bluuebunny/crossref_metadata_2025 huggingface dataset:
1. The roots of biochemistry
Authors: Lorch Mark
Published: May 2021

This chapter traces the history of biochemistry, which is linked to the understanding of arguably the oldest uses of biotechnology—fermentation and the production of alcoholic beverages and cheese. In the 19th century, at the same time as the fermentation debates and enzymology flourished, the nature of proteins was under scrutiny. The chapter then considers the contribution that X-ray crystallography has made to structural biology. By the mid-20th century, the structures of the two massive molecular players, protein and nucleic acids (DNA along with ribonucleic acid), and their myriad roles were in place. It was becoming apparent that these were the fundamental molecular machines that marshal the chemistry within cells.
3. Proteins
Authors: Lorch Mark
Published: May 2021

This chapter examines proteins, the dominant proportion of cellular machinery, and the relationship between protein structure and function. The multitude of biological processes needed to keep cells functioning are managed in the organism or cell by a massive cohort of proteins, together known as the proteome. The twenty amino acids that make up the bulk of proteins produce the vast array of protein structures. However, amino acids alone do not provide quite enough chemical variety to complete all of the biochemical activity of a cell, so the chapter also explores post-translation modifications. It finishes by looking as some dynamic aspects of proteins, including enzyme kinetics and the protein folding problem.
6. Manufacturing and maintaining DNA
Authors: Lorch Mark
Published: May 2021

This chapter assesses DNA replication. The double-helix of DNA could easily be separated into two individual strands, each of which acts as a template for the manufacturing of a new complementary strand. This became known as semi-conservative replication, to indicate that each daughter DNA double-helix contained one new strand and one old strand, conserved from the parent molecule. Discovering the ways by which cells replicate their DNA led to the question: can we harness these amazing natural machines to shed light on DNA itself? The chapter then examines two key biotechnological advances: DNA sequencing and the polymerase chain reaction (PCR).
Creativity: A Very Short Introduction
Authors: Glăveanu Vlad
Published: May 2021

Creativity: A Very Short Introduction explores the history, theory, and practice of creativity from a psychological perspective. For thousands of years humanity has engaged in creative expression, allowing us to relate to other people, build an identity, and give meaning to our existence. From the painted caves in Lascaux and the invention of the first tools to modern day advertising campaigns and inventors’ labs, creativity has a long past. This VSI discusses how one can understand creative people and their creations within the social, material, and historical context that made them possible. It addresses the meaning and value of creativity beyond its contribution to economic growth and personal well-being.
6. The why of creativity
Authors: Glăveanu Vlad
Published: May 2021

This chapter addresses why people engage in creativity. This question can be answered at different levels. On the one hand, one can refer to what motivates creative people to do what they do. On the other hand, the question addresses a deeper level, that of how societies today are built and how they, in turn, construct the meaning and value of creativity. Nowadays, people consider creativity intrinsically valuable largely because of its direct and indirect economic benefits. However, creative expression also has a role for health and well-being. Creativity also relates to meaning in life. The chapter then considers how creativity can be used for good or for evil.
7. Creativity
Authors: Glăveanu Vlad
Published: May 2021

This chapter explores the future of creativity, launching two calls for creativity research in the 21st century. The first one concerns what can be called the democratization of creativity—the effort to be more inclusive in who we identify as creative, expand our view of creative outcomes, and generally increase everyone’s participation in creative activities. The second, related call is to socialize creativity, which means to take the role of other people, society, and culture more seriously in the understanding of this phenomenon. Both these aims can be achieved through research that cuts across disciplinary boundaries. The chapter then outlines what a multidisciplinary science of creativity would look like.
4. Sensation
Authors: Davies Jamie A.
Published: May 2021

This chapter examines sensation, which is a catch-all term for monitoring any state and feeding it into a physiological process. When people talk of their ‘senses’ they usually mean the five senses by which they consciously monitor features of the outside world. These senses—vision, hearing, smell, taste, and touch—provide rich flows of information and most make use of specialized organs. In all five cases, the sensory system combines two functions: measurement of a stimulus and encoding it in a way that can be transmitted via a nerve into the brain. In addition, the brain may signal back to the sensing system to modulate the way that it works.
7. Defence
Authors: Davies Jamie A.
Published: May 2021

This chapter describes how the human body protects its internal conditions against micro-organisms and the environment. The body’s first line of defence is the mechanical barrier provided by the skin, a part of the integumentary system. When the integument is breached, the body’s immediate priority is to seal the hole by coagulation of the leaking blood. The next line of defence is chemical: the secretions that cover the surfaces of eyes and the inside of the nose contain a variety of proteins that attack bacteria. Within the blood and fluids that bathe internal tissues are proteins of the complement system. The chapter then considers the innate and the adaptive immune systems.
8. Reproduction
Authors: Davies Jamie A.
Published: May 2021

This chapter explores the physiology of reproduction. It spans the making of gametes, making a potential home for an embryo in the mother, arranging that fertilization takes place, supporting the developing embryos, making a supply of milk (lactation) in time for the birth, and, of course, developing from a single cell into an adult capable of repeating the whole process. The chapter then looks at the determination of biological sex in humans. The scientific understanding of reproductive physiology now gives people choices. People can now choose to limit their reproduction by measures such as sexual abstinence, condoms, and oral contraceptive pills.
Temperature effects on forest understorey plants in hedgerows: a combined warming and transplant experiment
Authors: Vanneste Thomas , Van Den Berge Sanne , Brunet Jörg , Hedwall Per-Ola , Verheyen Kris , De Frenne Pieter
Published: May 2021

Background and Aims

Hedgerows have been shown to improve forest connectivity, leading to an increased probability of species tracking the shifting bioclimatic envelopes. However, it is still unknown how species in hedgerows respond to temperature changes, and whether effects differ compared with those in nearby forests. We aimed to elucidate how ongoing changes in the climate system will affect the efficiency of hedgerows in supporting forest plant persistence and migration in agricultural landscapes.

Methods

Here we report results from the first warming experiment in hedgerows. We combined reciprocal transplantation of plants along an 860-km latitudinal transect with experimental warming to assess the effects of temperature on vegetative growth and reproduction of two common forest herbs (Anemone nemorosa and Geum urbanum) in hedgerows versus forests.

Key Results

Both species grew taller and produced more biomass in forests than in hedgerows, most likely due to higher competition with ruderals and graminoids in hedgerows. Adult plant performance of both species generally benefitted from experimental warming, despite lower survival of A. nemorosa in heated plots. Transplantation affected the species differently: A. nemorosa plants grew taller, produced more biomass and showed higher survival when transplanted at their home site, indicating local adaptation, while individuals of G. urbanum showed greater height, biomass, reproductive output and survival when transplanted northwards, likely owing to the higher light availability associated with increasing photoperiod during the growing season.

Conclusions

These findings demonstrate that some forest herbs can show phenotypic plasticity to warming temperatures, potentially increasing their ability to benefit from hedgerows as ecological corridors. Our study thus provides novel insights into the impacts of climate change on understorey plant community dynamics in hedgerows, and how rising temperature can influence the efficiency of these corridors to assist forest species’ persistence and colonization within and beyond their current distribution range.
Acid or base? How do plants regulate the ecology of their phylloplane?
Authors: Gilbert Kadeem J , Renner Tanya
Published: May 2021

Plants interface with and modify the external environment across their surfaces, and in so doing, can control or mitigate the impacts of abiotic stresses and also mediate their interactions with other organisms. Botanically, it is known that plant roots have a multi-faceted ability to modify rhizosphere conditions like pH, a factor with a large effect on a plant’s biotic interactions with microbes. But plants can also modify pH levels on the surfaces of their leaves. Plants can neutralize acid rain inputs in a period of hours, and either acidify or alkalinize the pH of neutral water droplets in minutes. The pH of the phylloplane—that is, the outermost surface of the leaf—varies across species, from incredibly acidic (carnivorous plants: as low as pH 1) to exceptionally alkaline (species in the plant family, Malvaceae, up to pH 11). However, most species mildly acidify droplets on the phylloplane by 1.5 orders of magnitude in pH. Just as rhizosphere pH helps shape the plant microbiome and is known to influence belowground interactions, so too can phylloplane pH influence aboveground interactions in plant canopies. In this review, we discuss phylloplane pH regulation from the physiological, molecular, evolutionary, and ecological perspectives and address knowledge gaps and identify future research directions.
Effects of three-dimensional soil heterogeneity and species composition on plant biomass and biomass allocation of grass-mixtures
Authors: Liu Yongjie , Li Guoe , Wang Mingxia , Yan Wenjing , Hou Fujiang
Published: May 2021

Soil heterogeneity significantly affects plant dynamics such as plant growth and biomass. Most studies developed soil heterogeneity in two dimensions, i.e. either horizontally or vertically. However, soil heterogeneity in natural ecosystems varies both horizontally and vertically, i.e. in three dimensions. Previous studies on plant biomass and biomass allocation rarely considered the joint effects of soil heterogeneity and species composition. Thus, to investigate such joint effects on plant biomass and biomass allocation, a controlled experiment was conducted, where three levels of soil heterogeneity and seven types of species compositions were applied. Such soil heterogeneity was developed by filling nutrient-rich and nutrient-poor substrates in an alternative pattern in pots with different patch sizes (small, medium or large), and species compositions was achieved by applying three plant species (i.e. Festuca elata, Bromus inermis, Elymus breviaristatus) in all possible combinations (growing either in monoculture or in mixtures). Results showed that patch size significantly impacted plant biomass and biomass allocation, which differed among plant species. Specially, at the pot scale, with increasing patch size, shoot biomass decreased, while root biomass and R:S ratio increased, and total biomass tended to show a unimodal pattern, where the medium patch supported higher total biomass. Moreover, at the substrate scale, more shoot biomass and total biomass were found in nutrient-rich substrate. Furthermore, at the community scale, two of the three target plant species growing in monoculture had more shoot biomass than those growing together with other species. Thus, our results indicate soil heterogeneity significantly affected plant biomass and biomass allocation, which differ among plant species, though more research is needed on the generalization on biomass allocation. We propose that soil heterogeneity should be considered more explicitly in studies with more species in long-term experiments.
Zooming through the MIST
Authors: Owens Mathew , Allanson Oliver , Maunder Megan
Published: May 2021

Mathew Owens, Oliver Allanson and Megan Maunder report on the 51st annual Magnetosphere, Ionosphere, and Solar–Terrestrial (MIST) meeting
Using interpretable deep learning to model cancer dependencies
Authors: Lin Chih-Hsu , Lichtarge Olivier
Published: May 2021

Motivation

Cancer dependencies provide potential drug targets. Unfortunately, dependencies differ among cancers and even individuals. To this end, visible neural networks (VNNs) are promising due to robust performance and the interpretability required for the biomedical field.

Results

We design Biological visible neural network (BioVNN) using pathway knowledge to predict cancer dependencies. Despite having fewer parameters, BioVNN marginally outperforms traditional neural networks (NNs) and converges faster. BioVNN also outperforms an NN based on randomized pathways. More importantly, dependency predictions can be explained by correlating with the neuron output states of relevant pathways, which suggest dependency mechanisms. In feature importance analysis, BioVNN recapitulates known reaction partners and proposes new ones. Such robust and interpretable VNNs may facilitate the understanding of cancer dependency and the development of targeted therapies.

Availability and implementation

Code and data are available at https://github.com/LichtargeLab/BioVNN

Supplementary information

Supplementary data are available at Bioinformatics online.
SAMF: a self-adaptive protein modeling framework
Authors: Ding Wenze , Xu Qijiang , Liu Siyuan , Wang Tong , Shao Bin , Gong Haipeng , Liu Tie-Yan
Published: May 2021

Motivation

Gradient descent-based protein modeling is a popular protein structure prediction approach that takes as input the predicted inter-residue distances and other necessary constraints and folds protein structures by minimizing protein-specific energy potentials. The constraints from multiple predicted protein properties provide redundant and sometime conflicting information that can trap the optimization process into local minima and impairs the modeling efficiency.

Results

To address these issues, we developed a self-adaptive protein modeling framework, SAMF. It eliminates redundancy of constraints and resolves conflicts, folds protein structures in an iterative way, and picks up the best structures by a deep quality analysis system. Without a large amount of complicated domain knowledge and numerous patches as barriers, SAMF achieves the state-of-the-art performance by exploiting the power of cutting-edge techniques of deep learning. SAMF has a modular design and can be easily customized and extended. As the quality of input constraints is ever growing, the superiority of SAMF will be amplified over time.

Availability and implementation

The source code and data for reproducing the results is available at https://msracb.blob.core.windows.net/pub/psp/SAMF.zip.

Supplementary information

Supplementary data are available at Bioinformatics online.
Sodium–glucose cotransporter 2 inhibitors: renal outcomes according to baseline albuminuria
Authors: Delanaye Pierre , Wissing Karl Martin , Scheen Andre J
Published: May 2021

Sodium–glucose co-transporter 2 inhibitors (SGLT2is) reduce albuminuria and hard renal outcomes (decline of renal function, renal replacement therapy and renal death) in patients with/without type 2 diabetes at high cardiovascular or renal risk. The question arises whether baseline albuminuria also influences renal outcomes with SGLT2is as reported with renin–angiotensin–aldosterone system inhibitors. Post hoc analyses focusing on albuminuria and renal outcomes of four cardiovascular outcome trials [EMPA-REG OUTCOME (Empagliflozin Cardiovascular Outcome Event Trial in Type 2 Diabetes Mellitus Patients), CANVAS (Canagliflozin Cardiovascular Assessment Study), DECLARE-TIMI 58 (Multicenter Trial to Evaluate the Effect of Dapagliflozin on the Incidence of Cardiovascular Events–Thrombolysis in Myocardial Infarction 58) and VERTIS CV (Evaluation of Ertugliflozin Efficacy and Safety Cardiovascular Outcomes Trial)] and some renal data from two heart failure trials [Dapagliflozin and Prevention of Adverse Outcomes in Heart Failure (DAPA-HF) and EMPEROR-Reduced (Empagliflozin Outcome Trial in Patients With Chronic Heart Failure With Reduced Ejection Fraction)] showed renal protection with SGLT2is without significant interaction (P > 0.10) when comparing renal outcomes according to baseline levels (A1, A2 and A3) of urinary albumin:creatinine ratio (UACR), a finding confirmed in a dedicated meta-analysis. Two trials [CREDENCE (Evaluation of the Effects of Canagliflozin on Renal and Cardiovascular Outcomes in Participants With Diabetic Nephropathy) and DAPA-CKD (Dapagliflozin and Prevention of Adverse Outcomes in Chronic Kidney Disease)] specifically recruited patients with CKD and UACRs of 200–5000 mg/g. A post hoc analysis of CREDENCE that distinguished three subgroups according to UACR (300–1000, 1000–3000 and >3000 mg/g) showed a greater relative reduction in UACR in patients with lower baseline albuminuria levels (P for interaction = 0.03). Patients with a UACR >1000 mg/g showed a significantly greater reduction in absolute (P for interaction < 0.001) and a trend in relative (P for interaction = 0.25) risk of renal events versus those with lower UACR levels. In conclusion, baseline UACR levels do not significantly influence the nephroprotection by SGLT2is, yet the greater protection in patients with very high UACRs in CREDENCE deserves confirmation. The underlying mechanisms of renal protection with SGLT2is might be different in patients with or without (high) UACR.
The second warning to humanity: contributions and solutions from conservation physiology
Authors: Madliger Christine L , Franklin Craig E , Chown Steven L , Fuller Andrea , Hultine Kevin R , Costantini David , Hopkins William A , Peck Myron A , Rummer Jodie L , Sack Lawren , Willis Craig K R , Cooke Steven J
Published: May 2021

In 1992, the Union of Concerned Scientists shared their ‘World Scientists’ Warning to Humanity’ with governmental leaders worldwide, calling for immediate action to halt the environmental degradation that threatens the systems that support life on Earth. A follow-up ‘Second Warning’ was released in 2017, with over 15 000 scientists as signatories, describing the lack of progress in adopting the sustainable practices necessary to safeguard the biosphere. In their ‘Second Warning’, Ripple and colleagues provided 13 ‘diverse and effective steps humanity can take to transition to sustainability.’ Here, we discuss how the field of conservation physiology can contribute to six of these goals: (i) prioritizing connected, well-managed reserves; (ii) halting the conversion of native habitats to maintain ecosystem services; (iii) restoring native plant communities; (iv) rewilding regions with native species; (v) developing policy instruments; and (vi) increasing outdoor education, societal engagement and reverence for nature. Throughout, we focus our recommendations on specific aspects of physiological function while acknowledging that the exact traits that will be useful in each context are often still being determined and refined. However, for each goal, we include a short case study to illustrate a specific physiological trait or group of traits that is already being utilized in that context. We conclude with suggestions for how conservation physiologists can broaden the impact of their science aimed at accomplishing the goals of the ‘Second Warning’. Overall, we provide an overview of how conservation physiology can contribute to addressing the grand socio-environmental challenges of our time.
Presynaptic Gαo (GOA-1) signals to depress command neuron excitability and allow stretch-dependent modulation of egg laying in Caenorhabditis elegans
Authors: Ravi Bhavya , Zhao Jian , Chaudhry Sana I , Signorelli Rossana , Bartole Mattingly , Kopchock Richard J , Guijarro Christian , Kaplan Joshua M , Kang Lijun , Collins Kevin M
Published: May 2021

Egg laying in the nematode worm Caenorhabditis elegans is a two-state behavior modulated by internal and external sensory input. We have previously shown that homeostatic feedback of embryo accumulation in the uterus regulates bursting activity of the serotonergic HSN command neurons that sustains the egg-laying active state. How sensory feedback of egg release signals to terminate the egg-laying active state is less understood. We find that Gαo, a conserved Pertussis Toxin-sensitive G protein, signals within HSN to inhibit egg-laying circuit activity and prevent entry into the active state. Gαo signaling hyperpolarizes HSN, reducing HSN Ca2+ activity and input onto the postsynaptic vulval muscles. Loss of inhibitory Gαo signaling uncouples presynaptic HSN activity from a postsynaptic, stretch-dependent homeostat, causing precocious entry into the egg-laying active state when only a few eggs are present in the uterus. Feedback of vulval opening and egg release activates the uv1 neuroendocrine cells which release NLP-7 neuropeptides which signal to inhibit egg laying through Gαo-independent mechanisms in the HSNs and Gαo-dependent mechanisms in cells other than the HSNs. Thus, neuropeptide and inhibitory Gαo signaling maintain a bi-stable state of electrical excitability that dynamically controls circuit activity in response to both external and internal sensory input to drive a two-state behavior output.
The hazard of coseismic gaps: the 2021 Fukushima earthquake
Authors: Kiser Eric , Kehoe Haiyang
Published: May 2021

Subduction zones are associated with significant seismic hazards around the world and determining the future locations of large earthquakes within these systems is a perpetual challenge of the Earth sciences. This study presents back-projection results from the 2021 Mw 7.1 Fukushima earthquake which show that the rupture area of this event filled a previously identified coseismic gap within the rupture area of the 2011 Mw 9.1 Tohoku-oki earthquake. These results, combined with observations of a similar coseismic gap from the 2010 Mw 8.8 Maule, Chile earthquake that was subsequently filled by a Mw 7.1 aftershock, demonstrate that future assessments of seismic hazards following giant earthquakes should include the identification of coseismic gaps left within main shock rupture areas.
The Development and Neuronal Complexity of Bipinnaria Larvae of the Sea StarAsterias rubens
Authors: Carter Hugh F , Thompson Jeffrey R , Elphick Maurice R , Oliveri Paola
Published: May 2021

Synopsis

Free-swimming planktonic larvae are a key stage in the development of many marine phyla, and studies of these organisms have contributed to our understanding of major genetic and evolutionary processes. Although transitory, these larvae often attain a remarkable degree of tissue complexity, with well-defined musculature and nervous systems. Among the best studied are larvae belonging to the phylum Echinodermata, but with work largely focused on the pluteus larvae of sea urchins (class Echinoidea). The greatest diversity of larval strategies among echinoderms is found in the class Asteroidea (sea stars), organisms that are rapidly emerging as experimental systems for genetic and developmental studies. However, the bipinnaria larvae of sea stars have only been studied in detail in a small number of species and although they have been relatively well described neuro-anatomically, they are poorly understood neurochemically. Here, we have analyzed embryonic development and bipinnaria larval anatomy in the common North Atlantic sea star Asterias rubens, using a variety of staining methods in combination with confocal microscopy. Importantly, the chemical complexity of the nervous system of bipinnaria larvae was revealed through use of a diverse set of antibodies, with identification of at least three centers of differing neurochemical signature within the previously described nervous system: the anterior apical organ, oral region, and ciliary bands. Furthermore, the anatomy of the musculature and sites of cell division in bipinnaria larvae was analyzed. Comparisons of developmental progression and molecular anatomy across the Echinodermata provided a basis for hypotheses on the shared evolutionary and developmental processes that have shaped this group of animals. We conclude that bipinnaria larvae appear to be remarkably conserved across ∼200 million years of evolutionary time and may represent a strong evolutionary and/or developmental constraint on species utilizing this larval strategy.
Obsessive Compulsive Disorder During Coronavirus Disease 2019 (COVID-19): 2- and 6-Month Follow-Ups in a Clinical Trial
Authors: Carmi Lior , Ben-Arush Oded , Fostick Leah , Cohen Hagit , Zohar Joseph
Published: May 2021

Background

Psychiatric patients are perceived to be especially vulnerable during a pandemic, as it increases stress and uncertainty. Several current publications have considered obsessive-compulsive disorder (OCD) patients to be particularly vulnerable during the coronavirus disease 2019 (COVID-19), and clinicians were advised to adjust treatments accordingly. The purpose of this study was to evaluate the 2- and 6-month impacts of COVID-19 on the symptom severity of OCD patients.

Methods

A cohort of OCD patients actively treated with Exposure and Response Prevention (ERP) combined with pharmacological treatment was evaluated as part of their regular psychiatric assessment twice: 113 patients were evaluated at their 2-month follow-up and 90 patients (from that cohort) were evaluated at their 6-month follow up.

Results

Obsessive-compulsive symptom deterioration was not present in 84% of the patients at the 2-month follow-up and 96% of the patients at the 6-month follow-up. The results were also replicated in the OCD subgroup that included patients with contamination (washers) and illness obsessions, who were believed to be particularly vulnerable considering their obsessional content.

Conclusions

OCD patients (including those with obsessions related to contamination and health) who were under active ERP and pharmacological treatment did not experience exacerbated symptoms during COVID-19 at their 2- and 6-month follow-ups.
The Evaluation of the Containment Efficacy of Semi-Rigid Isolators for Housing Cages of Laboratory Animals Infected With BSL-3 Agents
Authors: DeTolla Louis , Johnson David K , Reynolds Scott D , Sanchez Rigoberto , Weichbrod Robert H , Terzi Matthew C
Published: May 2021

Research animals models infected with Biosafety Level-3 (BSL-3) agents need to be housed in specialized biocontainment caging. Most of these specialized cages have input and exhaust that is high efficiency particulate air filtered and sealed to prevent escape of the BSL-3 agent. An alternative to the use of the above BSL-3 biocontainment caging is the use of a flexible film or modified semi-rigid plastic film isolator that has its own high efficiency particulate air–filtered input and exhaust and is sealed with respect to the animal room environment, thus preventing BSL-3 agent escape. Standard caging can be housed within such an isolator. Computational fluid dynamics was used to evaluate the integrity of modified semi-rigid isolators for containment of aerosolized BSL-3 agents. Three isolators were located inside an animal BSL-3 room to provide an extra tier of protection and to permit different infectious studies within the same room while reducing or eliminating the risk of cross-contamination. The isolators were sized to house caging for rabbits and smaller non-human primates such as marmosets, African greens, and macaques. Multiple case studies of failure scenarios were investigated, including isolator breaches through the plastic membrane seam separation and rips, and exhaust fan failure. Breaching the level of containment provided by the isolators required the improbable simultaneous event of a plastic membrane rip in addition to the rare malfunction of the back-up exhaust fans. Each isolator was equipped with 2 blower motors connected in parallel to a common exhaust plenum and a battery backup. Even with this rare double (simultaneous) event, the animal BSL-3 room air exhaust system was able to contain the few droplets released in the simulated computational fluid dynamics breach. The modified semi-rigid isolators with negative airflow proved safe and effective for aerosol studies using BSL-3 agents, even in the unlikely event of a breach in containment.
Patient data ownership: who owns your health?
Authors: Liddell Kathleen , Simon David A , Lucassen Anneke
Published: May 2021

This article answers two questions from the perspective of United Kingdom law and policy: (i) is health information property? and (ii) should it be? We argue that special features of health information make it unsuitable for conferral of property rights without an extensive system of data-specific rules, like those that govern intellectual property. Additionally, we argue that even if an extensive set of rules were developed, the advantages of a property framework to govern health information would be slight: propertization is unlikely to enhance patient self-determination, increase market efficiency, provide patients a foothold in the data economy, clarify legal uses of information, or encourage data-driven innovation. The better approach is to rely less, not more, on property. We recommend a regulatory model with four signature features: (i) substantial protection for personal health data similar to the GDPR with transparent limits on how, when, and by whom patient data can be accessed, used, and transmitted; (ii) input from relevant stakeholders; (iii) interoperability; and (iv) greater research into a health-data service, rather than goods, model.
The Effects of Person-Centered Social Support Messages on Recipient Distress Over Time within a Conversation
Authors: Rains Stephen A , High Andrew C
Published: May 2021

Although prior research documents the benefits of supportive messages containing higher levels of verbal person centeredness (VPC), the effects of this message property over time within a discussion are not well understood. This project evaluated predictions about the effects of high and low VPC messages over time drawn from the theory of conversationally induced reappraisals and the dual-process model of supportive communication outcomes. Participants (N = 281) completed an interaction with a computerized support provider in which the level of VPC was manipulated. Before and after the interaction and after receiving each of four supportive messages, participants rated their emotional distress, reappraisal, and validation. Participants in the high and low VPC conditions exhibited a significant reduction in emotional distress from before to after their interaction. Receiving subsequent messages with high levels of VPC produced a non-linear trend in distress reduction, whereas receiving subsequent low VPC messages fostered little change.
Axisymmetric model of the sealing cylinder in service: analytical solutions
Authors: Jin Lan , Cheng Yonggui , Zhang Kai , Xue Zhangna , Liu Jianlin
Published: May 2021

The stress state analysis of the sealing cylinder is of great significance for the safe operation of the sealing system. In this study, we probe a sealing system that can be simplified as an axisymmetric problem. In service, the rubber around the central pipe contacts the casing under the action of the axial pressure, and thus the sealing function is realized. The analytical solution of the stress at the sealing interface is derived based on the Love strain function in the axisymmetric configuration. Then, the relationship between the axial pressure and the gap (between the sealing cylinder and the casing) is presented, and the contact pressure at the contact interface is also given. The numerical simulation is performed, which is in agreement with the analytical solutions in the two deformation stages. The obtained results in the current work have also been comprehensively compared with the previous results, to give suggestions for engineering selection. These findings are beneficial to obtain a deep understanding on the mechanism of the sealing process, and provide some inspirations on the new types of sealing tools for mechanical engineering, chemical engineering, petroleum engineering, etc.
Prognostic significance of inflammatory response markers for locally advanced squamous cell carcinoma of the external auditory canal and middle ear
Authors: Makita Kenji , Hamamoto Yasushi , Takata Noriko , Ishikawa Hirofumi , Tsuruoka Shintaro , Uwatsu Kotaro , Hato Naohito , Kido Teruhito
Published: May 2021

We investigated the prognostic significance and treatment outcomes of pretreatment inflammatory response markers for locally advanced squamous cell carcinoma (SCC) of the external auditory canal (EAC) and middle ear (ME). Between July 2003 and July 2019, 21 patients with SCC of the EAC (n = 18) or ME (n = 3) who received radiotherapy with or without surgery or systemic therapy (radiotherapy alone [n = 2], radiotherapy + systemic therapy [n = 6], radiotherapy + surgery [n = 7], radiotherapy + surgery + systemic therapy [n = 6]) were retrospectively examined. The median radiation dose was 66.0 (range, 50.4–70.0) Gy, with daily fractions of 1.8–2.0 Gy. The median follow-up period was 25 months (range, 6–137). The two-year overall survival (OS), progression-free survival (PFS), and locoregional control (LC) rates were 61%, 48%, and 55%, respectively. OS, PFS, and LC did not differ significantly according to patient- (age, sex), tumor- (Pittsburgh stage, pretreatment neurological findings), and treatment-related (surgery or systemic therapy, radiation dose, prophylactic neck irradiation) factors. Conversely, there were significant differences in OS, PFS, and LC between patients with high and low pretreatment C-reactive protein-to-albumin ratios (p = 0.002, 0.003, and 0.004, respectively). OS also differed significantly between patients with high and low pretreatment neutrophil-to-lymphocyte ratios (NLR; p = 0.037). Other inflammatory response markers, including platelet-to-lymphocyte ratio (PLR) and albumin-to-globulin ratio (AGR), did not influence OS, PFS, or LC. Our findings suggest that pretreatment C-reactive protein-to-albumin ratio and NLRs have a significant impact on treatment outcomes in patients with locally advanced SCC of the EAC and ME.
Stakeholder perspectives on the development and implementation of approaches to municipal rat management
Authors: Lee Michael J , Byers Kaylee A , Cox Susan M , Stephen Craig , Patrick David M , Himsworth Chelsea G
Published: May 2021

Rats evoke public health and economic concern in cities globally. Rapid urbanization exacerbates pre-existing rat problems, requiring the development and adoption of more effective methods of prevention, monitoring and mitigation. While previous studies have indicated that city-wide municipal management approaches often fail, such outcomes are often left without specific explanation. To determine how municipalities could more effectively develop and implement large-scale approaches, we interviewed stakeholders in municipal rat management programs to document their opinions, recommendations and the challenges they face. Using a thematic framework method, this study collates and analyzes in-depth interviews with 39 stakeholders from seven cities across the United States. Overall, stakeholders’ recommendations for municipal rat management aligned with many conceptual attributes of effective management reported in the literature. Specifically, stakeholders highlighted the need to prioritize the reduction of resources available to sustain rat infestations (e.g. food, water and harborage), to focus on proactive (vs. reactive) measures, and to implement large-scale data collection to increase the efficiency of cross-city rat control. Stakeholders also suggested novel approaches to management, such as mitigating rat-associated risks for vulnerable populations specifically and developing tailored initiatives based on the specific needs and desires of residents. We synthesize these recommendations in light of reported barriers, such as resource limitations, and consider several opportunities that may help municipalities reconceptualize their approaches to city-wide rat management.
How deep is the ocean? Exploring the phase structure of water-rich sub-Neptunes
Authors: Nixon Matthew C , Madhusudhan Nikku
Published: May 2021

Understanding the internal structures of planets with a large H2O component is important for the characterization of sub-Neptune planets. The finding that the mini-Neptune K2-18b could host a liquid water ocean beneath a mostly hydrogen envelope motivates a detailed examination of the phase structures of water-rich planets. To this end, we present new internal structure models for super-Earths and mini-Neptunes that enable detailed characterization of a planet’s water component. We use our models to explore the possible phase structures of water worlds and find that a diverse range of interiors are possible, from oceans sandwiched between two layers of ice to supercritical interiors beneath steam atmospheres. We determine how the bulk properties and surface conditions of a water world affect its ocean depth, finding that oceans can be up to hundreds of times deeper than on Earth. For example, a planet with a 300 K surface can possess H2O oceans with depths from 30–500 km, depending on its mass and composition. We also constrain the region of mass–radius space in which planets with H/He envelopes could host liquid H2O, noting that the liquid phase can persist at temperatures up to 647 K at high pressures of 218–$7\times 10^4$ bar. Such H/He envelopes could contribute significantly to the planet radius while retaining liquid water at the surface, depending on the planet mass and temperature profile. Our findings highlight the exciting possibility that habitable conditions may be present on planets much larger than Earth.
The AARTFAAC 60 MHz transients survey
Authors: Kuiack Mark , Wijers Ralph A M J , Shulevski Aleksandar , Rowlinson Antonia , Huizinga Folkert , Molenaar Gijs , Prasad Peeyush
Published: May 2021

We report the experimental set-up and overall results of the AARTFAAC wide-field radio survey, which consists of observing the sky within 50° of Zenith, with a bandwidth of 3.2 MHz, at a cadence of 1 s, for 545 h. This yielded nearly 4 million snapshots, two per second, of on average 4800 square degrees and a sensitivity of around 60 Jy. We find two populations of transient events, one originating from PSR B0950+08 and one from strong ionospheric lensing events, as well as a single strong candidate for an extragalactic transient, with a peak flux density of 80 ± 30 Jy and a dispersion measure of $73\pm 3\, \mathrm{~pc~cm^{-3}}$. We also set a strong upper limit of 1.1 all-sky per day to the rate of any other populations of fast, bright transients. Lastly, we constrain some previously detected types of transient sources by comparing our detections and limits with other low-frequency radio transient surveys.
Chemical abundances in the nuclear region of nearby galaxies from the Palomar Survey
Authors: Pérez-Díaz B , Masegosa J , Márquez I , Pérez-Montero E
Published: May 2021

We estimate chemical abundances and ionization parameters in the nuclear region of a sample of 143 galaxies from the Palomar Spectroscopic Survey, composed by star-forming galaxies (87), Seyferts 2 (16), and LINERs (40) using the hii-chi-mistry code. We also study for each spectral type the correlation of the derived quantities with other different properties of the host galaxies, such as morphology, stellar mass, luminosity, and mass of their supermassive black holes. The results obtained for star-forming galaxies are used to check the soundness of our methodology. Then, we replicate a similar study for our sample of AGN, distinguishing between Seyferts 2 and LINERs. We report a saturation of Oxygen abundances for the nuclear regions of SFG. The correlations between chemical abundances and their host galaxy properties for SFG are in good agreement with previous studies. We find that Seyferts 2 present slightly higher chemical abundances but this result must be reexamined in larger samples of Seyfert galaxies. In contrast, we obtain lower chemical abundances for LINERs than for SFG. We confirm these relatively lower abundances for another sample of infrared luminous LINERs in the same stellar mass range. Our analysis of AGNs (both LINERs and Seyferts) shows that their host galaxy properties are not correlated with our estimated chemical abundances.
Strong lens modelling: comparing and combining Bayesian neural networks and parametric profile fitting
Authors: Pearson James , Maresca Jacob , Li Nan , Dye Simon
Published: May 2021

The vast quantity of strong galaxy–galaxy gravitational lenses expected by future large-scale surveys necessitates the development of automated methods to efficiently model their mass profiles. For this purpose, we train an approximate Bayesian convolutional neural network (CNN) to predict mass profile parameters and associated uncertainties, and compare its accuracy to that of conventional parametric modelling for a range of increasingly complex lensing systems. These include standard smooth parametric density profiles, hydrodynamical EAGLE galaxies, and the inclusion of foreground mass structures, combined with parametric sources and sources extracted from the Hubble Ultra Deep Field. In addition, we also present a method for combining the CNN with traditional parametric density profile fitting in an automated fashion, where the CNN provides initial priors on the latter’s parameters. On average, the CNN achieved errors 19 ± 22 per cent lower than the traditional method’s blind modelling. The combination method instead achieved 27 ± 11 per cent lower errors over the blind modelling, reduced further to 37 ± 11 per cent when the priors also incorporated the CNN-predicted uncertainties, with errors also 17 ± 21 per cent lower than the CNN by itself. While the CNN is undoubtedly the fastest modelling method, the combination of the two increases the speed of conventional fitting alone by factors of 1.73 and 1.19 with and without CNN-predicted uncertainties, respectively. This, combined with greatly improved accuracy, highlights the benefits one can obtain through combining neural networks with conventional techniques in order to achieve an efficient automated modelling approach.
On the Origin of Frameshift-Robustness of the Standard Genetic Code
Authors: Xu Haiqing , Zhang Jianzhi
Published: May 2021

The standard genetic code (SGC) has been extensively analyzed for the biological ramifications of its nonrandom structure. For instance, mismatch errors due to point mutation or mistranslation have an overall smaller effect on the amino acid polar requirement under the SGC than under random genetic codes (RGCs). A similar observation was recently made for frameshift errors, prompting the assertion that the SGC has been shaped by natural selection for frameshift-robustness—conservation of certain amino acid properties upon a frameshift mutation or translational frameshift. However, frameshift-robustness confers no benefit because frameshifts usually create premature stop codons that cause nonsense-mediated mRNA decay or production of nonfunctional truncated proteins. We here propose that the frameshift-robustness of the SGC is a byproduct of its mismatch-robustness. Of 564 amino acid properties considered, the SGC exhibits mismatch-robustness in 93–133 properties and frameshift-robustness in 55 properties, respectively, and that the latter is largely a subset of the former. For each of the 564 real and 564 randomly constructed fake properties of amino acids, there is a positive correlation between mismatch-robustness and frameshift-robustness across one million RGCs; this correlation arises because most amino acid changes resulting from a frameshift are also achievable by a mismatch error. Importantly, the SGC does not show significantly higher frameshift-robustness in any of the 55 properties than RGCs of comparable mismatch-robustness. These findings support that the frameshift-robustness of the SGC need not originate through direct selection and can instead be a site effect of its mismatch-robustness.
Effect of Inadequate Empiric Antibacterial Therapy on Hospital Outcomes in SARS-CoV-2-Positive and -Negative US Patients With a Positive Bacterial Culture: A Multicenter Evaluation From March to November 2020
Authors: Puzniak Laura , Bauer Karri A , Yu Kalvin C , Moise Pamela , Finelli Lyn , Ye Gang , De Anda Carisa , Vankeepuram Latha , Gupta Vikas
Published: May 2021

Background

Increased utilization of antimicrobial therapy has been observed during the coronavirus disease 2019 pandemic. We evaluated hospital outcomes based on the adequacy of antibacterial therapy for bacterial pathogens in US patients.

Methods

This multicenter retrospective study included patients with ≥24 hours of inpatient admission, ≥24 hours of antibiotic therapy, and discharge/death from March to November 2020 at 201 US hospitals in the BD Insights Research Database. Included patients had a test for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and a positive bacterial culture (gram-positive or gram-negative). We used generalized linear mixed models to evaluate the impact of inadequate empiric therapy (IET), defined as therapy not active against the identified bacteria or no antimicrobial therapy in the 48 hours following culture, on in-hospital mortality and hospital and intensive care unit length of stay (LOS).

Results

Of 438 888 SARS-CoV-2-tested patients, 39 203 (8.9%) had positive bacterial cultures. Among patients with positive cultures, 9.4% were SARS-CoV-2 positive, 74.4% had a gram-negative pathogen, 25.6% had a gram-positive pathogen, and 44.1% received IET for the bacterial infection. The odds of mortality were 21% higher for IET (odds ratio [OR], 1.21; 95% CI, 1.10–1.33; P < .001) compared with adequate empiric therapy. IET was also associated with increased hospital LOS (LOS, 16.1 days; 95% CI, 15.5–16.7 days; vs LOS, 14.5 days; 95% CI, 13.9–15.1 days; P < .001). Both mortality and hospital LOS findings remained consistent for SARS-CoV-2-positive and -negative patients.

Conclusions

Bacterial pathogens continue to play an important role in hospital outcomes during the pandemic. Adequate and timely therapeutic management may help ensure better outcomes.
Spontaneous cervical swelling syndrome as a rare cause of neck edema: case series and literature review
Authors: Betrains Albrecht , Hermans Robert , Gheysens Olivier , Poorten Vincent Vander , Peetermans Willy E , Vanderschueren Steven
Published: May 2021

Spontaneous cervical swelling syndrome (SCSS) is a rare disorder characterized by unprovoked, self-limiting and often unilateral cervical edema. SCSS is a recurrent disorder that predominantly affects adult women and is not associated with laboratory abnormalities. We report on eight female patients with a mean age of 56 (38–82) years at the time of the first presentation. The episodes were characterized by an acute onset in all patients and had a mean duration of 3.8 (1–7) days. Biochemical analysis did not reveal any related abnormalities. Imaging of the neck and chest demonstrated diffuse edema in the supraclavicular fossa and left infrahyoid region in all patients. At the time of the acute event, lymphatic scintigraphy revealed tracer accumulation in the left supraclavicular region in three patients and could not demonstrate any abnormalities in the in-between episodes in two patients.