bluuebunny/crossref_metadata_2025 huggingface dataset:
A Novel Hybrid Point Defect of Oxygen Vacancy and Phosphorus Doping in TiO2 Anode for High-Performance Sodium Ion Capacitor
Authors: Chen Daming , Wu Youchun , Huang Zhiquan , Chen Jian
Published: August 2022

Although sodium ion capacitors (SICs) are considered as one of the most promising electrochemical energy storage devices (organic electrolyte batteries, aqueous batteries and supercapacitor, etc.) due to the combined merits of battery and capacitor, the slow reaction kinetics and low specific capacity of anode materials are the main challenges. Point defects including vacancies and heteroatoms doping have been widely used to improve the kinetics behavior and capacity of anode materials. However, the interaction between vacancies and heteroatoms doping have been seldomly investigated. In this study, a hybrid point defects (HPD) engineering has been proposed to synthesize TiO2 with both oxygen vacancies (OVs) and P-dopants (TiO2/C-HPD). In comparison with sole OVs or P-doping treatments, the synergistic effects of HPD on its electrical conductivity and sodium storage performance have been clarified through the density functional theory calculation and sodium storage characterization. As expected, the kinetics and electronic conductivity of TiO2/C-HPD3 are significantly improved, resulting in excellent rate performance and outstanding cycle stability. Moreover, the SICs assembled from TiO2/C-HPD3 anode and nitrogen-doped porous carbon cathode show outstanding power/energy density, ultra-long life with good capacity retention. This work provides a novel point defect engineering perspective for the development of high-performance SICs electrode materials.

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AI Ethics, Ethics Washing, and the Need to Politicize Data Ethics
Authors: van Maanen Gijs
Published: August 2022

Many commercial actors in the tech sector publish ethics guidelines as a means to ‘wash away’ concerns raised about their policies. For some academics, this phenomenon is reason to replace ethics with other tools and methods in an attempt to make sure that the tech sector does not cross any moral Rubicons. Others warn against the tendency to reduce a criticism of ‘ethics washing’ into one of ethics simpliciter. In this essay, I argue firstly that the dominant focus on principles, dilemmas, and theory in conventional ethical theories and practices could be an explanation of it lacking resistance to abuse by dominant actors, and hence its rather disappointing capacity to stop, redirect, or at least slow down big tech’s course. Secondly, drawing from research on casuistry and political philosopher Raymond Geuss, this essay will make a case for a question, rather than theory or principle-based ethical data practice. The emphasis of this approach is placed on the acquisition of a thorough understanding of a social-political phenomenon like tech development. This approach should be replenished with one extra component to the picture of the repoliticized data ethics drawn so far: the importance of ‘exemplars,’ or stories. Precisely the fact that one should acquire an in-depth understanding of the problem in practice will also allow one to look in the past, present, or future for similar and comparable stories from which one can learn.
Gastric outlet obstruction as a rare presentation of peritoneal hydatid disease: A case report
Authors: Shammas Ibrahim , Alorfhli Ibrahim , Shammas Lora , Abbas Aram , Alahmar Fadi Obaied
Published: August 2022

ABSTRACT

Introduction and importance:

Peritoneal hydatid cyst is a rare disease which transplants by eggs of Echinococcus. Peritoneal cysts are divided into primary and secondary. This case shows an unusual manifestation of peritoneal hydatid cysts, adding to the already known manifestations of this disease in medical literature. It is important because peritoneal hydatid cysts maybe life-threatening if it is not managed carefully.

Case presentation:

In this case, we present a patient with history of recurrent hepatic hydatid cysts who presented with symptoms of gastric outlet obstruction. CT showed multiple peritoneal cysts consisting with peritoneal hydatid cysts located at the level of stomach pylorus. Although the patient suffered from multiple surgeries for recurrent hydatid cysts, she accepted the surgical option. The patient was discharged 10 days later after a non-complicated surgery. Albendazole was recommended after surgery.

Clinical discussion:

The mechanism of peritoneal hydatid cysts is still unknown, but one of theories declares that microrupture can explain the disease.

Conclusion:

This case emphasizes the idea that peritoneal hydatid cysts should be considered even in patients presenting with atypical symptom (eg, Gastric outlet obstruction).

Highlights
The changing roles of frontline bureaucrats in the digital welfare state: The case of a data dashboard in Rotterdam’s Work and Income department
Authors: Kersing Margot , van Zoonen Liesbet , Putters Kim , Oldenhof Lieke
Published: August 2022

The welfare state is currently undergoing a transition toward data-driven policies, management, and execution. This has important repercussions for frontline bureaucrats in such a “digital welfare state.” So far, impact of data-driven tools on frontline bureaucrats is primarily described in terms of curtailing or enlarging their discretionary space to make decisions. It is unclear, however, how daily work practices and role identities of frontline bureaucrats change in situ and which norms they develop to work with new data tools. In this article, we present an empirical study about the impact of a data dashboard in the Work and Income department of the municipality of Rotterdam. We answer the following research question: Which role identities, work practices, and norms of appropriate behavior of frontline bureaucrats in the social domain are reshaped by the introduction of a data dashboard? We use a multiple methods design consisting of semi-structured interviews, ethnographic observations, and document analysis. Our results reveal two role identities among frontline bureaucrats: (a) the client coach, and (b) the caseload manager. We show that the implementation of the dashboard stimulates a shift from a client coach role identity toward a caseload manager role identity. This shift is contested as it leads to role identity conflicts among frontline bureaucrats with a client coach role. Furthermore, we establish that the accommodation of the institutional void in which the introduction of the dashboard takes place, is centered around three themes of contestation: (a) data quality, (b) quality of service provision, and (c) data representations.
Epistemic Side-Effect Effect: A Meta-Analysis
Authors: Maćkiewicz Bartosz , Kuś Katarzyna , Paprzycka-Hausman Katarzyna , Zaręba Marta
Published: August 2022

Beebe and Buckwalter (2010) made the surprising discovery that people are more inclined to attribute knowledge when norms are violated than when they are conformed to. The epistemic side-effect effect (ESEE) is the analogue of the Knobe effect (Knobe 2003a). ESEE was replicated in a number of experiments. It was also studied under various conditions. We have carried out a meta-analysis of research on ESEE. The results suggest that ESEE is a robust finding but its magnitude is highly variable. Two study-level covariates influence its size: the subject of the knowledge attribution (agent vs third-party) and the type of norm that is violated or complied with. The effect size is not influenced, however, by the manipulation of chances, by whether the story is about a side effect or not, by language or by question phrasing. The impact of the Gettierization of the story is marginally significant.
Banking Nationalism and Resolution in Italy and Spain
Authors: Donnelly Shawn , Pometto Gaia
Published: August 2022

This article contributes to the comparative literatures on varieties of financial capitalism, economic nationalism and bank resolution with a focus on Spain and Italy's management of bank insolvency and resolution between 2008 and 2018. Both countries' alternative banks faced enormous challenges through prolonged economic decline and declining loan repayments, both turned to depositors to become investors in lieu of attracting arm's-length investors to inject capital, and both had strong connections with local political authorities that resisted bank reform. But Spanish banks were restructured successfully in accordance with EU law while local government ties complicated Italian resolutions. We explain this outcome through two factors: state strength buttressed by outside assistance from the European Stability Mechanism; and strong international marketization, which enhanced the drive to restructure quickly. Spain's decision to ask for loans from the European Stability Mechanism to help restructure its heavily marketized savings banks allowed it to finish reforms after 2012.
Substance use and self-harm emergency department presentations during COVID19: evidence from a National Clinical Programme for Self-Harm
Authors: Maguire E. , Kavalidou K. , Bannan N. , Doherty A. M. , Jeffers A.
Published: August 2022

Introduction:

Given the evidence that drinking patterns and self-harm hospital presentations have changed during COVID-19, this study aimed to examine any change in self-harm and suicide-related ideation presentations, together with any possible contribution made by alcohol or substance misuse, to Irish Emergency Departments in 2020, compared with 2018 and 2019.

Methods:

A population-based cohort with self-harm and suicide-related ideation presenting to Irish hospitals derived from the National Clinical Programme for Self-Harm was analysed. Descriptive analyses were conducted based on sociodemographic variables and types of presentation for the period January to August 2020 and compared with the same period in 2018 and 2019. Binomial regression analyses were performed to investigate the independent effect of demographic characteristics and pre/during COVID-19 periods on the use of substances as contributory factors in the self-harm and suicide-related ideation presentations.

Results:

12,075 presentations due to self-harm and suicide-related ideation were recorded for the periods January–August 2018–2020 across nine emergency departments. The COVID-19 year was significantly associated with substances contributing to self-harm and suicide-related ideation ED presentations (OR = 1.183; 95% CI, 1.075–1.301, p < 0.001). No changes in the demographic characteristics were found for those with self-harm or suicide-related ideation across the years. Suicide-related ideation seemed to be increased after May 2020 compared with previous years. In terms of self-harm episodes with comorbid drug and alcohol overdose and poisoning, these were significantly increased in January–August 2020, compared with previous timepoints (χ2 = 42.424, df = 6, p < 0.001).

Conclusion:

An increase in suicide-related ideation and substance-related self-harm presentations may indicate longer term effects of the pandemic and its relevant restrictions. Future studies might explore whether those presenting with ideation will develop a risk of suicide in post-pandemic periods.
Dynamic stabilisation of Rayleigh–Plateau modes on a liquid cylinder
Authors: Patankar Sagar , Basak Saswata , Dasgupta Ratul
Published: August 2022

We demonstrate dynamic stabilisation of axisymmetric Fourier modes susceptible to the classical Rayleigh–Plateau (RP) instability on a liquid cylinder by subjecting it to a radial oscillatory body force. Viscosity is found to play a crucial role in this stabilisation. Linear stability predictions are obtained via Floquet analysis demonstrating that RP unstable modes can be stabilised using radial forcing. We also solve the linearised, viscous initial-value problem for free-surface deformation obtaining an equation governing the amplitude of a three-dimensional Fourier mode. This equation generalizes the Mathieu equation governing Faraday waves on a cylinder derived earlier in Patankaret al.(J. Fluid Mech., vol. 857, 2018, pp. 80–110), is non-local in time and represents the cylindrical analogue of its Cartesian counterpart (Beyer & Friedrich,Phys. Rev.E, vol. 51, issue 2, 1995, p. 1162). The memory term in this equation is physically interpreted and it is shown that, for highly viscous fluids, its contribution can be sizeable. Predictions from the numerical solution to this equation demonstrate the predicted RP mode stabilisation and are in excellent agreement with simulations of the incompressible Navier–Stokes equations (up to the simulation time of several hundred forcing cycles).
Direct numerical simulation of the turbulent kinetic energy and energy dissipation rate in a cylinder wake
Authors: Jiang Hongyi , Hu Xiaoyuan , Cheng Liang , Zhou Tongming
Published: August 2022

The turbulent kinetic energy and energy dissipation rate in the wake of a circular cylinder are examined at a Reynolds number of 1000. The turbulence characteristics are quantified using direct numerical simulation, which provides a comprehensive dataset that is almost impossible to acquire from physical experiments. The energy dissipation rate is decomposed into the components due to the mean flow, the coherent primary vortices and the remainder. It is found that the remainder component, which develops only in a three-dimensional turbulent wake and resides mainly in the regions of vortices, accounts for 95 % and 97 % of the total dissipation rate for 10 and 20 cylinder diameters downstream of the cylinder, respectively (while the remainder accounts for 62 % and 83 % of the total turbulent kinetic energy). Based on the remainder component, the validity of local isotropy, local axisymmetry, local homogeneity and homogeneity in they–zplane for the turbulent dissipation in the wake is examined. The analysis reveals that the turbulent dissipation is largely locally homogeneous, but not locally isotropic or axisymmetric, even after the annihilation of the primary vortex street. In addition, the performances of the four corresponding surrogates to the true dissipation rate are evaluated. Owing to the general validity of local homogeneity, the surrogates of local homogeneity and homogeneity in they–zplane perform well. Although local axisymmetry does not hold, the corresponding surrogate performs well, because errors from different terms largely cancel out. However, the surrogate of local isotropy generally underestimates the true dissipation rate.
Optimal timing of endoscopic sinus surgery for the retention cyst of maxillary sinus
Authors: Sato K , Chitose S , Sato K , Sato F , Ono T , Umeno H
Published: August 2022

Objective

The optimal timing of functional endoscopic sinus surgery for odontogenic infections precipitated by retention cysts of the maxillary sinus was investigated.

Methods

Five adults who underwent functional endoscopic sinus surgery were examined.

Results

The root apexes of all teeth that had odontogenic infection protruded into the maxillary sinus. All teeth with odontogenic infections precipitated by the retention cysts had percussion pain, indicating they had periodontitis and pulpitis around the root apex. They were vital teeth, indicating they did not have pulp necrosis. The small area of cyst wall attached to the floor of the maxillary sinus and root apex were left intact. The teeth that had odontogenic infections precipitated by retention cysts continued to be vital with no symptoms.

Conclusion

Functional endoscopic sinus surgery should be performed before periodontitis and pulpitis of the root apex progress to ascending pulpitis and pulp necrosis. In other words, functional endoscopic sinus surgery should be performed while the affected tooth is still vital.
A phonetic case study of Tŝilhqot’in /z/ and /zʕ/
Authors: Bird Sonya , Onosson Sky
Published: August 2022

This paper provides an acoustic description of /z/ and /zʕ/ in Tŝilhqot’in (Northern Dene). These sounds are noted by Cook (1993, 2013) to show lenition and some degree of laterality in coda position. Based on recordings made in 2014 with a single, mother-tongue speaker of Tŝilhqot’in, we describe their acoustic properties and examine their distribution as a function of prosodic position and segmental environment. We find that they vary along three dimensions: manner (fricative–approximant), degree of retraction (non-retracted–retracted), and laterality (non-lateral–lateral). In addition, some tokens have a characteristic ‘buzziness’, which has been associated with the Chinese front apical vowel (Shao & Ridouane 2018, 2019) and the Swedish ‘Viby-i’ (Westberger 2019). We argue that ‘lenition’ (Kirchner 2004, Ennever, Meakins & Round 2017) can only account for some of the observed variation and suggest that both /z/ and /zʕ/ are specified for two tongue articulations: tongue tip/blade and tongue body (Laver 1994), encompassing laterality (and concomitant retraction) in addition to the primary coronal gesture.
The development of single molecule force spectroscopy: from polymer biophysics to molecular machines
Authors: Bustamante Carlos , Yan Shannon
Published: August 2022

The advent of single-molecule force spectroscopy represents the introduction of forces, torques, and displacements as controlled variables in biochemistry. These methods afford the direct manipulation of individual molecules to interrogate the forces that hold together their structure, the forces and torques that these molecules generate in the course of their biochemical reactions, and the use of force, torque, and displacement as tools to investigate the mechanisms of these reactions. Because of their microscopic nature, the signals detected in these experiments are often dominated by fluctuations, which, in turn, play an important role in the mechanisms that underlie the operation of the molecular machines of the cell. Their direct observation and quantification in single-molecule experiments provide a unique window to investigate those mechanisms, as well as a convenient way to investigate fundamental new fluctuation theorems of statistical mechanics that bridge the equilibrium and non-equilibrium realms of this discipline. In this review we have concentrated on the developments that occurred in our laboratory on the characterization of biopolymers and of molecular machines of the central dogma. Accordingly, some important areas like the study of cytoskeletal motors have not been included. While we adopt at times an anecdotal perspective with the hope of conveying the personal circumstances in which these developments took place, we have made every effort, nonetheless, to include the most important developments that were taking place at the same time in other laboratories.
Impact of interdisciplinary counselling for parental decision-making in cases of pregnancies with prenatally diagnosed CHD
Authors: Schneider Katja , Bousi Dafni , Stressig Rüdiger
Published: August 2022

Introduction:

Parental counselling after antenatal diagnosis of a congenital heart defect requires a high degree of professional and emotional competence and ultimately a sense of responsibility on the part of the consulting physicians. However, little is known about parents` perceptions and evaluation of these consultations.

Material/Methods:

Survey on 425 women who received interdisciplinary counselling after antenatal diagnosis of a complex fetal congenital heart defect in a specialized prenatal outpatient clinic with an affiliated paediatric heart centre. Two questionnaires were used to retrospectively evaluate the parental perception and impact on counselling, particularly on decision-making. Questionnaires differed between women conceiving the child and women who terminated the pregnancy.

Results:

400 women continued, 25 women terminated the pregnancy after diagnosis and counselling. Good quality of life was reported for 68% of the children, 15% died postnatally in the further course. 95% rated the counselling as good or very good regardless of the child´s outcome. 73% described the counselling as highly important for their subsequent decision. The possibility of termination of pregnancy was discussed with 37% of the respondents, 22% of them found it outrageous or very distressing. Of all respondents, one woman would have made a different decision regarding continuation of the pregnancy in retrospect.

Conclusion:

Retrospectively, parents rate prenatal counselling extremely positively, irrespective of the severity of the child´s heart defect. It can be assumed that the consistent joint interdisciplinary consultation and the high reputation of the cooperating heart centre have had an influence on the below-average rate of termination of pregnancy.
Early taphonomic processes in a microbial-based sedimentary system from a temperate salt-pan site (Cervia salterns, Italy)
Authors: Barbieri Roberto , Cavalazzi Barbara
Published: August 2022

In the only salt evaporation pond retaining its natural setting of the historic Salina di Cervia (Italy), the northernmost salterns of the Mediterranean area, a number of potentially preservable textures derive from the interactions between photosynthetic mat producers and the sedimentary substrate. These morphologies occur at the beginning of the taphonomic processes when repeated emerged-submerged conditions take place. In these conditions the cohesive nature of the diatom- and cyanobacterial-derived mucilage favours the stabilization of otherwise ephemeral structures. Surface micromorphologies for which diatoms and cyanobacteria have played some active role when still living in the soft microlayer and down to the sediment-water interface, such as during the gliding motility, can overcome the surface layer of most intense mixing (i.e., the taphonomically active zone) and keep traces of them in the fossil record either as body fossils or as texture contributors. Tiny microbial-derived remnants, such as filaments and biofilm strands of halotolerant microorganisms, while fragile upon their formation, can therefore stabilize as biosignatures when combined with salt precipitation. Halophilic and halotolerant ecosystems are models for life in extreme environments (analogue sites) with similarity to those strongly suspected to occur and/or have occurred on Mars and on other planetary bodies. The study of hypersaline systems such as Salina di Cervia which harbour diverse and abundant microbial life, can be relevant for astrobiology since it allows the investigation of potential biosignatures and their preservation, and of further understand the range of conditions and the planetary processes sustaining potentially habitable systems.
“You think you got it down and then the moment comes”: The certainty of uncertainty in end-of-life decision making
Authors: Clair Catherine A. , Abshire Saylor Martha , Nolan Marie T. , Gallo Joseph J.
Published: August 2022

Objectives

Some observers have proposed that physicians may die differently compared with the average patient. Semi-structured interviews with family members of physicians who died offer an opportunity to better understand how patient preferences and wishes are perceived and acted on by family members at the end of life. The decision-making experiences of these family members for a loved one who was a physician may have implications for the lay person at end of life.

Methods

The Johns Hopkins Precursors Study includes individuals who matriculated into the graduating classes of 1948 to 1964 of the Johns Hopkins University School of Medicine. From this cohort, we interviewed 26 family members of physicians who died. Interviews were coded and analyzed using a comparative, iterative process.

Results

We found that family members of physicians who died described the uncertainty at end of life. This overarching theme was organized into the following: (a) the certainty of uncertainty; (b) the preparation for uncertainty; and (c) brokering of decisions in the face of uncertainty. Despite careful end-of-life preparation by well-informed physicians, family members were still left to broker decisions as they navigated the wishes of the physician and what the family and medical care team believed to be in the best interest of the physician.

Significance of results

Our findings suggest that our family members were not immune to uncertainty. The clinical momentum at the end of life may contribute to challenges faced by patients and family members when brokering decisions. Normalizing uncertainty in medical training and for families may aid in addressing the stress of uncertainty at end of life.
Strengthening health system governance in Germany: looking back, planning ahead
Authors: Schmitt Tugce , Haarmann Alexander , Shaikh Mujaheed
Published: August 2022

Health system governance has been receiving increasing attention in health system research since the 1980s. The contemporary challenges that the German health system is faced with are often closely linked to governance issues. Although Germany has the highest health expenditure as a share of Gross Domestic Product (GDP) in the European Union (EU), the spending on healthcare is out of proportion to the health outcomes of the population. The reason for this lies mainly in the complexity of the German health system which is hard to steer due to several administrative levels in the country and numerous policy actors to whom the decision-making power on healthcare provision is delegated. In this paper, we present the results of focus group discussions on governance and build upon the insights gained through theNeustartproject of the Robert Bosch Foundation. Based on an internationally recognised health governance framework from the World Health Organization (WHO), experts who work in, on or for the German health system addressed health governance challenges. They provided evidence-based recommendations for the new legislative period (2021-2025) on transparency, accountability, participation, integrity and capacity of the German health system.
Transcriptomic diversity in human medullary thymic epithelial cells
Authors: Carter Jason A. , Strömich Léonie , Peacey Matthew , Chapin Sarah R. , Velten Lars , Steinmetz Lars M. , Brors Benedikt , Pinto Sheena , Meyer Hannah V.
Published: August 2022

The induction of central T cell tolerance in the thymus depends on the presentation of peripheral self-epitopes by medullary thymic epithelial cells (mTECs). This promiscuous gene expression (pGE) drives mTEC transcriptomic diversity, with non-canonical transcript initiation, alternative splicing, and expression of endogenous retroelements (EREs) representing important but incompletely understood contributors. Here we map the expression of genome-wide transcripts in immature and mature human mTECs using high-throughput 5’ cap and RNA sequencing. Both mTEC populations show high splicing entropy, potentially driven by the expression of peripheral splicing factors. During mTEC maturation, rates of global transcript mis-initiation increase and EREs enriched in long terminal repeat retrotransposons are up-regulated, the latter often found in proximity to differentially expressed genes. As a resource, we provide an interactive public interface for exploring mTEC transcriptomic diversity. Our findings therefore help construct a map of transcriptomic diversity in the healthy human thymus and may ultimately facilitate the identification of those epitopes which contribute to autoimmunity and immune recognition of tumor antigens.
Iron mobilization during lactation reduces oxygen stores in a diving mammal
Authors: Shero Michelle R. , Kirkham Amy L. , Costa Daniel P. , Burns Jennifer M.
Published: August 2022

The profound impacts that maternal provisioning of finite energy resources has on offspring survival have been extensively studied across mammals. This study shows that in addition to calories, high hemoprotein concentrations in diving mammals necessitates exceptional female-to-pup iron transfer. Numerous indices of iron mobilization (ferritin, serum iron, total-iron-binding-capacity, transferrin saturation) were significantly elevated during lactation in adult female Weddell seals (Leptonychotes weddellii), but not in skip-breeders. Iron was mobilized from endogenous stores for incorporation into the Weddell seal’s milk at concentrations up to 100× higher than terrestrial mammals. Such high rates of iron offload to offspring drew from the female’s own heme stores and led to compromised physiologic dive capacities (hemoglobin, myoglobin, and total body oxygen stores) after weaning their pups, which was further reflected in shorter dive durations. We demonstrate that lactational iron transfer shapes physiologic dive thresholds, identifying a cost of reproduction to a marine mammal.
Multiplex base editing to convert TAG into TAA codons in the human genome
Authors: Chen Yuting , Hysolli Eriona , Chen Anlu , Casper Stephen , Liu Songlei , Yang Kevin , Liu Chenli , Church George
Published: August 2022

Whole-genome recoding has been shown to enable nonstandard amino acids, biocontainment and viral resistance in bacteria. Here we take the first steps to extend this to human cells demonstrating exceptional base editing to convert TAG to TAA for 33 essential genes via a single transfection, and examine base-editing genome-wide (observing ~40 C-to-T off-target events in essential gene exons). We also introduce GRIT, a computational tool for recoding. This demonstrates the feasibility of recoding, and highly multiplex editing in mammalian cells.
Systematic strategies for developing phage resistant Escherichia coli strains
Authors: Zou Xuan , Xiao Xiaohong , Mo Ziran , Ge Yashi , Jiang Xing , Huang Ruolin , Li Mengxue , Deng Zixin , Chen Shi , Wang Lianrong , Lee Sang Yup
Published: August 2022

Phages are regarded as powerful antagonists of bacteria, especially in industrial fermentation processes involving bacteria. While bacteria have developed various defense mechanisms, most of which are effective against a narrow range of phages and consequently exert limited protection from phage infection. Here, we report a strategy for developing phage-resistant Escherichia coli strains through the simultaneous genomic integration of a DNA phosphorothioation-based Ssp defense module and mutations of components essential for the phage life cycle. The engineered E. coli strains show strong resistance against diverse phages tested without affecting cell growth. Additionally, the resultant engineered phage-resistant strains maintain the capabilities of producing example recombinant proteins, D-amino acid oxidase and coronavirus-encoded nonstructural protein nsp8, even under high levels of phage cocktail challenge. The strategy reported here will be useful for developing engineered E. coli strains with improved phage resistance for various industrial fermentation processes for producing recombinant proteins and chemicals of interest.
Engineering micro oxygen factories to slow tumour progression via hyperoxic microenvironments
Authors: Wang Weili , Zheng Huizhen , Jiang Jun , Li Zhi , Jiang Dongpeng , Shi Xiangru , Wang Hui , Jiang Jie , Xie Qianqian , Gao Meng , Chu Jianhong , Cai Xiaoming , Xia Tian , Li Ruibin
Published: August 2022

While hypoxia promotes carcinogenesis, tumour aggressiveness, metastasis, and resistance to oncological treatments, the impacts of hyperoxia on tumours are rarely explored because providing a long-lasting oxygen supply in vivo is a major challenge. Herein, we construct micro oxygen factories, namely, photosynthesis microcapsules (PMCs), by encapsulation of acquired cyanobacteria and upconversion nanoparticles in alginate microcapsules. This system enables a long-lasting oxygen supply through the conversion of external radiation into red-wavelength emissions for photosynthesis in cyanobacteria. PMC treatment suppresses the NF-kB pathway, HIF-1α production and cancer cell proliferation. Hyperoxic microenvironment created by an in vivo PMC implant inhibits hepatocarcinoma growth and metastasis and has synergistic effects together with anti-PD-1 in breast cancer. The engineering oxygen factories offer potential for tumour biology studies in hyperoxic microenvironments and inspire the exploration of oncological treatments.
Genomic architecture of adaptive radiation and hybridization in Alpine whitefish
Authors: De-Kayne Rishi , Selz Oliver M. , Marques David A. , Frei David , Seehausen Ole , Feulner Philine G. D.
Published: August 2022

Adaptive radiations represent some of the most remarkable explosions of diversification across the tree of life. However, the constraints to rapid diversification and how they are sometimes overcome, particularly the relative roles of genetic architecture and hybridization, remain unclear. Here, we address these questions in the Alpine whitefish radiation, using a whole-genome dataset that includes multiple individuals of each of the 22 species belonging to six ecologically distinct ecomorph classes across several lake-systems. We reveal that repeated ecological and morphological diversification along a common environmental axis is associated with both genome-wide allele frequency shifts and a specific, larger effect, locus, associated with the geneedar. Additionally, we highlight the possible role of introgression between species from different lake-systems in facilitating the evolution and persistence of species with unique trait combinations and ecology. These results highlight the importance of both genome architecture and secondary contact with hybridization in fuelling adaptive radiation.
Highly efficient and selective extraction of gold by reduced graphene oxide
Authors: Li Fei , Zhu Jiuyi , Sun Pengzhan , Zhang Mingrui , Li Zhenqing , Xu Dingxin , Gong Xinyu , Zou Xiaolong , Geim A. K. , Su Yang , Cheng Hui-Ming
Published: August 2022

Materials capable of extracting gold from complex sources, especially electronic waste (e-waste), are needed for gold resource sustainability and effective e-waste recycling. However, it remains challenging to achieve high extraction capacity and precise selectivity if only a trace amount of gold is present along with other metallic elements . Here we report an approach based on reduced graphene oxide (rGO) which provides an ultrahigh capacity and selective extraction of gold ions present in ppm concentrations (>1000 mg of gold per gram of rGO at 1 ppm). The excellent gold extraction performance is accounted to the graphene areas and oxidized regions of rGO. The graphene areas spontaneously reduce gold ions to metallic gold, and the oxidized regions allow good dispersibility of the rGO material so that efficient adsorption and reduction of gold ions at the graphene areas can be realized. By controlling the protonation of the oxidized regions of rGO, gold can be extracted exclusively, without contamination by the other 14 co-existing elements typically present in e-waste. These findings are further exploited to demonstrate recycling gold from real-world e-waste with good scalability and economic viability, as exemplified by using rGO membranes in a continuous flow-through process.
Golgi stress induces SIRT2 to counteract Shigella infection via defatty-acylation
Authors: Wang Miao , Zhang Yugang , Komaniecki Garrison P. , Lu Xuan , Cao Ji , Zhang Mingming , Yu Tao , Hou Dan , Spiegelman Nicole A. , Yang Ming , Price Ian R. , Lin Hening
Published: August 2022

Enzymes from pathogens often modulate host protein post-translational modifications (PTMs), facilitating survival and proliferation of pathogens. Shigella virulence factors IpaJ and IcsB induce proteolytic cleavage and lysine fatty acylation on host proteins, which cause Golgi stress and suppress innate immunity, respectively. However, it is unknown whether host enzymes could reverse such modifications introduced by pathogens’ virulence factors to suppress pathogenesis. Herein, we report that SIRT2, a potent lysine defatty-acylase, is upregulated by the transcription factor CREB3 under Golgi stress induced by Shigella infection. SIRT2 in turn removes the lysine fatty acylation introduced by Shigella virulence factor IcsB to enhance host innate immunity. SIRT2 knockout mice are more susceptible to Shigella infection than wildtype mice, demonstrating the importance of SIRT2 to counteract Shigella infection.
Associations between aerobic fitness, negative symptoms, cognitive deficits and brain structure in schizophrenia—a cross-sectional study
Authors: Maurus Isabel , Röll Lukas , Keeser Daniel , Karali Temmuz , Papazov Boris , Hasan Alkomiet , Schmitt Andrea , Papazova Irina , Lembeck Moritz , Hirjak Dusan , Thieme Cristina E. , Sykorova Eliska , Münz Susanne , Seitz Valentina , Greska David , Campana Mattia , Wagner Elias , Löhrs Lisa , Pömsl Johannes , Roeh Astrid , Malchow Berend , Keller-Varady Katriona , Ertl-Wagner Birgit , Stöcklein Sophia , Meyer-Lindenberg Andreas , Falkai Peter
Published: August 2022

Negative symptoms and cognitive deficits are common in individuals with schizophrenia, greatly affect their outcome, and have been associated with alterations in cerebral gray and white matter volume (GMV, WMV). In the last decade, aerobic endurance training has emerged as a promising intervention to alleviate these symptoms and improved aerobic fitness has been suggested as a key moderator variable. In the present study, we investigated, whether aerobic fitness is associated with fewer cognitive deficits and negative symptoms and with GMVs and WMVs in individuals with schizophrenia in a cross-sectional design. In the largest study to date on the implications of fitness in individuals with schizophrenia, 111 participants at two centers underwent assessments of negative symptoms, cognitive functioning, and aerobic fitness and 69 underwent additional structural magnetic resonance imaging. Multilevel Bayesian partial correlations were computed to quantify relationships between the variables of interest. The main finding was a positive association of aerobic fitness with right hippocampal GMV and WMVs in parahippocampal and several cerebellar regions. We found limited evidence for an association of aerobic fitness with cognitive functioning and negative symptoms. In summary, our results strengthen the notion that aerobic fitness and hippocampal plasticity are interrelated which holds implications for the design of exercise interventions in individuals with schizophrenia.
Daily 1 km terrain resolving maps of surface fine particulate matter for the western United States 2003–2021
Authors: Swanson Alan , Holden Zachary A. , Graham Jon , Warren D. Allen , Noonan Curtis , Landguth Erin
Published: August 2022

We developed daily maps of surface fine particulate matter (PM2.5) for the western United States. We used geographically weighted regression fit to air quality station observations with Moderate Resolution Imaging Spectroradiometer (MODIS) aerosol optical depth (AOD) data, and meteorological data to produce daily 1-kilometer resolution PM2.5 concentration estimates from 2003–2020. To account for impacts of stagnant air and inversions, we included estimates of inversion strength based on meteorological conditions, and inversion potential based on human activities and local topography. Model accuracy based on cross-validation was R2 = 0.66. AOD data improve the model in summer and fall during periods of high wildfire activity while the stagnation terms capture the spatial and temporal dynamics of PM2.5 in mountain valleys, particularly during winter. These data can be used to explore exposure and health outcome impacts of PM2.5 across spatiotemporal domains particularly in the intermountain western United States where measurements from monitoring station data are sparse. Furthermore, these data may facilitate analyses of inversion impacts and local topography on exposure and health outcome studies.
Evaluation of entropy driven jet symmetry transitions
Authors: Pease Leonard F. , Mahoney Lenna A. , Yokuda S. Thomas , Bamberger Judith A. , Minette Michael J.
Published: August 2022

Here we determine whether entropy drives planar turbulent jets into round turbulent jets. Determining when a jet flow transitions from one symmetry to the next is an important but incompletely resolved problem. The constructal view argues that the transition between symmetries of jet flows is governed by the minimization or maximization of entropy. Here we explore whether entropy increases with the transition of a planar turbulent jet into a round turbulent jet and whether entropy maximization (or minimization) predicts the same location of symmetry transition as velocity matching. We find that entropy considerations presented do not predict this transition.
Rhythm but not melody processing helps reading via phonological awareness and phonological memory
Authors: Sousa José , Martins Marta , Torres Nathércia , Castro São Luís , Silva Susana
Published: August 2022

Despite abundant evidence that music skills relate to enhanced reading performance, the mechanisms subtending this relation are still under discussion. The Temporal Sampling Framework (TSF) provides a well-defined explanation for the music-reading link: musical rhythm perception would relate to reading because it helps to encode speech units, which, in turn, is fundamental to reading. However, in spite of this clear mediation-based prediction (effect of music skills mediated by the encoding of speech units), the tests made to it so far remain inconclusive, either due to the use of hybrid measures (rhythm perception and production, musical and non-musical rhythm) or to underspecified mediation results (unclear presence of partial mediation). In the present study, we addressed these potential weaknesses of previous studies and investigated whether phonological memory and phonological awareness (proxies of speech encoding abilities) mediate the effects of rhythm perception abilities on reading in late first-graders. To test for the specificity of musical rhythm in this relation, we examined the same hypothesis for melody perception. Results showed full mediation for effects of musical rhythm perception, while melody perception did not even relate to reading. Our findings support the predictions embedded in the TSF and highlight the potential of rhythm-based interventions in early stimulation.
An analysis of the significance of the Tre2/Bub2/CDC 16 (TBC) domain protein family 8 in colorectal cancer
Authors: Liu Yuan-jie , Li Jie-pin , Li Hui-ru , Zeng Shu-hong , Chen Yu-gen , Han Mei , Ye Qian-wen , Zhou Jin-yong , Liu Shen-lin , Zou Xi
Published: August 2022

The TBC (Tre-2/Bub2/Cdc16, TBC) structural domain is now considered as one of the factors potentially regulating tumor progression. However, to date, studies on the relationship between TBC structural domains and tumors are limited. In this study, we identified the role of TBC1 domain family member 8 (TBC1D8) as an oncogene in colorectal cancer (CRC) by least absolute shrinkage and selection operator (LASSO) and Cox regression analysis, showing thatTBC1D8may independently predict CRC outcome. Functional enrichment and single-cell analysis showed thatTBC1D8levels were associated with hypoxia.TBC1D8levels were also positively correlated with M2 macrophage infiltration, which may have a complex association with hypoxia. Taken together, these results show that theTBC1D8gene is involved in colorectal carcinogenesis, and the underlying molecular mechanisms may include hypoxia and immune cell infiltration.
Isolation and identification of antioxidative peptides from crocodile meat hydrolysates using silica gel chromatography
Authors: Yang Liu , Xing Yan , Chen Rui , Ni He , Li Hai-Hang
Published: August 2022

Crocodiles are cultured in large numbers in Asia and other places in order to protect wild resources and meet the needs of human life. In this study, crocodile (Crocodylus siamensis) meat proteins were extracted and hydrolyzed into peptides, their antioxidant peptides were isolated and purified by silica gel chromatography and identified by LC/MS. Crocodile meat proteins were optimally extracted with water and hydrolyzed by papain based on the degree of hydrolysis and antioxidant activity. The hydrolysates were fractionated by ultrafiltration into 3 kDa, 3–30 kDa, and ≥ 30 kDa fractions. The 3 kDa fraction showed most antioxidant activity of the hydrolysates. Its active peptides were separated by silica gel column chromatography and purified by silica gel TLC, based on TLC bio-autographic assays of the activity. Four highly active peptides were identified by LC/MS as SSLTIQFVEGQFVDSYDPTIENTFTK, VPPHIY, VAPEEHPVLLTEAPLNPK, and RNGLPGPIGPAG. The identified peptides were synthesized and showed 50% free radical scavenging activities at 1.0 mg/mL, equal or higher to ascorbic acid at 0.5 mg/mL, in both DPPH and ABTS assays. The results indicated that the 3 kDa hydrolyzed peptides of crocodile meat had high antioxidant activity and the active peptides can be effectively separated and purified by silica gel column chromatography and TLC.
Reciprocal perspective as a super learner improves drug-target interaction prediction (MUSDTI)
Authors: Dick Kevin , Kyrollos Daniel G. , Cosoreanu Eric D. , Dooley Joseph , Fryer Joshua S. , Gordon Shaun M. , Kharbanda Nikhil , Klamrowski Martin , LaCasse Patrick N. L. , Leung Thomas F. , Nasir Muneeb A. , Qiu Chang , Robinson Aisha S. , Shao Derek , Siromahov Boyan R. , Starlight Evening , Tran Christophe , Wang Christopher , Yang Yu-Kai , Green James R.
Published: August 2022

The identification of novel drug-target interactions (DTI) is critical to drug discovery and drug repurposing to address contemporary medical and public health challenges presented by emergent diseases. Historically, computational methods have framed DTI prediction as a binary classification problem (indicating whether or not a drug physically interacts with a given protein target); however, framing the problem instead as a regression-based prediction of the physiochemical binding affinity is more meaningful. With growing databases of experimentally derived drug-target interactions (e.g. Davis, Binding-DB, and Kiba), deep learning-based DTI predictors can be effectively leveraged to achieve state-of-the-art (SOTA) performance. In this work, we formulated a DTI competition as part of the coursework for a senior undergraduate machine learning course and challenged students to generate component DTI models that might surpass SOTA models and effectively combine these component models as part of a meta-model using the Reciprocal Perspective (RP) multi-view learning framework. Following 6 weeks of concerted effort, 28 student-produced component deep-learning DTI models were leveraged in this work to produce a new SOTA RP-DTI model, denoted the Meta Undergraduate Student DTI (MUSDTI) model. Through a series of experiments we demonstrate that (1) RP can considerably improve SOTA DTI prediction, (2) our new double-cold experimental design is more appropriate for emergent DTI challenges, (3) that our novel MUSDTI meta-model outperforms SOTA models, (4) that RP can improve upon individual models as an ensembling method, and finally, (5) RP can be utilized for low computation transfer learning. This work introduces a number of important revelations for the field of DTI prediction and sequence-based, pairwise prediction in general.
Exploring synthetic lethal network for the precision treatment of clear cell renal cell carcinoma
Authors: Liu Zhicheng , Lin Dongxu , Zhou Yi , Zhang Linmeng , Yang Chen , Guo Bin , Xia Feng , Li Yan , Chen Danyang , Wang Cun , Chen Zhong , Leng Chao , Xiao Zhenyu
Published: August 2022

The emerging targeted therapies have revolutionized the treatment of advanced clear cell renal cell carcinoma (ccRCC) over the past 15 years. Nevertheless, lack of personalized treatment limits the development of effective clinical guidelines and improvement of patient prognosis. In this study, large-scale genomic profiles from ccRCC cohorts were explored for integrative analysis. A credible method was developed to identify synthetic lethality (SL) pairs and a list of 72 candidate pairs was determined, which might be utilized to selectively eliminate tumors with genetic aberrations using SL partners of specific mutations. Further analysis identified BRD4 and PRKDC as novel medical targets for patients with BAP1 mutations. After mapping these target genes to the comprehensive drug datasets, two agents (BI-2536 and PI-103) were found to have considerable therapeutic potentials in the BAP1 mutant tumors. Overall, our findings provided insight into the overview of ccRCC mutation patterns and offered novel opportunities for improving individualized cancer treatment.