To our knowledge, this is the first study to isolate the role of CORT in HPG genomic transcription during a stress response. We present an extensive and openly accessible view of the role corticosterone in the HPG transcriptomic stress response. Because the HPG system is well conserved across vertebrates, these data have the potential to inspire new therapeutic strategies for reproductive dysregulation in multiple vertebrate systems, including our own.

Artificial intelligence applied to musculoskeletal oncology: a systematic review.

Developments in artificial intelligence have the potential to improve the care of patients with musculoskeletal tumors. We performed a systematic review of the published scientific literature to identify the current state of the art of artificial intelligence applied to musculoskeletal oncology, including both primary and metastatic tumors, and across the radiology, nuclear medicine, pathology, clinical research, and molecular biology literature. Through this search, we identified 252 primary research articles, of which 58 used deep learning and 194 used other machine learning techniques. Articles involving deep learning have mostly involved bone scintigraphy, histopathology, and radiologic imaging. Articles involving other machine learning techniques have mostly involved transcriptomic analyses, radiomics, and clinical outcome prediction models using medical records. These articles predominantly present proof-of-concept work, other than the automated bone scan index for bone metastasis quantification, which has translated to clinical workflows in some regions. We systematically review and discuss this literature, highlight opportunities for multidisciplinary collaboration, and identify potentially clinically useful topics with a relative paucity of research attention. Musculoskeletal oncology is an inherently multidisciplinary field, and future research will need to integrate and synthesize noisy siloed data from across clinical, imaging, and molecular datasets. Building the data infrastructure for collaboration will help to accelerate progress towards making artificial intelligence truly useful in musculoskeletal oncology.

Morphologic Characteristics and Length-Weight Relationships of Sciaena umbra (Linnaeus, 1758) in the Black Sea Coast

In this study, the morphological characteristics and length-weight relationships of Sciaena umbra (Linnaeus, 1758) belonging to the Sciaenidae family, which is represented by five species in the Mediterranean basin and two species in the Black Sea, were investigated. Sampling was carried out in the Black Sea Region (Samsun, Ordu, Giresun, Trabzon) between March 2019 and February 2020. A total 54 of individuals were sampled and 15 different metric measurements were performed in each sample to determine their morphological characteristics. The mean total length and weight were estimated as 357.8 mm (117-580) and 845.3 g (16.4-2485.1), respectively. Total length was compared with morphometric characters and the lowest ratio was found with eye diameter (4.3%) and the highest ratio was with anal distance (59.9%). In the relation between the total length and morphological characters of the highest and the lowest correlation were observed in dorsal distance with r2=0.993 and the anal height with r2=0.938. A strong correlation (r2=0.993) was found between the total length and wet relationship and the growth was positive allometric b>3. This paper reports the first documented of morphometric characteristics of the species. It is considered to contribute to fisheries biology and international scientific literature.

Families of periodic orbits: Closed 1-forms and global continuability

We investigate global continuation of periodic orbits of a differential equation depending on a parameter, assuming that a closed 1-form satisfying certain properties exists. We begin by extending the global continuation theory of Alexander, Alligood, Mallet-Paret, Yorke, and others to this situation, formulating a new notion of global continuability and a new global continuation theorem tailored for this situation. In particular, we show that the existence of such a 1-form ensures that local continuability of periodic orbits implies global continuability. Using our general theory, we then develop continuation-based techniques for proving the existence of periodic orbits. In contrast to previous work, a key feature of our results is that existence of periodic orbits can be proven (i) without finding trapping regions for the dynamics and (ii) without establishing a priori upper bounds on the periods of orbits. We illustrate the theory in examples inspired by the synthetic biology literature.

Brachionus rotifers as a model for investigating dietary and metabolic regulators of aging.

Because every species has unique attributes relevant to understanding specific aspects of aging, using a diversity of study systems and a comparative biology approach for aging research has the potential to lead to novel discoveries applicable to human health. Monogonont rotifers, a standard model for studies of aquatic ecology, evolutionary biology, and ecotoxicology, have also been used to study lifespan and healthspan for nearly a century. However, because much of this work has been published in the ecology and evolutionary biology literature, it may not be known to the biomedical research community. In this review, we provide an overview of Brachionus rotifers as a model to investigate nutritional and metabolic regulators of aging, with a focus on recent studies of dietary and metabolic pathway manipulation. Rotifers are microscopic, aquatic invertebrates with many advantages as a system for studying aging, including a two-week lifespan, easy laboratory culture, direct development without a larval stage, sexual and asexual reproduction, easy delivery of pharmaceuticals in liquid culture, and transparency allowing imaging of cellular morphology and processes. Rotifers have greater gene homology with humans than do established invertebrate models for aging, and thus rotifers may be used to investigate novel genetic mechanisms relevant to human lifespan and healthspan. The research on caloric restriction; dietary, pharmaceutical, and genetic interventions; and transcriptomics of aging using rotifers provide insights into the metabolic regulators of lifespan and health and suggest future directions for aging research. Capitalizing on the unique biology of Brachionus rotifers, referencing the vast existing literature about the influence of diet and drugs on rotifer lifespan and health, continuing the development of genetic tools for rotifers, and growing the rotifer research community will lead to new discoveries a better understanding of the biology of aging.

A Review of Heterolytic Synthesis Methodologies for Organotri- and Organotetrasulfane Synthesis

AbstractIt has been ten years since the last comprehensive review on polysulfanes, and during the intervening period, organodi-, organotri- and organotetrasulfanes have featured prominently in both the chemistry and biology literature. This timely update presents both a mechanistic and historical account of synthesis methodology available for organotri- and organotetrasulfanes involving heterolytic S–S bond formation.