bluuebunny/crossref_metadata_2025 huggingface dataset:
Supporting Inclusive Learning Environments and Professional Development in Medical Education Through an Identity and Inclusion Initiative
Authors: Woodruff James N. , Vela Monica B. , Zayyad Zaina , Johnson Tyrone A. , Kyalwazi Beverly , Amegashie Courtney , Silverman Rebecca , Levinson Dana , Blythe Kate , Lee Wei Wei , Thomas Shanetha , Parrish Walter , Humphrey Holly J.
Published: September 2020

In 2015, the Pritzker School of Medicine experienced increasing student interest in the changing sociopolitical landscape of the United States and the interaction of these events with student and patient identity. To address this interest, an Identity and Inclusion Steering Committee was formed and formally charged with “providing ongoing direction for programs and/or curricula at Pritzker that support an inclusive learning environment and promote respectful and effective communication with diverse patients and colleagues around issues of identity.” The authors describe this committee’s structure and steps taken by the committee to create an inclusive community of students at Pritzker characterized by learning through civil discourse. Initiatives were guided by a strategy of continuous quality improvement consisting of regular iterative evaluation, ongoing school-wide engagement, and responsiveness to issues and concerns as they emerged. Data collected over the committee’s 4-year existence demonstrate significant improvement in students’ sense of inclusion and respect for different perspectives on issues related to identity, such as access to health care, racialized medicine, safe spaces, and nursing labor strikes. The authors discuss several principles that support the development of an inclusive community of students as well as challenges to the implementation of such programming. They conclude that a strategy of continuous quality improvement guided by values of social justice, tolerance, and civil discourse can build community inclusion and enhance medical training for the care of diverse patient populations.
Alpha Omega Alpha in the 21st Century: One School’s Approach
Authors: Cifu Adam S. , Dorsey Chelsea , Humphrey Holly J.
Published: September 2020

Recent data suggest that students from population groups that have been underrepresented in medicine are disproportionately excluded from admission into the national medical honor society, Alpha Omega Alpha (AΩA). This finding, in combination with increasing concerns about bias in medical student assessment, has led some medical schools to reexamine their AΩA selection process and/or their relationship with the organization. The Pritzker School of Medicine at the University of Chicago formed a task force to study the schools process of choosing students for recognition and to make recommendations regarding this issue.
Medical Education’s Wicked Problem: Achieving Equity in Assessment for Medical Learners
Authors: Lucey Catherine R. , Hauer Karen E. , Boatright Dowin , Fernandez Alicia
Published: September 2020

Despite a lack of intent to discriminate, physicians educated in U.S. medical schools and residency programs often take actions that systematically disadvantage minority patients. The approach to assessment of learner performance in medical education can similarly disadvantage minority learners. The adoption of holistic admissions strategies to increase the diversity of medical training programs has not been accompanied by increases in diversity in honor societies, selective residency programs, medical specialties, and medical school faculty. These observations prompt justified concerns about structural and interpersonal bias in assessment. This manuscript characterizes equity in assessment as a “wicked problem” with inherent conflicts, uncertainty, dynamic tensions, and susceptibility to contextual influences. The authors review the underlying individual and structural causes of inequity in assessment. Using an organizational model, they propose strategies to achieve equity in assessment and drive institutional and systemic improvement based on clearly articulated principles. This model addresses the culture, systems, and assessment tools necessary to achieve equitable results that reflect stated principles. Three components of equity in assessment that can be measured and evaluated to confirm success include intrinsic equity (selection and design of assessment tools), contextual equity (the learning environment in which assessment occurs), and instrumental equity (uses of assessment data for learner advancement and selection and program evaluation). A research agenda to address these challenges and controversies and demonstrate reduction in bias and discrimination in medical education is presented.
Rank Equity Index: Measuring Parity in the Advancement of Underrepresented Populations in Academic Medicine
Authors: Fassiotto Magali , Flores Brenda , Victor Robert , Altamirano Jonathan , Garcia Luis C. , Kotadia Shaila , Maldonado Yvonne
Published: September 2020

As educators, researchers, clinicians, and administrators, faculty serve pivotal roles in academic medical centers (AMCs). Thus, the quality of faculty members’ experiences is inseparable from an AMC’s success. In seeking new methods to assess equity in advancement in academic medicine, the authors developed the Rank Equity Index (REI)—adapted from the Executive Parity Index, a scale previously implemented within the business sector—to examine national data on gender and racial/ethnic equity across faculty ranks. The REI was employed on self-reported demographic data, collected by the Association of American Medical Colleges, from U.S. medical school faculty in 2017, to make pairwise rank comparisons of the professoriate by demographic characteristics and department. Overall results indicated that women did not attain parity at any pairwise rank comparison, while men were above parity at all ranks. Similar results were observed across all departments surveyed: women in the basic sciences had REIs closest to parity, women in pediatrics had the highest representation but had REIs that were further from parity than REIs in the basic sciences, and women in surgery demonstrated the lowest REIs. Nationally, REIs were below 1.00 for all racial/ethnic group rank comparisons except for White and, in one case, multiple-race non-Hispanic/Latinx. Across all analyzed departments, Black/African American, Asian, Hispanic/Latinx, and multiple-race Hispanic/Latinx faculty had REIs below parity at all ranks except in 2 cases. In a comparison of 2017 and 2007 data, REIs across both race/ethnicity and gender were lower in 2007 for nearly all groups. REI analyses can highlight inequities in faculty rank that may be masked when using aggregate faculty proportions, which do not account for rank. The REI provides AMCs with a new tool to better analyze institutional data to inform efforts to increase parity across all faculty ranks.
Cost-effective analysis of infertility treatment in women with anovulatory polycystic ovarian syndrome
Authors: Saad-Naguib Michael H. , Timmons Douglas , Krishnamoorthy Kavitha , Attia George R.
Published: September 2020

Introduction:

Polycystic ovarian syndrome (PCOS) is a common cause of female infertility. Clomiphene citrate (CC) is a first line treatment for infertility secondary to PCOS, in addition to Letrozole. After unsuccessful cycles using CC and timed intercourse, pregnancy may be achieved using in-vitro fertilization (IVF), bypassing gonadotropins. We explore the most efficient and cost-effective way to obtain at least 70% live-birth rate in PCOS patients who fail first-line treatment.

Materials and methods:

A review of relevant trials using PUBMED was performed to obtain pregnancy rates of women with PCOS undergoing various treatments. Six randomized trials were included in this study. We used 761 cycles from these trials. Four different protocols were structured: protocol 1 consisted of 3 cycles of CC/intrauterine insemination (IUI) followed by 3 cycles of human menopausal gonadotropin stimulation with IUI followed by 2 cycles of IVF/intracytoplasmic sperm injection (ICSI). Protocol 2 involved 3 cycles of CC/IUI followed by 2 cycles of IVF/ICSI. Protocol 3 was comprised of 3 cycles of human menopausal gonadotropin/IUI followed by 2 cycles of IVF/ICSI, and protocol 4 was composed of 2 cycles of IVF/ICSI and 1 cycle of frozen embryo transfer. Each protocol was analyzed for cost per live birth and time to live birth.

Results:

Protocol 1 yielded a live-birth rate of 75%, costing $34,923 per live-birth achieved over a 10-month period. Protocol 2 yielded a pregnancy rate of 71%, costing $32,172 over 7 months. Protocol 3 yielded a pregnancy rate of 73%, costing $39,812 over 7 months. Lastly, protocol 4 yielded a pregnancy rate of 70%, costing $37,884 per pregnancy over a 5-month period.

Conclusion:

Protocol 4 was the most efficient, reaching a 70% live birth rate in a 5-month period. Protocol 2 was the most cost-effective, with a total cost of $32,172 per live birth. These results will assist physicians in counseling PCOS patients with subfertility to determine the optimal treatment method.
SARS-CoV-2 Vaccine
Authors: Walker Karrie
Published: September 2020

With the SARS-CoV-2 pandemic creating such a wide-reaching health crisis, it is imperative that a safe and effective vaccine be developed promptly for global availability. As such, there are several vaccine development projects currently underway aiming to meet this critical demand. However, COVID vaccine development is not immune to the inherent limitations and challenges that are encountered during vaccine clinical trials.
Controversies in the Treatment of Peripheral T‐cell Lymphoma
Authors: Bachy Emmanuel , Broccoli Alessandro , Dearden Claire , de Leval Laurence , Gaulard Philippe , Koch Raphael , Morschhauser Franck , Trümper Lorenz , Zinzani Pier Luigi
Published: September 2020

Peripheral T‐cell lymphomas are a heterogeneous group of rare diseases with an aggressive behavior and dismal prognosis. Their classification is complex and still evolving, and several biomolecular markers now help refine the prognosis of specific disease entities, although still have limited impact in tailoring the treatment. First‐line treatment strategies can cure only a minority of patients and relapsed‐refractory disease still represents the major cause of failure. Frontline autologous transplantation may have an impact in the consolidation of response; however, its role is still questioned as far as complete responses obtained after induction chemotherapy are concerned. Newer drugs are now being evaluated in clinical trials, but effective salvage strategies for those who experience treatment failures are lacking. Here we review and discuss the most controversial aspects of diagnosis and treatment of peripheral T‐cell lymphomas.
Sex differences in the perception of itch and quality of life in patients with chronic pruritus in the United States
Authors: Kursewicz Christina , Fowler Emilie , Rosen Jordan , Castillo David , Chan Yiong Huak , Nattkemper Leigh , Yosipovitch Gil
Published: September 2020

Using cross-sectional survey data from 335 patients with chronic itch, we analyzed differences in itch intensity, characteristics, and quality of life between males and females. The intensity of chronic pruritus was significantly greater in females compared with males (7.70 vs. 6.95; P<0.05) and females more often described their pruritus as dreadful, unbearable, hurting, and oppressive (P<0.05). In addition, females achieved a greater overall quality of life mean score compared with males (3.65 vs. 3.19; P<0.05), indicating a more negative impact on quality of life. Overall, our study shows that significant differences exist between females and males with chronic pruritus, and clinicians should be aware of these distinctions.
Greater mechanical temporal summation of pain in Latinx-Americans and the role of adverse life experiences
Authors: Rassu Fenan S. , Luedke Jessica C. , Nanavaty Namrata , Mathur Vani A. , Meagher Mary W.
Published: September 2020

Introduction:

Adverse life experiences disproportionately impact Latinx-Americans and are related to greater chronic pain rates. However, little is known about how adversities interact with central pain mechanisms for the development of later pain among Latinx-Americans.

Objectives:

The current study examined the relationship between adverse life experiences (eg, trauma and ethnic discrimination) and correlates (eg, social status) with mechanical temporal summation of pain (a proxy measure of central sensitization) between pain-free U.S. native Latinx (n = 65) and non-Hispanic White (NHW) (n = 51) adults.

Methods:

Participants completed self-report adverse life experience and correlational measures regarding childhood and adulthood and a mechanical temporal summation protocol.

Results:

Relative to NHWs, Latinx-Americans reported experiencing significantly greater trauma, discrimination, and lower social status during childhood and adulthood, along with greater temporal summation. Contrary to hypotheses, recent and lifetime experiences of ethnic discrimination significantly correlated with less temporal summation among Latinx-Americans. Decreases in objective and subjective social status across the lifespan (childhood to present day) correlated with greater temporal summation for Latinx-Americans. However, r-to-z transformation analyses confirmed that significant adversity and social status correlations observed among the Latinx group did not significantly differ from NHW participants.

Conclusions:

The present findings highlight the complex association between adverse experiences, adverse experience risk factors, and pain for Latinx-Americans. Given the disproportion of experienced pain and adversity among Latinx-Americans, the current findings suggest that a better understanding of the unique adversities for this sample may help elucidate the mechanisms underlying the relationship between adversities, adversity correlates, and pain risk for Latinx-Americans.
Inpatient postoperative undesirable side effects of analgesics management: a pediatric patients and parental perspective
Authors: Chabot Bianca , Ferland Catherine E. ,   on behalf of the Quebec Consortium on Adverse Effects of Pain Medications
Published: September 2020

Introduction:

The use of analgesics for the treatment of post-operative pain is common, however, such medications are known to have potential side effects. These undesirable secondary effects can have an important impact on patients and impede their recovery.

Objectives:

A review of the literature was conducted in order to gain a better understanding of the challenges confronted by pediatric patients in the acute post-operative period in terms of the side effects of analgesics.

Methods:

An online search of keywords (pediatric, analgesic, pain medication, side effects, adverse effects, nausea and vomiting, post-operative, post-discharge, self-care, self-management, management, self-care strategies, patient expectations, patient concerns and education) using PubMed, Medline and Scopus databases, and using the snowballing method of reference tracking was conducted.

Results:

A total of 10 studies (N = 10, 871 participants) published between 1990 and 2019 were reviewed. Common side effects experienced by patients were nausea, vomiting, and pruritus. Patients' parents reported having many concerns about analgesic use and reported a lack of knowledge on pain medications and side-effect management.

Conclusion:

Areas of improvement in clinical practice include providing the patient and their parents with more information about the post-operative period, analgesic use, and side effects as well as prescribing appropriate treatments to alleviate side effects. This review reveals a lack of qualitative data on pain management and related undesired side effects in pediatric patients having undergone inpatient surgery in addition to the consequences on patients' daily living and on the self-care strategies they engage in to attenuate such effects.
TAK1: a potent tumour necrosis factor inhibitor for the treatment of inflammatory diseases
Authors: Totzke Juliane , Scarneo Scott A. , Yang Kelly W. , Haystead Timothy A. J.
Published: September 2020

Aberrant tumour necrosis factor (TNF) signalling is a hallmark of many inflammatory diseases including rheumatoid arthritis (RA), irritable bowel disease and lupus. Maladaptive TNF signalling can lead to hyper active downstream nuclear factor (NF)-κβ signalling in turn amplifying a cell's inflammatory response and exacerbating disease. Within the TNF intracellular inflammatory signalling cascade, transforming growth factor-β-activated kinase 1 (TAK1) has been shown to play a critical role in mediating signal transduction and downstream NF-κβ activation. Owing to its role in TNF inflammatory signalling, TAK1 has become a potential therapeutic target for the treatment of inflammatory diseases such as RA. This review highlights the current development of targeting the TNF-TAK1 signalling axis as a novel therapeutic strategy for the treatment of inflammatory diseases.
Phenotypes from cell-free DNA
Authors: Zukowski Alexis , Rao Satyanarayan , Ramachandran Srinivas
Published: September 2020

Cell-free DNA (cfDNA) has the potential to enable non-invasive detection of disease states and progression. Beyond its sequence, cfDNA also represents the nucleosomal landscape of cell(s)-of-origin and captures the dynamics of the epigenome. In this review, we highlight the emergence of cfDNA epigenomic methods that assess disease beyond the scope of mutant tumour genotyping. Detection of tumour mutations is the gold standard for sequencing methods in clinical oncology. However, limitations inherent to mutation targeting in cfDNA, and the possibilities of uncovering molecular mechanisms underlying disease, have made epigenomics of cfDNA an exciting alternative. We discuss the epigenomic information revealed by cfDNA, and how epigenomic methods exploit cfDNA to detect and characterize cancer. Future applications of cfDNA epigenomic methods to act complementarily and orthogonally to current clinical practices has the potential to transform cancer management and improve cancer patient outcomes.
Exploiting aneuploidy-imposed stresses and coping mechanisms to battle cancer
Authors: Zhou Lin , Jilderda Laura J. , Foijer Floris
Published: September 2020

Aneuploidy, an irregular number of chromosomes in cells, is a hallmark feature of cancer. Aneuploidy results from chromosomal instability (CIN) and occurs in almost 90% of all tumours. While many cancers display an ongoing CIN phenotype, cells can also be aneuploid without displaying CIN. CIN drives tumour evolution as ongoing chromosomal missegregation will yield a progeny of cells with variable aneuploid karyotypes. The resulting aneuploidy is initially toxic to cells because it leads to proteotoxic and metabolic stress, cell cycle arrest, cell death, immune cell activation and further genomic instability. In order to overcome these aneuploidy-imposed stresses and adopt a malignant fate, aneuploid cancer cells must develop aneuploidy-tolerating mechanisms to cope with CIN. Aneuploidy-coping mechanisms can thus be considered as promising therapeutic targets. However, before such therapies can make it into the clinic, we first need to better understand the molecular mechanisms that are activated upon aneuploidization and the coping mechanisms that are selected for in aneuploid cancer cells. In this review, we discuss the key biological responses to aneuploidization, some of the recently uncovered aneuploidy-coping mechanisms and some strategies to exploit these in cancer therapy.
Term Matrix: a novel Gene Ontology annotation quality control system based on ontology term co-annotation patterns
Authors: Wood Valerie , Carbon Seth , Harris Midori A. , Lock Antonia , Engel Stacia R. , Hill David P. , Van Auken Kimberly , Attrill Helen , Feuermann Marc , Gaudet Pascale , Lovering Ruth C. , Poux Sylvain , Rutherford Kim M. , Mungall Christopher J.
Published: September 2020

Biological processes are accomplished by the coordinated action of gene products. Gene products often participate in multiple processes, and can therefore be annotated to multiple Gene Ontology (GO) terms. Nevertheless, processes that are functionally, temporally and/or spatially distant may have few gene products in common, and co-annotation to unrelated processes probably reflects errors in literature curation, ontology structure or automated annotation pipelines. We have developed an annotation quality control workflow that uses rules based on mutually exclusive processes to detect annotation errors, based on and validated by case studies including the three we present here: fission yeast protein-coding gene annotations over time; annotations for cohesin complex subunits in human and model species; and annotations using a selected set of GO biological process terms in human and five model species. For each case study, we reviewed available GO annotations, identified pairs of biological processes which are unlikely to be correctly co-annotated to the same gene products (e.g. amino acid metabolism and cytokinesis), and traced erroneous annotations to their sources. To date we have generated 107 quality control rules, and corrected 289 manual annotations in eukaryotes and over 52 700 automatically propagated annotations across all taxa.
Diversity from similarity: cellular strategies for assigning particular identities to actin filaments and networks
Authors: Boiero Sanders Micaela , Antkowiak Adrien , Michelot Alphée
Published: September 2020

The actin cytoskeleton has the particularity of being assembled into many functionally distinct filamentous networks from a common reservoir of monomeric actin. Each of these networks has its own geometrical, dynamical and mechanical properties, because they are capable of recruiting specific families of actin-binding proteins (ABPs), while excluding the others. This review discusses our current understanding of the underlying molecular mechanisms that cells have developed over the course of evolution to segregate ABPs to appropriate actin networks. Segregation of ABPs requires the ability to distinguish actin networks as different substrates for ABPs, which is regulated in three different ways: (1) by the geometrical organization of actin filaments within networks, which promotes or inhibits the accumulation of ABPs; (2) by the identity of the networks' filaments, which results from the decoration of actin filaments with additional proteins such as tropomyosin, from the use of different actin isoforms or from covalent modifications of actin; (3) by the existence of collaborative or competitive binding to actin filaments between two or multiple ABPs. This review highlights that all these effects need to be taken into account to understand the proper localization of ABPs in cells, and discusses what remains to be understood in this field of research.
A simple experiment on global warming
Authors: Levendis Yiannis A. , Kowalski Gregory , Lu Yang , Baldassarre Gregory
Published: September 2020

A simple experiment has been developed to demonstrate the global warming potential of carbon dioxide (CO
2
) gas in the Earth's atmosphere. A miniature electric resistance heating element was placed inside an inflatable balloon. The balloon was filled with either air or CO
2
. Whereas the CO
2
partial pressure on the earth's atmosphere is approximately 4 × 10
−4
atm, in this experiment, a high partial pressure of CO
2
(1 atm) was used to compensate for the short radiation absorption path in the balloon. The element was heated to approximately 50°C, the power was then switched off and the element's cooling trends in air and in CO
2
were monitored. It took a longer time to cool the heating element back to ambient temperature in CO
2
than in air. It also took longer times to cool the element in larger size balloons and in pressurized balloons when they were filled with CO
2
. To the contrary, the balloon size or pressure made no difference when the balloons were filled with air. A simple mathematical model was developed, and it confirmed that the radiative heat loss from the element decreased significantly in CO
2
. This investigation showed that the cooling rate of an object, with surface temperature akin to temperatures found on Earth, is reduced in a CO
2
-rich atmosphere because of the concomitant lower heat loss to its environment.
Photocatalytic degradation of methylene blue under natural sunlight using iron titanate nanoparticles prepared by a modified sol–gel method
Authors: Vasiljevic Z. Z. , Dojcinovic M. P. , Vujancevic J. D. , Jankovic-Castvan I. , Ognjanovic M. , Tadic N. B. , Stojadinovic S. , Brankovic G. O. , Nikolic M. V.
Published: September 2020

The aim of this work was to synthesize semiconducting oxide nanoparticles using a simple method with low production cost to be applied in natural sunlight for photocatalytic degradation of pollutants in waste water. Iron titanate (Fe
2
TiO
5
) nanoparticles with an orthorhombic structure were successfully synthesized using a modified sol–gel method and calcination at 750°C. The as-prepared Fe
2
TiO
5
nanoparticles exhibited a moderate specific surface area. The mesoporous Fe
2
TiO
5
nanoparticles possessed strong absorption in the visible-light region and the band gap was estimated to be around 2.16 eV. The photocatalytic activity was evaluated by the degradation of methylene blue under natural sunlight. The effect of parameters such as the amount of catalyst, initial concentration of the dye and pH of the dye solution on the removal efficiency of methylene blue was investigated. Fe
2
TiO
5
showed high degradation efficiency in a strong alkaline medium that can be the result of the facilitated formation of OH radicals due to an increased concentration of hydroxyl ions.
Do bats use guano and urine stains to find new roosts? Tests with three group-living bats
Authors: Brown Bridget K. G. , Leffer Lauren , Valverde Yesenia , Toshkova Nia , Nystrom Jessica , Page Rachel A. , Carter Gerald G.
Published: September 2020

Many animals use social cues to find refuges. Bats can find roosts using the echolocation and social calls of conspecifics, but they might also use scent cues, a possibility which is less studied. The entrances of bat roosts are often marked by guano and urine, providing possible scent cues. We conducted eight experiments to test whether bats use the scent of guano and urine to find potential roosts. In field experiments, we tested if
Molossus molossus
(velvety free-tailed bats) in Panama and
Eptesicus fuscus
(big brown bats) in Ohio would investigate artificial roost boxes that were scented with guano and urine more often than a paired unscented control. We did not detect any difference in flights near the scented versus unscented roosts, and we detected only one entrance into any artificial roost (scented). In six captive experiments, we tested for the attraction of
Desmodus rotundus
(common vampire bats) and
Molossus molossus
to areas scented with guano and urine, under several conditions. Results were mixed, but overall suggested that the scent of guano and urine does not act as a strong lure for the tested bat species. We suggest that further tests of olfaction-based roost choice in bats should manipulate existing scent cues on familiar roosts.
Analysis of self-equilibrated networks through cellular modelling
Authors: Aloui O. , Orden D. , Bel Hadj Ali N. , Rhode-Barbarigos L.
Published: September 2020

Network equilibrium models represent a versatile tool for the analysis of interconnected objects and their relationships. They have been widely employed in both science and engineering to study the behaviour of complex systems under various conditions, including external perturbations and damage. In this paper, network equilibrium models are revisited through graph-theory laws and attributes with special focus on systems that can sustain equilibrium in the absence of external perturbations (self-equilibrium). A new approach for the analysis of self-equilibrated networks is proposed; they are modelled as a collection of cells, predefined elementary network units that have been mathematically shown to compose any self-equilibrated network. Consequently, the equilibrium state of complex self-equilibrated systems can be obtained through the study of individual cell equilibria and their interactions. A series of examples that highlight the flexibility of network equilibrium models are included in the paper. The examples attest how the proposed approach, which combines topological as well as geometrical considerations, can be used to decipher the state of complex systems.
Evolution of local motifs and topological proximity in self-assembled quasi-crystalline phases
Authors: Cramer Pedersen Martin , Robins Vanessa , Mortensen Kell , Kirkensgaard Jacob J. K.
Published: September 2020

Using methods from the field of topological data analysis, we investigate the self-assembly and emergence of three-dimensional quasi-crystalline structures in a single-component colloidal system. Combining molecular dynamics and persistent homology, we analyse the time evolution of persistence diagrams and particular local structural motifs. Our analysis reveals the formation and dissipation of specific particle constellations in these trajectories, and shows that the persistence diagrams are sensitive to nucleation and convergence to a final structure. Identification of local motifs allows quantification of the similarities between the final structures in a topological sense. This analysis reveals a continuous variation with density between crystalline clathrate, quasi-crystalline, and disordered phases quantified by ‘topological proximity’, a visualization of the Wasserstein distances between persistence diagrams. From a topological perspective, there is a subtle, but direct connection between quasi-crystalline, crystalline and disordered states. Our results demonstrate that topological data analysis provides detailed insights into molecular self-assembly.
Corrugation of an unpaved road surface under vehicle weight
Authors: Matsuyama C. , Tanaka Y. , Sato M. , Shima H.
Published: September 2020

Road corrugation refers to the formation of periodic, transverse ripples on unpaved road surfaces. It forms spontaneously on an initially flat surface under heavy traffic and can be considered to be a type of unstable growth phenomenon, possibly caused by the local volume contraction of the underlying soil due to a moving vehicle’s weight. In the present work, we demonstrate a possible mechanism for road corrugation using experimental data of soil consolidation and numerical simulations. The results indicate that the vertical oscillation of moving vehicles, which is excited by the initial irregularities of the surface, plays a key role in the development of corrugation.
Transmission efficiency drives host–microbe associations
Authors: Leftwich Philip T. , Edgington Matthew P. , Chapman Tracey
Published: September 2020

Sequencing technologies have fuelled a rapid rise in descriptions of microbial communities associated with hosts, but what is often harder to ascertain is the evolutionary significance of these symbioses. Here, we review the role of vertical (VT), horizontal (HT), environmental acquisition and mixed modes of transmission (MMT), in the establishment of animal host–microbe associations. We then model four properties of gut microbiota proposed as key to promoting animal host–microbe relationships: modes of transmission, host reproductive mode, host mate choice and host fitness. We found that: (i) MMT led to the highest frequencies of host–microbe associations, and that some environmental acquisition or HT of microbes was required for persistent associations to form unless VT was perfect; (ii) host reproductive mode (sexual versus asexual) and host mate choice (for microbe carriers versus non-carriers) had little impact on the establishment of host–microbe associations; (iii) host mate choice did not itself lead to reproductive isolation, but could reinforce it; and (iv) changes in host fitness due to host–microbe associations had a minimal impact upon the formation of co-associations. When we introduced a second population, into which host–microbe carriers could disperse but in which environmental acquisition did not occur, highly efficient VT was required for host–microbe co-associations to persist. Our study reveals that transmission mode is of key importance in establishing host–microbe associations.
The effects of animal personality on the ideal free distribution
Authors: DiNuzzo Eleanor R. , Griffen Blaine D.
Published: September 2020

The ideal free distribution (IFD) has been used to predict the distribution of foraging animals in a wide variety of systems. However, its predictions do not always match observed distributions of foraging animals. Instead, we often observe that there are more consumers than predicted in low-quality patches and fewer consumers than predicted in high-quality patches (i.e. undermatching). We examine the possibility that animal personality is one explanation for this undermatching. We first conducted a literature search to determine how commonly studies document the personality distribution of populations. Second, we created a simple individual-based model to conceptually demonstrate why knowing the distribution of personalities is important for studies of populations of foragers in context of the IFD. Third, we present a specific example where we calculate the added time to reach the IFD for a population of mud crabs that has a considerable number of individuals with relatively inactive personalities. We suggest that animal personality, particularly the prevalence of inactive personality types, may inhibit the ability of a population to track changes in habitat quality, therefore leading to undermatching of the IFD. This may weaken the IFD as a predictive model moving forward.
The evolution and fate of diversity under hard and soft selection
Authors: Chen Patrick , Kassen Rees
Published: September 2020

How genetic variation arises and persists over evolutionary time despite the depleting effects of natural selection remains a long-standing question. Here, we investigate the impacts of two extreme forms of population regulation—at the level of the total, mixed population (hard selection) and at the level of local, spatially distinct patches (soft selection)—on the emergence and fate of diversity under strong divergent selection. We find that while the form of population regulation has little effect on rates of diversification, it can modulate the long-term fate of genetic variation, diversity being more readily maintained under soft selection compared to hard selection. The mechanism responsible for coexistence is negative frequency-dependent selection which, while present initially under both forms of population regulation, persists over the long-term only under soft selection. Importantly, coexistence is robust to continued evolution of niche specialist types under soft selection but not hard selection. These results suggest that soft selection could be a general mechanism for the maintenance of ecological diversity over evolutionary time scales.
De novo biosynthesis of simple aromatic compounds by an arthropod (
Archegozetes longisetosus
)
Authors: Brückner Adrian , Kaltenpoth Martin , Heethoff Michael
Published: September 2020

The ability to synthesize simple aromatic compounds is well known from bacteria, fungi and plants, which all share an exclusive biosynthetic route—the shikimic acid pathway. Some of these organisms further evolved the polyketide pathway to form core benzenoids via a head-to-tail condensation of polyketide precursors. Arthropods supposedly lack the ability to synthesize aromatics and instead rely on aromatic amino acids acquired from food, or from symbiotic microorganisms. The few studies purportedly showing de novo biosynthesis via the polyketide synthase (PKS) pathway failed to exclude endosymbiotic bacteria, so their results are inconclusive. We investigated the biosynthesis of aromatic compounds in defence secretions of the oribatid mite
Archegozetes longisetosus
. Exposing the mites to a diet containing high concentrations of antibiotics removed potential microbial partners but did not affect the production of defensive benzenoids. To gain insights into benzenoid biosynthesis, we fed mites with stable-isotope labelled precursors and monitored incorporation with mass spectrometry. Glucose, malonic acid and acetate, but not phenylalanine, were incorporated into the benzenoids, further evidencing autogenous biosynthesis. Whole-transcriptome sequencing with hidden Markov model profile search of protein domain families and subsequent phylogenetic analysis revealed a putative PKS domain similar to an actinobacterial PKS, possibly indicating a horizontal gene transfer.
Honeybees solve a multi-comparison ranking task by probability matching
Authors: MaBouDi HaDi , Marshall James A. R. , Barron Andrew B.
Published: September 2020

Honeybees forage on diverse flowers which vary in the amount and type of rewards they offer, and bees are challenged with maximizing the resources they gather for their colony. That bees are effective foragers is clear, but how bees solve this type of complex multi-choice task is unknown. Here, we set bees a five-comparison choice task in which five colours differed in their probability of offering reward and punishment. The colours were ranked such that high ranked colours were more likely to offer reward, and the ranking was unambiguous. Bees' choices in unrewarded tests matched their individual experiences of reward and punishment of each colour, indicating bees solved this test not by comparing or ranking colours but by basing their colour choices on their history of reinforcement for each colour. Computational modelling suggests a structure like the honeybee mushroom body with reinforcement-related plasticity at both input and output can be sufficient for this cognitive strategy. We discuss how probability matching enables effective choices to be made without a need to compare any stimuli directly, and the use and limitations of this simple cognitive strategy for foraging animals.
Investigating the effect of national government physical distancing measures on depression and anxiety during the COVID-19 pandemic through meta-analysis and meta-regression
Authors: Castaldelli-Maia João M. , Marziali Megan E. , Lu Ziyin , Martins Silvia S.
Published: September 2020

Abstract (following PRISMA statement)

Background

COVID-19 physical distancing measures can potentially increase the likelihood of mental disorders. It is unknown whether these measures are associated with depression and anxiety.

Objectives

To investigate meta-analytic global levels of depression and anxiety during the COVID-19 pandemic and how implementation of mitigation strategies (i.e. public transportation closures, stay-at-home orders, etc.) impacted such disorders.

Data sources

Pubmed, MEDLINE, Web of Science, BIOSIS Citation Index, Current Content Connect, PsycINFO, CINAHL, medRxiv, and PsyArXiv databases for depression and anxiety prevalences; Oxford Covid-19 Government Response Tracker for the containment and closure policies indexes; Global Burden of Disease Study for previous levels of depression and anxiety.

Study eligibility criteria

Original studies conducted during COVID-19 pandemic, which assessed categorical depression and anxiety, using PHQ-9 and GAD-7 scales (cutoff ≥ 10).

Participants and interventions

General population, healthcare providers, students, and patients. National physical distancing measures.

Study appraisal and synthesis methods

Meta-analysis and meta-regresssion.

Results

In total, 226,638 individuals were assessed within the 60 included studies. Global prevalence of both depression and anxiety during COVID-19 pandemic were 24.0% and 21.3%, respectively. There was a wide variance in the prevalence of both anxiety and depression reported in different regions of the world and countries. Asia, and China particularly, had the lowest prevalence of both disorders. Regarding the impact of mitigation strategies on mental health, only public transportation closures increased anxiety prevalence.

Limitations

Country-level data on physical distancing measures and previous anxiety/depression may not necessarily reflect local (i.e., city-specific) contexts.

Conclusions and implications of key findings

Mental health concerns should not be viewed only as a delayed consequence of the COVID-19 pandemic, but also as a concurrent epidemic. Our data provides support for policy-makers to consider real-time enhanced mental health services, and increase initiatives to foster positive mental health outcomes.

Systematic review registration number

https://doi.org/10.17605/OSF.IO/JQGSF
Severity Prediction for COVID-19 Patients via Recurrent Neural Networks
Authors: Lee Junghwan , Kim Jae Hyun , Ta Casey , Liu Cong , Weng Chunhua
Published: September 2020

The novel coronavirus disease-2019 (COVID-19) pandemic has threatened the health of tens of millions of people worldwide and posed enormous burden on the global healthcare systems. Many prediction models have been proposed to fight against the pandemic. In this paper, we propose a model to predict whether a patient infected with COVID-19 will develop severe outcomes based only on the patient’s historical electronic health records (EHR) using recurrent neural networks (RNN). The predicted severity risk score represents the probability for a person to progress into severe status (mechanical ventilation, tracheostomy, or death) after being infected with COVID-19. While many of the existing models use features obtained after diagnosis of COVID-19, our proposed model only utilizes a patient’s historical EHR so that it can enable proactive risk management before or at the time of hospital admission.
Quantifying the Risk of Indoor Drainage System in Multi-unit Apartment Building as a Transmission Route of SARS-CoV-2
Authors: Shi Kuang-Wei , Huang Yen-Hsiang , Quon Hunter , Ou-Yang Zi-Lu , Wang Chengwen , Jiang Sunny C.
Published: September 2020

The COVID-19 pandemic has had a profound impact on human society. The isolation of SARS-CoV-2 from patients’ feces on human cell line raised concerns of possible transmission through human feces including exposure to aerosols generated by toilet flushing and through the indoor drainage system. Currently, routes of transmission, other than the close contact droplet transmission, are still not well understood. A quantitative microbial risk assessment was conducted to estimate the health risks associated with two aerosol exposure scenarios: 1) toilet flushing, and 2) faulty connection of a floor drain with the building’s main sewer pipe. SARS-CoV-2 data were collected from the emerging literature. The infectivity of the virus in feces was estimated based on a range of assumption between viral genome equivalence and infectious unit. The human exposure dose was calculated using Monte Carlo simulation of viral concentrations in aerosols under each scenario and human breathing rates. The probability of COVID-19 illness was generated using the dose-response model for SARS-CoV-1, a close relative of SARS-CoV-2, that was responsible for the SARS outbreak in 2003. The results indicate the median risks of developing COVID-19 for a single day exposure is 1.11 x 10-10and 3.52 x 10-11for toilet flushing and faulty drain scenario, respectively. The worst case scenario predicted the high end of COVID-19 risk for the toilet flushing scenario was 5.78 x 10-4(at 95thpercentile). The infectious viral loads in human feces are the most sensitive input parameter and contribute significantly to model uncertainty.
COVID-19 and Multisystem Inflammatory Syndrome in Latin American children: a multinational study
Authors: Antúnez-Montes Omar Yassef , Escamilla Maria Isabel , Figueroa-Uribe Augusto Flavio , Arteaga-Menchaca Erick , Lavariega-Saráchaga Manuel , Salcedo-Lozada Perla , Melchior Priscilla , de Oliveira Rodrigo Beréa , Caballero Juan Carlos Tirado , Redondo Hernando Pinzon , Fontalvo Laura Vanessa Montes , Hernandez Roger , Chavez Carolina , Campos Francisco , Uribe Fadia , Aguila Olguita del , Aida Jorge Alberto Rios , Buitrago Andrea Parra , Londoño Lina Maria Betancur , Vega León Felipe Mendoza , Hernández Carolina Almeida , Sali Michela , Palacio Julian Esteban Higuita , Gomez-Vargas Jessica , Yock-Corrales Adriana , Buonsenso Danilo
Published: September 2020

Background

To date, there are no comprehensive data on pediatric COVID-19 from Latin America. This study aims to assess COVID-19 and Multisystem Inflammatory Syndrome (MIS-C) in Latin American children, in order to appropriately plan and allocate resources to face the pandemic on a local and International lever

Methods

Ambispective multicentre cohort study from five Latin American countries. Children aged 18 years or younger with microbiologically confirmed SARS-CoV-2 infection were included.

Findings

409 children were included, with a median age of 53.0 years (IQR 0.6–9.0). Of these, 95 191 (23.2%) were diagnosed with MIS-C. 191 (46.7%) children were admitted to hospital and 52 (12.7%) required admission to a Pediatric Intensive Care Unite (PICU). 92 (22.5%) patients required oxygen support: 8 (2%) were started on continuous positive airway pressure (CPAP) and 29 (7%) on mechanical ventilation. 35 (8.5%) patients required inotropic support. The following factors were associated with PICU admission: pre-existing medical condition (P < 0.0001), immunodeficiency (P = 0.01), lower respiratory tract infection (P< 0.0001), gastrointestinal symptoms (P = 0.006), radiological changes suggestive of pneumonia and acute respiratory distress syndrome (P< 0.0001), low socioeconomic conditions (P 0.009).

Conclusions

This study shows a generally more severe form of COVID-19 and a high number of MIS-C in Latin American children, compared with studies from China, Europe and North America, and support current evidence of a more severe disease in Latin/Hyspanic children or in people of lower socioeconomic level. The findings highlight an urgent need of more data of COVID-19 in South America.
Plasma tissue plasminogen activator and plasminogen activator inhibitor-1 in hospitalized COVID-19 patients
Authors: Zuo Yu , Warnock Mark , Harbaugh Alyssa , Yalavarthi Srilakshmi , Gockman Kelsey , Zuo Melanie , Madison Jacqueline A. , Knight Jason S , Kanthi Yogendra , Lawrence Daniel A.
Published: September 2020

Background

Patients with coronavirus disease 19 (COVID-19) are at high risk for thrombotic arterial and venous occlusions. At the same time, bleeding complications have been observed in some patients. Better understanding the balance between coagulation and fibrinolysis will help inform optimal approaches to thrombosis prophylaxis and potential utility of fibrinolytic-targeted therapies.

Methods

118 hospitalized COVID-19 patients and 30 healthy controls were included in the study. We measured plasma antigen levels of tissue-type plasminogen activator (tPA) and plasminogen activator inhibitor-1 (PAI-1) and performed spontaneous clot lysis assays.

Findings

We found markedly elevated levels of tPA and PAI-1 among patients hospitalized with COVID-19. Both factors demonstrated a strong correlation with neutrophil counts and markers of neutrophil activation. High levels of tPA and PAI-1 were associated with worse respiratory status. High levels of tPA, in particular, were also strongly correlated with mortality and with a significant enhancement in spontaneous ex vivo clot lysis.

Interpretation

While both tPA and PAI-1 are elevated among COVID-19 patients, extremely high levels of tPA enhance spontaneous fibrinolysis and are significantly associated with mortality in some patients. These data indicate that fibrinolytic homeostasis in COVID-19 is complex with a subset of patients expressing a balance of factors that may favor fibrinolysis, and suggest that further study of tPA as a potential biomarker is warranted.

Funding

COVID-19 Cardiovascular Impact Research Ignitor Grant from the Michigan Medicine Frankel Cardiovascular Center, the National Institutes of Health, the A. Alfred Taubman Medical Research Institute, the Rheumatology Research Foundation, the Lupus Research Alliance, the Falk Medical Research Trust, the Burroughs Wellcome Fund, and the JOBST-American Venous Forum.