bluuebunny/crossref_metadata_2025 huggingface dataset:
Toxic and non-toxic dinoflagellates host distinct bacterial communities in their phycospheres
Authors: Deng Yunyan , Wang Kui , Hu Zhangxi , Hu Qiang , Tang Ying Zhong
Published: July 2023

Dinoflagellates encompass highly abundant and diverse toxin-producing species among marine phytoplankton. Previous works suggested that some bacterial taxa may affect toxins production in dinoflagellates, however, little is known about impact of toxic dinoflagellates on their co-existing bacterial flora. Here we characterized the bacterial communities associated with 22 clonal cultures of dinoflagellates using DNA metabarcoding method, including 11 confirmed toxic species and 11 species that have not been reported to be toxic. Beta diversity analysis revealed that all the 11 species in toxic group were clustered together and distinctly separated from non-toxic group, strongly suggesting the bacterial community composition was largely influenced by toxic dinoflagellate hosts. The toxic group was found to include higher relative abundance of non-carbohydrate utilizers and xenobiotic-degrading taxa and showed inhibitory effects on algicidal bacteria. These findings suggested that toxic dinoflagellates host bacterial communities distinctive from non-toxic species in multiple ways in their phycospheres.
The combination of metagenome and metabolome to compare the differential effects and mechanisms of fructose and sucrose on the metabolic disorders and gut microbiota in vitro and in vivo
Authors: Chen Qu , Ren Ruochen , Sun Yue , Xu Jing , Yang Hua , Li Xiaoqiong , Xiao Yingping , Li Jinjun , Lyu Wentao
Published: July 2023

The different responses of gut microbiota to excessive fructose or sucrose intake may lead to different effects on host health.
Non-precious metal-based heterostructure catalysts for hydrogen evolution reaction: mechanisms, design principles, and future prospects
Authors: Sun Mojie , Li Yalin , Wang Shijie , Wang Ziquan , Li Zhi , Zhang Ting
Published: July 2023

As a highly promising clean energy source to replace fossil fuels in the 21st century, hydrogen energy has garnered considerable attention, with water electrolysis emerging as a key hydrogen production technology.
The Smoluchowski–Kramer approximation of a generalized Langevin equation with state-dependent damping
Authors: Wang Shaoteng , Wang Wei
Published: July 2023

The small-mass limit is derived for a generalized Langevin equation (GLE) with state-dependent damping and a kernel expressed as an infinite sum of exponentials. The state dependence includes both the current and the past. By some bounded estimates and tightness, as the mass tends to 0, the GLE is shown to converge in distribution to a limit equation with additional drift terms that come from the current and the past state dependence, respectively.
Endurance Strength and Residual Life Assessment of T23 Steel after 96000 Hours of High Temperature and High Pressure Service
Authors: Yang Jia , Cai Yuanzong , Lu Li , Wang Yuwei , Liang Zhenxin , Cai Zhipeng , Sun Qian
Published: July 2023

The macroscopic morphology, oxide layer characteristics, rupture strength and residual life of T23 steel after 96000 hours of service at high temperature and high pressure were analyzed. The results show that T23 steel pipe has good macroscopic appearance, without obvious abnormal features such as cracks, folds, rolling breaks, double skin, scabs, delaminations and sharp scratches. The chemical composition of different pipe sections conforms to the standard, and the structure is mainly bainite, with uniform distribution and no obvious coarse phase. There is an obvious interface between the metal substrate and the internal oxide layer, and there is an obvious wavy line at the interface. The oxide layer is relatively dense and continuous. The tensile properties at room temperature and high temperature are good. At room temperature, the yield strength exceeds 420MPa, the tensile strength exceeds 540MPa, and the elongation exceeds 19%. After 96000 hours of use, the remaining creep life of T23 split platen superheater submitted for inspection is 84000 hours, and the remaining creep life of T23 rear platen superheater submitted for inspection is 40000 hours.
Fuzzy Structured Element Integrated Decision of Metamorphism on Coal Dust Ignition Hazard Rating
Authors: Dong Xiaoting , Liu Tianqi , Wang Xiaoyi , Xu Xiaoliang
Published: July 2023

To discuss the coal dust ignition hazard rating of different metamorphism, the fuzzy structure element integrated decision model about “no danger”, “weak danger”, “general danger”, and “strong danger” of coal dust ignition is established. 40 kinds of coal samples are selected to carry out coal quality analysis test, overpressure test, temperature test, flame propagation properties test and particle size distribution test. Based on this, coal dust ignition hazard rating decision-making index system is built. The triangular structure element is added to fuzzy comprehensive decision model, by sequencing weighted Hamming distance between fuzzy index value function and fuzzy maximal function, the coal dust ignition hazard rating of different coal quality can be decided. The result shows that: with increasing metamorphic grade, coal dust ignition hazard rating is decreasing, which provides study basis for relation between metamorphism and ignition hazard rating.
Numerical Simulation of Train-Induced Structural Vibration
Authors: Lin Gang , Liu Donghuan
Published: July 2023

Train-induced structural vibration caused more and more attentions nowadays, and the present paper developed a numerical approach of train-induced structural vibration simulation with ANSYS software. The finite element model is composed by buildings, rail, sleepers, ballast and several layers of soil, and the moving load is represented by wheel-rail coupling forces, and both solid element, shell element and beam element are used in the finite element model. Acceleration time history and vibration levels of the key point on the buildings are given, and effect of different wheel-rail coupling forces and the dynamic response of the building are also numerically investigated. Comparisons of free boundary, symmetric boundary, fixed boundary and transmitting boundary conditions on the dynamic responses are also illustrated. Numerical results show that, both boundary condition and load type could affect the dynamic response of the structures near the train tracks, and validation test should be performed firstly to determine the proper boundary condition and load amplitude and frequency. The proposed numerical method provides a powerful technic tool for numerically predicting the dynamic response of train-induce structural vibration, and could also be employed to evaluate the vibration control results of different approaches.
Research on Local Structure Plastic Damage of Cylindrical Shell under Near-field Underwater Explosion
Authors: Yang Di , Luo Wei , Li Fei , Gong Yufeng , Zhao Yongcai , Li Sheng
Published: July 2023

The local structure of the cylindrical shell produces plastic deformation under the near-field underwater explosion load, based on the fact that the ring rib is the strong support of reinforced cylindrical shell plate, this paper simplifies the reinforced cylindrical shell model into a rigid slatted beam model at both ends, and lists the equations of slatted beams under the action of shock wave and bubble pulsation load. This equation takes the initial damage caused by shock wave into account, and compares the calculation results obtained by the theoretical method with the experimental data, which verifies the correctness of this mechanical model. At the same time, it is explained that this calculation method can better predict the plastic damage of the local structure of the cylindrical shell under the action of near-field underwater explosion.
Multi-strategy Improved Sparrow Search Algorithm
Authors: Liu Zichang , Bai Yongsheng , Jia Xisheng
Published: July 2023

The multi-strategy improved sparrow search algorithm (MSISSA) is proposed to address the problems that the sparrow search algorithm (SSA) is not rich in population diversity, and is prone to fall into local optimality and poor accuracy in solving multi-dimensional functions. Firstly, Cat mapping is used to initialize the SSA population. Secondly, an elite reverse learning strategy is introduced to increase the population diversity and improve the global search ability of SSA. Then, the number of discoverers and the number of aware-at-risk sparrows are dynamically adjusted by improving the scaling factor. Finally, individuals are subjected to Cauchy variation or Tent chaos perturbation according to their fitness values to effectively solve the problem of their falling into local optimality. Simulation results show that MSISSA has higher performance in finding the optimum compared with classical optimization algorithms such as SSA.
The plot must thicken: a call for increased attention to social surprises in scenarios of climate futures
Authors: Keys Patrick W
Published: July 2023

Climate change scenarios are typically based on trajectories of greenhouse gas emissions out into the future. These emissions are then incorporated into climate and earth system models to simulate pathways of global climate change. These pathways are often communicated as the average of numerous model simulations. Though essential for calculating the role of greenhouse gas emissions on the climate system, this approach inadvertently masks the fact that our future will conform to something akin to a single model simulation, or storyline—rather than the average of many simulations. Human responses to and interactions with these climate storylines will not necessarily be expected or rational. As such, potential social surprises could lead to multiple plotlines emerging from a single earth system storyline. Such social surprises are explored in three examples: net zero emissions achievement, low climate sensitivity, and solar climate intervention. Climate change scenarios are fundamentally dependent on policy pathways that in practice will be influenced by public perception and expectation. Thus, it is essential for climate change scenarios to recognize and incorporate the potential for heterogeneous social surprises to unexpected climate changes.
De-Internationalization: The Other Side of Internationalization
Authors: Benito Gabriel R. G.
Published: July 2023

Companies rightly regard internationalization decisions as strategic; they are long-term, require and bind up resources, and have important implications for companies’ performance. But internationalization is inherently demanding and risky, changes are likely to happen, and there is no guarantee of a positive outcome. The notion of de-internationalization captures the other side of internationalization: actions that reduce a company’s engagement in or exposure to international or border-crossing activities. One important dimension of de-internationalization is its extent, which ranges from a total withdrawal from international operations to partial retractions, such as exiting from a particular market, and minor adjustments, such as downscaling activities. Another key dimension is the volition aspect of de-internationalization, which distinguishes between de-internationalization decisions that are principally taken by the companies themselves, and those that have been imposed upon the companies by other actors, such as host-country authorities. There are three main types of de-internationalization: reductions in trade volume, market withdrawals, and divestments. Extant research, while limited, has tended to take either a behavioral perspective or an economics perspective. The latter takes a choice (or decision) perspective on de-internationalization, while the former emphasizes the process aspects of such actions. De-internationalization does not need to be the end of the road for companies’ foreign involvement. There is mounting evidence that de-internationalization can be temporary, with companies re-entering foreign markets after a time-out period, often by implementing better suited approaches when retrying.
Memorable Messages in Families
Authors: Horstman Haley Kranstuber , Jordan Ellen , Yue Jinwen
Published: July 2023

Families are (one of) the first and most influential socializing agents of our lives. Among the innumerable messages family members convey to each other, a select few are regarded as “memorable.” Memorable messages are “distinct communication units considered influential over the course of a person’s life.” Those messages that are most memorable are typically brief, direct, oral messages delivered by a higher-status, older, and likable individual to the recipient during their teen or young adult years. Although memorable messages were initially regarded as having positive implications for the receiver’s life, newer research has provided space for the negative implications and perceptions of these messages. Nonverbal communication elements and relational contexts and qualities are influential to the receptivity of memorable messages. Although memorable messages often originate from a family member, the sources of memorable messages can also be friends/peers, teachers, coworkers, or, in some cases, the media. Research on memorable messages has been largely concentrated in health and interpersonal/family communication contexts; organizational and instructional contexts have also been explored. Memorable message research in families has focused much on health topics (i.e., mental health, sexual health, body image and weight), socialization (i.e., around school, work, race, other topics), and coping with hardship. In these studies, memorable messages have largely been investigated through mixed-method survey-based research, but also through purely quantitative (i.e., survey-based) and qualitative (i.e., interview) methods as well. This research has been largely atheoretical but has been grounded in control theory and, more recently, the theory of memorable messages and communicated narrative sense-making theory. Future research and practical applications of family memorable message research include informing health campaigns and family life education programming.
Social Identity Theory
Authors: Gaffney Amber M. , Hogg Michael A.
Published: July 2023

The self-concept provides people with a fundamental frame of reference for navigating their social world. People understand and interpret social interactions using knowledge of their personal self (e.g., How do I as an individual usually respond in this or a similar situation?), their relational self, in which the focus of interaction is their role defined by attachment bonds with specific significant other people, and their collective self in which interactions are fully defined by their membership in a distinct social group or category. Social context is the determinant of which level of self is the dominating feature driving interaction and relevant contextual knowledge of the self. The social identity perspective focuses on the part of the self-concept that people derive from their important group memberships—their social identities—and how group memberships can become a compass for an individual’s interactions within specific groups and how self and social categorization processes set the normative boundaries for intergroup relationships.
Leadership That Bridges Arts and Social-Emotional Learning
Authors: Nava Marco A. , Nava Imelda L. , Kirsch Jan
Published: July 2023

Over the last 40 years, due to the combination of cuts to school and district budgets and an overemphasis on standardized testing, arts instruction has been severely cut back in public schools. Minority and low-income students are the ones most negatively impacted, as the schools they attend generally have lower standardized test scores. A study, Arts and Social-Emotional Learning (ASEL), provided training for 44 elementary school administrators serving high-needs students. Through a theoretical framework of social-emotional and brain-based learning, participating administrators received 40 hours of professional development that supported them in creating safe classroom learning environments to foster creativity, innovation, and collaboration. The research may provide insights to assist school and district leaders to provide all students with equitable access to the arts and social-emotional learning.
Teacher Education in India
Authors: Mohanty Sunil Behari
Published: July 2023

In the last part of the 19th century, the consecutive model of teacher education followed in England was introduced in India by the English rulers. In the 1960s, the concurrent model-integrated teacher education program found in the United States was started by a private college at Kurukshetra, Haryana State. After 2 years, admission to this course was closed. In 1963, the National Council of Educational Research and Training launched pre-service teacher training program through this integrated B.A./B.Sc. and B.Ed. course meant for school leavers along with a 1-year B.Ed. for graduates in its four Regional Colleges of Education. The concurrent model for secondary school teacher training could not even draw the attention of the governments of the states in which these colleges are located. In spite of the efforts of the central government to bring uniformity, after-school education came under the concurrent list of the constitution of India, could not be successful. The complexity found in the school system is also reflected in the teacher education system. Central government schemes to improve quality of a certain number of state government teacher training colleges could not succeed. Transferring the task of controlling curricula for secondary school teacher training from state governments to universities also did not succeed, as some universities utilized B.Ed. courses for untrained teachers as a source of revenue generation. The Indian central government tried to regulate teacher education by having a statutory body-National Council for Teacher Education. This body increased the duration of the B.Ed. course through correspondence to 2 years, while face to face mode B.Ed. course continued to be of 1 year duration. In 2014, this body replaced 1 year B.Ed. course by 2 year B.Ed. course without increasing appropriate duration of B.Ed. correspondence (distance mode) course. The new education policy of 2020 has suggested implementing a 1-year B.Ed. course for postgraduates to be delivered by multidisciplinary institutions. The policy has made the future teacher education scenario more complicated by hoping that by 2030 all teacher training shall be provided through integrated teacher training programs.
Slavery in Egypt under the Mamluks
Authors: Ali Adam
Published: July 2023

The Muslim polity commonly referred to as the Mamluk Sultanate ruled Egypt and Syria during the late medieval period (1250–1517). Slaves played a big role at every level of society in Mamluk Egypt. A slave’s race, origins, and network (if he had one) determined the prospects of his life and career. Most slaves formed the lowest stratum in society as domestic servants and laborers. Such slaves could be Africans, Caucasians, Turks, Europeans, Greeks, Armenians, or Mongols. However, some slaves occupied the highest positions. These military slaves, the mamluks, dominated the army and the government and formed a military-political elite caste in Egyptian society. In fact, so-called military slaves played an important role in the history of the Muslim world for a millennium, starting from the 9th century. Even after the Ottoman conquest of Egypt in 1517, the mamluks continued to exist as an elite socio-military class in Egypt.
Global Abolitionist Movements
Authors: Rossi Benedetta
Published: July 2023

Abolitionism succeeded thanks to the struggles of many movements, some genuinely global, others national or local but interconnected at a global level. This article takes a pluralist approach to global abolitionism. Since the late 17th century, the membership, objectives, and strategies of different abolitionist movements have been varied, but they shared the same objective: to impose their understanding of slavery as an aberration that ought to be de-legalized and eventually prohibited worldwide. This article periodizes global abolitionism in three main stages characterized, successively, by the primacy of egalitarianism, imperialism, and internationalism. By the mid-20th century, pro-slavery ideologies were obsolete in Euro-America and had disappeared from official policy globally. They survived in circumscribed contexts in which anti-slavery activists are struggling against the lingering vitality of pro-slavery ideas in the 21st century.
Popular Infrastructures in West Africa
Authors: Chalfin Brenda
Published: July 2023

Popular infrastructures in West Africa encompass a broad array of basic utilities enabling access to water, sanitation, power, communication, and transportation networks. Though characterized as “by the people, for the people” formulations, popular infrastructures are rarely stand-alone and intersect with services sponsored by states, international investors, and humanitarian organizations. These amalgams evince a complex politics where self-determination vies with elite accommodation and infrastructural operations command labor and impinge upon public and private life. Most notable across the region is the overwhelming inadequacy of state-based infrastructural orders and the heightened role of corporate capital and commodification to meet and modify basic infrastructural needs and installations. This is evident in the rise of both digital communication networks and high-tech megaports and extractive enterprise across this wide swath of nation-states, the one intensifying social relations and interdependencies, the other promoting de-peopling and alienation. Like the “just-in-time” humanitarian infrastructural aid packages that mark the region’s crisis zones, they each carry their own chimera of promise. Received and reflected on by a diverse populace, these offerings and impositions combine with infrastructural strategies already in place—evident in revitalized tea circles in Niger and Burkina Faso; repair, care, and fabrication networks in Guinea, Ghana, Togo, and Nigeria; public points of gathering in Gambia, Cote d’Ivoire, and Benin; or new conventions of domesticity in Mali, Senegal, Liberia, and Sierra Leone. Irreducible to resistance or accommodation, popular infrastructural solutions prioritize opportunity and security in the face of the near inevitable predations of large-scale infrastructural interventions motivated by profit, development, or both.
Maritime Archaeology of the Post-Ancient World (1400–1946)
Authors: Delgado James P.
Published: July 2023

Maritime archaeology is a relatively new aspect of anthropological inquiry into the past and examines humanity’s interaction with the aquatic world. It specifically examines the archaeological remains of human interaction with the world’s waters. These are primarily shipwrecks, or sunken craft of all types and sizes, ranging from antiquity to the modern era. It includes the contents of shipwrecks, usually cargoes, but also personal effects such as baggage or ships’ equipment. Historic submerged resources in maritime archaeological research include now-inundated former ports, harbors, and settlements of the modern era and modern human-made artifacts that are preserved because they now rest under water, such as aircraft, particularly those associated with naval aviation.

The means by which these sites have been and are now interpreted has changed from a 20th-century approach of treating them as adjuncts to history and historical narratives to an anthropological approach in which they are interpreted as aspects of human societies and behavior. This includes ships and seafaring as key players in developing regional and global economies and their role in cultural exchange, colonial endeavors, warfare, and technological advances. The development of a theory of maritime archaeology, which examines the topic from both a submerged and nonsubmerged approach, evolved in the later 20th century and is now the dominant anthropological approach to assessing maritime and marine resources regardless of the context of where a site is located.
Moser, Mentona
Authors: Schmelz Andrea
Published: July 2023

Mentona Moser (1874–1971) was a pioneer of social work in Switzerland. Following the ideas of the settlement movement, Moser initiated and contributed to fundamental social welfare activities in Zurich until the end of World War I. As a communist, from the early 1920s on, she worked on several projects of radical social work in the context of the Red Aid.
An Intestinal Th17 Subset is Associated with Inflammation in Crohn’s Disease and Activated by Adherent-invasive Escherichia coli
Authors: Paroni Moira , Leccese Gabriella , Ranzani Valeria , Moschetti Giorgia , Chiara Matteo , Perillo Federica , Ferri Sara , Clemente Francesca , Noviello Daniele , Conforti Francesco Simone , Ferrero Stefano , Karnani Bhavna , Bosotti Roberto , Vasco Chiara , Curti Serena , Crosti Maria Cristina , Gruarin Paola , Rossetti Grazisa , Conte Maria Pia , Vecchi Maurizio , Pagani Massimiliano , Landini Paolo , Facciotti Federica , Abrignani Sergio , Caprioli Flavio , Geginat Jens
Published: July 2023

IFNγ-producing ex-Th17 cells [‘Th1/17’] were shown to play a key pathogenic role in experimental colitis and are abundant in the intestine. Here, we identified and characterised a novel, potentially colitogenic subset of Th17 cells in the intestine of patients with Crohn’s disease [CD]. Human Th17 cells expressing CCR5 [‘pTh17’] co-expressed T-bet and RORC/γt and produced very high levels of IL-17, together with IFN-γ. They had a gene signature of Th17 effector cells and were distinct from established Th1/17 cells. pTh17 cells, but not Th1/17 cells, were associated with intestinal inflammation in CD, and decreased upon successful anti-TNF therapy with infliximab. Conventional CCR5[-]Th17 cells differentiated to pTh17 cells with IL-23 in vitro. Moreover, anti-IL-23 therapy with risankizumab strongly reduced pTh17 cells in the intestine. Importantly, intestinal pTh17 cells were selectively activated by adherent-invasive Escherichia coli [AIEC], but not by a commensal/probiotic E. coli strain. AIEC induced high levels of IL-23 and RANTES from dendritic cells [DC]. Intestinal CCR5+Th1/17 cells responded instead to cytomegalovirus and were reduced in ulcerative colitis [UC], suggesting an unexpected protective role. In conclusion, we identified an IL-23–inducible subset of human intestinal Th17 cells. pTh17 cells produced high levels of pro-inflammatory cytokines, were selectively associated with intestinal inflammation in CD, and responded to CD-associated AIEC, suggesting a key colitogenic role.
Predictors of pituitary tumour behaviour: an analysis from long-term follow-up in 2 tertiary centres
Authors: Lenders Nèle F , Earls Peter E , Wilkinson Adam C , Costin Monique , Hofer Monika , Shein Tint T , Harvey Richard J , Krishnan Gayathri , Picallo Maria , Pal Aparna , Wass John , McCormack Ann I
Published: July 2023

Objectives

To determine the clinical utility of assessment of tumour invasion, markers of proliferation, and the French clinicopathological classification in pituitary tumour prognostication.

Methods

This is a retrospective evaluation of adult patients undergoing pituitary surgery at Oxford University and St Vincent's Hospitals, between 1989 and 2016, with at least 12 months of clinical data. Invasion was assessed radiologically, proliferative markers (Ki67, mitotic count, p53) by immunohistochemistry. Tumours were graded according to the clinicopathological classification. Intra- and interlaboratory variability of histopathology reporting was evaluated.

Outcomes

(1) Tumour recurrence (radiological or reintervention ≥12 months postoperatively) and/or (2) “aggressive behaviour” (≥4 interventions and/or invasive tumour with recurrence/reintervention between 12 and 24 months postoperatively).

Results

A total of 386 patients were included, age at surgery was 56 (interquartile range [IQR] 41-67) years, 54% were male, and median follow-up was 90 months (range 44-126). Tumours were predominantly clinically nonfunctioning (252, 65%), with overall 53% invasive, and 10% that demonstrated ≥2 proliferative marker positivity. Recurrence was predicted by invasiveness (hazards ratio [HR] 1.6 [1.10-2.37], P .02), elevated mitotic count (HR 2.17 [1.21-3.89], P .01), grade (2b vs 1a HR 2.32 [1.06-5.03], P .03), and absence of gross total resection (HR 3.70 [1.72-8.00], P .01). Clinically defined aggressiveness was associated with elevated Ki67, mitotic count, and invasiveness. Ki67 reporting methodologies showed moderate correlation across laboratories (Phi 0.620), whereas p53 reporting reproducibility was poor (Phi 0.146).

Conclusions

Proliferative markers, including Ki67 and mitotic count, but not p53, are important in predicting the development of aggressive pituitary tumour behaviour.
Chromosome-level genome assembly of Hydractinia symbiolongicarpus
Authors: Kon-Nanjo Koto , Kon Tetsuo , Horkan Helen R , Febrimarsa  , Steele Robert E , Cartwright Paulyn , Frank Uri , Simakov Oleg
Published: July 2023

Hydractinia symbiolongicarpus is a pioneering model organism for stem cell biology, being one of only a few animals with adult pluripotent stem cells (known as i-cells). However, the unavailability of a chromosome-level genome assembly has hindered a comprehensive understanding of global gene regulatory mechanisms underlying the function and evolution of i-cells. Here, we report the first chromosome-level genome assembly of H. symbiolongicarpus (HSymV2.0) using PacBio HiFi long-read sequencing and Hi-C scaffolding. The final assembly is 483 Mb in total length with 15 chromosomes representing 99.8% of the assembly. Repetitive sequences were found to account for 296 Mb (61%) of the total genome; we provide evidence for at least two periods of repeat expansion in the past. A total of 25,825 protein-coding genes were predicted in this assembly, which include 93.1% of the metazoan Benchmarking Universal Single-Copy Orthologs (BUSCO) gene set. 92.8% (23,971 genes) of the predicted proteins were functionally annotated. The H. symbiolongicarpus genome showed a high degree of macrosynteny conservation with the Hydra vulgaris genome. This chromosome-level genome assembly of H. symbiolongicarpus will be an invaluable resource for the research community that enhances broad biological studies on this unique model organism.
Parameter Estimation and Species Tree Rooting Using ALE and GeneRax
Authors: Williams Tom A , Davín Adrián A , Morel Benoit , Szánthó Lénárd L , Spang Anja , Stamatakis Alexandros , Hugenholtz Philip , Szöllősi Gergely J
Published: July 2023

ALE and GeneRax are tools for probabilistic gene tree–species tree reconciliation. Based on a common underlying statistical model of how gene trees evolve along species trees, these methods rely on gene vs. species tree discordance to infer gene duplication, transfer, and loss events, map gene family origins, and root species trees. Published analyses have used these methods to root species trees of Archaea, Bacteria, and several eukaryotic groups, as well as to infer ancestral gene repertoires. However, it was recently suggested that reconciliation-based estimates of duplication and transfer events using the ALE/GeneRax model were unreliable, with potential implications for species tree rooting. Here, we assess these criticisms and find that the methods are accurate when applied to simulated data and in generally good agreement with alternative methodological approaches on empirical data. In particular, ALE recovers variation in gene duplication and transfer frequencies across lineages that is consistent with the known biology of studied clades. In plants and opisthokonts, ALE recovers the consensus species tree root; in Bacteria—where there is less certainty about the root position—ALE agrees with alternative approaches on the most likely root region. Overall, ALE and related approaches are promising tools for studying genome evolution.
Science, Religion, and Morality
Authors: Stone Alison
Published: July 2023

The relations among science, morality, and religion were intensely debated by Victorian intellectuals, but generally, women’s contributions to these debates have been ignored. This chapter restores them to the record. It looks, first, at Frances Power Cobbe (1822–1904) and her account of how morality necessarily depends on religion, specifically Christianity. Second, the chapter considers the different engagements with Darwinism of Cobbe and Frances Julia Wedgwood (1833–1913). Third, the chapter introduces a pair of debates, one between Cobbe and Vernon Lee (1856–1935), the other between Cobbe and Annie Besant (1847–1933). Both Lee and Besant defended versions of secularism while Cobbe counterargued that no secularist morality was possible.
Augusta Ada Lovelace (1815–1852)
Authors: Krämer Sybille
Published: July 2023

In recent literature Ada Lovelace is considered the first programmer and a pioneer of information technology. But what justifies our interpreting her as an original philosopher as well? This chapter distinguishes three philosophical aspects of her thought: (1) The idea that the universality of the machine is not founded in the calculation of numbers, but in the computation of general symbols. (2) The idea of a “science of operations,” the core of which is to manipulate and combine not quantities, but patterns. This idea stands in the intellectual tradition of an ars combinatoria, a characteristica universalis, and a mathesis universalis. (3) A reflection on the relationship between human being and machine, not as a substitution and surpassing of humans by the machine, but from the perspective that human and machine can provide mutual assistance. Lovelace’s contribution to philosophy can be summarized as “ontology and ethics of operativity.”
Arendt, Poetry and Music
Authors: Sjöholm Cecilia
Published: July 2023

This chapter focuses on Hannah Arendt’s concept of sounding. It explores Arendt’s focus on music and poetry producing the phenomena of aesthetics and politics. Arendt’s assertion of an intrinsic relationship between music and poetry offers a way of interpreting musical and poetic works as inherently political. Mood, tone, and sounding belong to the world of appearances that hold inherent political capacity by displaying an explosive ability to give voice to the dispossessed. The chapter then considers Arendt’s basic assumption that music and poetry, as artworks, uphold an ontological status of permanence, while also referencing an immersion in emotions and radical subjectivity.
Expanding Phenomenological Methods
Authors: Høffding Simon
Published: July 2023

This chapter argues that musicking and musical absorption constitute a ripe field for phenomenological investigations because such musical activity engages a number of intertwined bodily, affective, and cognitive capacities, such as different forms of memory, attention, reflection and meta-cognition, imagination, mind wandering, and empathy. These capacities, in turn, connect back to core discussions in orthodox phenomenological philosophy. From here, the chapter ventures into a presentation of using qualitative, “phenomenological interviews” for enlightening the phenomenology of musical absorption while critically engaging with core insights in debates on expertise and the psychology of music. Finally, the chapter expands to include insights from physiological and psychological experimental science proposing how one could structure “research concerts” that integrate phenomenological, qualitative, and quantitative traditions into live citizen science events.
The osmotic stress–activated receptor-like kinase DPY1 mediates SnRK2 kinase activation and drought tolerance in Setaria
Authors: Zhao Meicheng , Zhang Qi , Liu Hong , Tang Sha , Shang Chunyue , Zhang Wei , Sui Yi , Zhang Yuxue , Zheng Chunyan , Zhang Hui , Liu Cuimei , Chu Jinfang , Jia Guanqing , Wang Haigang , Liu Xigang , An Diaoguo , Zhu Feng , Zhi Hui , Wu Chuanyin , Diao Xianmin
Published: July 2023

Plant genomes encode many receptor-like kinases (RLKs) that localize to the cell surface and perceive a wide variety of environmental cues to initiate downstream signaling cascades. Whether these RLKs participate in dehydration stress signaling in plants is largely unknown. DROOPY LEAF1 (DPY1), a leucine-rich repeat (LRR)-RLK, was recently shown to regulate plant architecture by orchestrating early brassinosteroid signaling in foxtail millet (Setaria italica). Here, we show that DPY1 is essential for the acclimation of foxtail millet to drought stress. DPY1 can be phosphorylated and activated in response to osmotic stress and is required for more than half of osmotic stress–induced global phosphorylation events, including the phosphorylation of sucrose nonfermenting kinase 2s (SnRK2s), the central kinases involved in osmotic stress. DPY1 acts upstream of STRESS-ACTIVATED PROTEIN KINASE 6 (SAPK6, a subclass I SnRK2) and is required for full SAPK6 activation, thereby allowing regulation of downstream genes to mount a response against drought stress. These signaling events are largely independent of DPY1-mediated brassinosteroid signaling. The DPY1-SAPK6 module is specific to seed plants and is absent in ancestral nonseed plants. Our findings reveal a dehydration stress–activated RLK that plays an indispensable role in osmotic stress signaling and mediates SnRK2 activation at the cell surface.
CardioMotion: identification of functional and structural cardiotoxic liabilities in small molecules through brightfield kinetic imaging
Authors: Stebbeds William , Raniga Kavita , Standing David , Wallace Iona , Bayliss James , Brown Andrew , Kasprowicz Richard , Dalmas Wilk Deidre , Deakyne Julianna , Clements Peter , Chaudhary Khuram W , Rossman Eric I , Bahinski Anthony , Francis Jo
Published: July 2023

Cardiovascular toxicity is an important cause of drug failures in the later stages of drug development, early clinical safety assessment, and even postmarket withdrawals. Early-stage in vitro assessment of potential cardiovascular liabilities in the pharmaceutical industry involves assessment of interactions with cardiac ion channels, as well as induced pluripotent stem cell-derived cardiomyocyte-based functional assays, such as calcium flux and multielectrode-array assays. These methods are appropriate for the identification of acute functional cardiotoxicity but structural cardiotoxicity, which manifests effects after chronic exposure, is often only captured in vivo. CardioMotion is a novel, label-free, high throughput, in vitro assay and analysis pipeline which records and assesses the spontaneous beating of cardiomyocytes and identifies compounds which impact beating. This is achieved through the acquisition of brightfield images at a high framerate, combined with an optical flow-based python analysis pipeline which transforms the images into waveform data which are then parameterized. Validation of this assay with a large dataset showed that cardioactive compounds with diverse known direct functional and structural mechanisms-of-action on cardiomyocytes are identified (sensitivity = 72.9%), importantly, known structural cardiotoxins also disrupt cardiomyocyte beating (sensitivity = 86%) in this method. Furthermore, the CardioMotion method presents a high specificity of 82.5%.
The Experiences of Nursing Students for Whom English Is an Additional Language in Preparing for and Taking Examinations
Authors: Cooper-Lara Peter
Published: July 2023

AIM

This study explored the experiences of prelicensure nursing students for whom English is an additional language when preparing for and taking course examinations.

BACKGROUND

English-as-an-additional-language students face challenges related to language comprehension on nursing examinations. Recognizing their unique obstacles may assist in designing equitable assessments and processes that improve outcomes.

METHOD

Responding to 14 semistructured, guided questions, 16 students discussed their experiences preparing for and taking nursing examinations.

RESULTS

Three primary themes related to student academic success emerged: psychological factors, perseverance, and factors affecting outcomes. Data revealed language as a factor that affected outcomes. Positive factors of note included self-confidence and diligence to succeed.

CONCLUSION

The results outline challenges faced by nursing students for whom English is an additional language and include strategies for promoting equity and academic success.
CONTOUR Australia: Condition of Submental Fullness and Treatment Outcomes with Belkyra Registry
Authors: Boxley Sarah G. , Lin Frank , Lee See Neville , St. Rose Suzanne , Battucci Simona , Simonyi Susan
Published: July 2023

Background:

Submental fat (SMF) contributes to an aged or overweight appearance that may negatively impact an individual’s psychological well-being. Deoxycholic acid (ATX-101) is an injectable formulation of deoxycholic acid approved to treat SMF. The Condition of Submental Fullness and Treatment Outcomes Registry (CONTOUR) Australia study was designed to understand treatment patterns and outcomes with ATX-101 in Australia.

Methods:

CONTOUR Australia was a phase 4, prospective, observational, multicenter registry that enrolled adults considering treatment for SMF reduction.

Results:

The registry enrolled 86 patients from six sites. Significant changes from baseline through the end of treatment indicated improvement in mild to moderate fullness associated with SMF on the Clinician-Reported SMF Rating Scale and the Patient-Reported SMF Rating Scale, improvement in SMF-associated psychological impact after treatment on the Patient-Reported SMF Impact Scale, no overall worsening in skin laxity based on Submental Skin Laxity Grade, and increased patient satisfaction with the face/chin on the Subject Self-Rating Scale after receiving treatment. Adverse events were all mild and mostly related to the injection site (ie, bruising and swelling).

Conclusion:

CONTOUR Australia observed clinically meaningful and significant outcomes and further supports ATX-101 as a well-tolerated and effective treatment for SMF reduction.
Markers of right ventricular dysfunction predict 30-day adverse prognosis of pulmonary embolism on pulmonary computed tomographic angiography
Authors: Hu Jie , Tian Xin , Liu Xiao-Wei , Liu Ya-Zhen , Gao Bu-Lang , Li Cai-Ying
Published: July 2023

To investigate the value of parameters of the pulmonary artery and right ventricular function in predicting the 30-day poor prognosis of patients with acute pulmonary embolism (APE). The heart rate, respiratory rate, systolic blood pressure, Wells score for APE, history of recent operation or immobilization, history of cancer, respiratory failure, smoking were significantly (P < .05) different among the control, good prognosis, and poor prognosis groups. The maximal short diameter of the right and left ventricle (RVD/LVD) ratio (P < .001) and left pulmonary artery (LPA) (P = .01) were significantly different between the good and poor prognosis groups. Systolic blood pressure (odds ratio [OR]: 0.98, P = .045) and the RVD/LVD ratio (OR: 12.57, P = .02) were significant independent risk factors for poor prognosis. The risk for poor prognosis significantly increased when the RVD/LVD ratio was >1.11 (cutoff value) with the area under the curve (AUC) of 0.71 (95% confidence interval [CI]: 0.61–0.80, P < .001). LPA (OR: 9.12, P = .01) and RVD/LVD (OR: 4.62, P = .012) were the significant independent risk factors for poor prognosis in the central pulmonary embolism. The LPA of 2.1 cm had the highest predictive value for poor prognosis in the central APE (AUC: 0.68; sensitivity 84.6%; specificity 53.1%). The RVD/LVD ratio and systolic blood pressure are significant risk factors for short-term prognosis in patients with APE. When the LPA is >2.1 cm in the central APE or the RVD/LVD is >1.11, the risk of poor prognosis increases, which can be used as important indicators for predicting the prognosis of patients with APE. Two hundred forty-three APE patients and 61 patients without APE who underwent computed tomographic pulmonary angiography (CTPA) were retrospectively enrolled as the experimental and the control group, respectively. APE patients who were followed up at the 30-day time point were divided into the good prognosis (n = 195) and poor prognosis group (n = 32). The main pulmonary artery (MPA) to the aorta (AO) ratio, maximal diameter of the LPA and right pulmonary artery (RPA), ratio of the RVD/LVD and the height and volume of the pulmonary artery (PAh and PAV, respectively) were analyzed after indexing to the body surface area.
A hybrid and poly-polish workflow for the complete and accurate assembly of phage genomes: a case study of ten przondoviruses
Authors: Elek Claire K. A. , Brown Teagan L. , Le Viet Thanh , Evans Rhiannon , Baker David J. , Telatin Andrea , Tiwari Sumeet K. , Al-Khanaq Haider , Thilliez Gaëtan , Kingsley Robert A. , Hall Lindsay J. , Webber Mark A. , Adriaenssens Evelien M.
Published: July 2023

Bacteriophages (phages) within the genus Przondovirus are T7-like podoviruses belonging to the subfamily Studiervirinae, within the family Autographiviridae, and have a highly conserved genome organisation. The genomes of these phages range from 37 to 42 kb in size, encode 50–60 genes and are characterised by the presence of direct terminal repeats (DTRs) flanking the linear chromosome. These DTRs are often deleted during short-read-only and hybrid assemblies. Moreover, long-read-only assemblies are often littered with sequencing and/or assembly errors and require additional curation. Here, we present the isolation and characterisation of ten novel przondoviruses targeting

Klebsiella

spp. We describe HYPPA, a HYbrid and Poly-polish Phage Assembly workflow, which utilises long-read assemblies in combination with short-read sequencing to resolve phage DTRs and correcting errors, negating the need for laborious primer walking and Sanger sequencing validation. Our assembly workflow utilised Oxford Nanopore Technologies for long-read sequencing for its accessibility, making it the more relevant long-read sequencing technology at this time, and Illumina DNA Prep for short-read sequencing, representing the most commonly used technologies globally. Our data demonstrate the importance of careful curation of phage assemblies before publication, and prior to using them for comparative genomics.