bluuebunny/crossref_metadata_2025 huggingface dataset:
Collaborative approaches in sustainable and resilient manufacturing
Authors: Camarinha-Matos Luis M. , Rocha Andre Dionisio , Graça Paula
Published: December 2022

In recent years, the manufacturing sector is going through a major transformation, as reflected in the concept of Industry 4.0 and digital transformation. The urge for such transformation is intensified when we consider the growing societal demands for sustainability. The notion of sustainable manufacturing has emerged as a result of this trend. Additionally, industries and the whole society face the challenges of an increasing number of disruptive events, either natural or human-caused, that can severely affect the normal operation of systems. Furthermore, the growing interconnectivity between organizations, people, and physical systems, supported by recent developments in information and communication technologies, highlights the important role that collaborative networks can play in the digital transformation processes. As such, this article analyses potential synergies between the areas of sustainable and resilient manufacturing and collaborative networks. The work also discusses how the responsibility for the various facets of sustainability can be distributed among the multiple entities involved in manufacturing. The study is based on a literature survey, complemented with the experience gained from various research projects and related initiatives in the area, and is organized according to various dimensions of Industry 4.0. A brief review of proposed approaches and indicators for measuring sustainability from the networked manufacturing perspective is also included. Finally, a set of key research challenges are identified to complement strategic research agendas in manufacturing.
Can Environmental Protection Behavior Enhance Farmers' Subjective Well-Being?
Authors: Qi Wenhao , Xu Wei , Qi Xiulin , Sun Meng
Published: December 2022

The significance of environmental protection activities is well known, but little literature has focused on the well-being effects of environmental protection behavior among farmer groups. This study provides new literature support for farmers and rural development issues. Using data from the 2013 China Integrated Social Survey, a systematic and robust examination of the happiness effects of environmental protection behavior among Chinese farmers and their transmission mechanisms was conducted with the help of multiple regression techniques and mediated impact analysis. The study found that Chinese farmers' environmental protection behavior can directly trigger the experience of well-being and also indirectly enhance subjective well-being by improving the quality of life in other areas, thanks to their characteristics in avoiding environmental risks and enhancing social interactions. Increased education may contribute to farmers being more motivated by benefits such as material rewards, experience, and skills, and thus experiencing less well-being from environmental protection behavior. The fact that farmers of all household incomes experience equal well-being from environmental protection behavior is consistent with the view of non-differential well-being experiences in the volunteering literature. The research in this paper adds new evidence to the existing literature and provides an essential reference for policymakers and participants in rural development in China. In addition, studying individual issues in environmental governance in rural China provides a Chinese case study and practical lessons for farmer development in other countries worldwide.
Isn’t there more than one way to bias a polar question?
Authors: Goodhue Daniel
Published: December 2022

I show that speaker bias inpolarity focus questions(PFQs) is context sensitive, while speaker bias inhigh negation questions(HNQs) is context insensitive. This leads me to develop separate accounts of speaker bias in each of these kinds of polar questions. I argue that PFQ bias derives from the fact that they are frequently used in conversational contexts in which an answer to the question has already been asserted by an interlocutor, thus expressing doubt about the prior assertion. This derivation explains their context sensitivity, and the fact that similar bias arises from polar questions that lack polarity focus. I also provide novel evidence that the prejacents of HNQs lack negation, and thus only have an outer negation reading (see, e.g., Ladd in Papers from the seventeenth regional meeting of the Chicago Linguistic Society, vol. 17, pp. 164–171, 1981; Romero and Han in Linguistics and Philosophy 27(5):609–658, 2004; Krifka in Contrastiveness in information structure, alternatives and scalar implicatures, pp. 359–398, 2017; AnderBois in Questions in discourse, pp. 118–171, 2019; Frana and Rawlins in Semantics and Pragmatics 12(16):1–48, 2019; Jeong in Journal of Semantics 38(1):49–94, 2020). Based on a treatment of HNQs as denoting unbalanced partitions (Romero and Han in Linguistics and Philosophy 27(5):609–658, 2004), and competition with their positive polar question alternatives, I propose a novel derivation of speaker bias in HNQs as a conversational implicature. Roughly, if the speaker is ignorant, then a positive polar question will be more useful because it is more informative, so the use of an HNQ conveys that the speaker is not ignorant. The denotation of the HNQ then makes clear which way the speaker is biased. The result separates high negation from verum focus, and I argue that it is more parsimonious and has better empirical coverage than prior accounts.
The correlation of honesty-humility and learning goals with academic cheating
Authors: Reinhardt Nina , Trnka Lina-Marie , Reinhard Marc-André
Published: December 2022

Academic cheating is a problem that affects many educational institutions and has become increasingly significant with the new challenges of online education. Recent studies have found that learning goals are correlated with cheating behavior among students. In this study, we investigated whether learning goals are still a predictor of cheating behavior when controlling for students’ Honesty-Humility (emanated from the HEXACO model of personality) within a sample of 311 German university students. Regrading students’ learning goals, we assessed their learning approach, performance approach, performance avoidance, and work avoidance. The result shows an intermediate negative and highly significant association between Honesty-Humility and academic cheating. Learning goals did not explain any incremental variance in academic cheating that goes beyond the Honesty-Humility factor. As the only exception, the work avoidance goal was found to also predict cheating behavior, but this positive association seems to be not as strong as the negative correlation between Honesty-Humility and academic cheating. We discuss the theoretical and practical implications of these results and make recommendations for future research.
Good practices and recommendations for using and benchmarking computational metabolomics metabolite annotation tools
Authors: de Jonge Niek F. , Mildau Kevin , Meijer David , Louwen Joris J. R. , Bueschl Christoph , Huber Florian , van der Hooft Justin J. J.
Published: December 2022

Background

Untargeted metabolomics approaches based on mass spectrometry obtain comprehensive profiles of complex biological samples. However, on average only 10% of the molecules can be annotated. This low annotation rate hampers biochemical interpretation and effective comparison of metabolomics studies. Furthermore, de novo structural characterization of mass spectral data remains a complicated and time-intensive process. Recently, the field of computational metabolomics has gained traction and novel methods have started to enable large-scale and reliable metabolite annotation. Molecular networking and machine learning-based in-silico annotation tools have been shown to greatly assist metabolite characterization in diverse fields such as clinical metabolomics and natural product discovery.

Aim of review

We highlight recent advances in computational metabolite annotation workflows with a special focus on their evaluation and comparison with other tools. Whilst the progress is substantial and promising, we also argue that inconsistencies in benchmarking different tools hamper users from selecting the most appropriate and promising method for their research. We summarize benchmarking strategies of the different tools and outline several recommendations for benchmarking and comparing novel tools.

Key scientific concepts of review

This review focuses on recent advances in mass spectral library-based and machine learning-supported metabolite annotation workflows. We discuss large-scale library matching and analogue search, the current bloom of mass spectral similarity scores, and how molecular networking has changed the field. In addition, the potentials and challenges of machine learning-supported metabolite annotation workflows are highlighted. Overall, recent developments in computational metabolomics have started to fundamentally change metabolomics workflows, and we expect that as a community we will be able to overcome current method performance ambiguities and annotation bottlenecks.
Conversion of Lithium Chloride into Lithium Hydroxide by Solvent Extraction
Authors: Nguyen Viet Tu , Deferm Clio , Caytan Ward , Riaño Sofía , Jones Peter Tom , Binnemans Koen
Published: December 2022

A hydrometallurgical process is described for conversion of an aqueous solution of lithium chloride into an aqueous solution of lithium hydroxide via a chloride/hydroxide anion exchange reaction by solvent extraction. The organic phase comprises a quaternary ammonium chloride and a hydrophobic phenol in a diluent. The best results were observed for a mixture of the quaternary ammonium chloride Aliquat 336 and 2,6-di-tert-butylphenol (1:1 molar ratio) in the aliphatic diluent Shellsol D70. The solvent extraction process involves two steps. In the first step, the organic phase is contacted with an aqueous sodium hydroxide solution. The phenol is deprotonated, and a chloride ion is simultaneously transferred to the aqueous phase, leading to in situ formation of a quaternary ammonium phenolate in the organic phase. The organic phase, comprising the quaternary ammonium phenolate, is contacted in the second step with an aqueous lithium chloride solution. This contact converts the phenolate into the corresponding phenol by protonation with water extracted to the organic phase, followed by a transfer of hydroxide ions to the aqueous phase and chloride ions to the organic phase. As a result, the aqueous lithium chloride solution is transformed into a lithium hydroxide solution. The process has been demonstrated in continuous counter-current mode in mixer–settlers. Solid battery-grade lithium hydroxide monohydrate was obtained from the aqueous solution by crystallization or by antisolvent precipitation with isopropanol. The process consumes no chemicals other than sodium hydroxide. No waste is generated, with the exception of an aqueous sodium chloride solution.

Graphical Abstract
Getting started in jail, prison, and legal system research
Authors: Glenn Jason , Wickliffe Joi , Kelly Patricia J.
Published: December 2022

Extensive health inequities exist for persons with criminal-legal involvement in the USA. Researchers, both novice and experienced, are critical in documenting these inequities and implementing programs that address the many health and social problems of this population. However, working with currently or formerly incarcerated persons brings new challenges to researchers that may have not been previously considered as necessary. Because incarcerated persons were systemically exploited by biomedical researchers until reform following the Civil Rights Movement, resulting in their designation as a vulnerable population in the Code of Federal Regulations, enhanced protections are necessary in implementing contemporary research involving incarcerated persons. These enhanced protections can delay or prolong the regulatory approval process, particularly to the novice carceral system researcher, which may discourage some from engaging with this important population. Drawing on the many years of experience working with incarcerated persons accumulated by the Sexual Health Empowerment (S)HE Team at the University of Kansas Medical Center (KUMC), this article offers some concrete steps toward getting started in this work.
Gendered radicalisation and ‘everyday practices’: An analysis of extreme right and Islamic State women-only forums
Authors: Veilleux-Lepage Yannick , Phelan Alexandra , Lokmanoglu Ayse D.
Published: December 2022

A growing amount of literature is being devoted to interrogating gendered dynamics in both violent extremism and terrorism, contributing to the integration of international and feminist security. This includes how such dynamics can shape differences in the motivations and participation of women and men. By critically analysing ideological gender constructs in two women-only extremist forums – the Women's Forum on Stormfront.org and Women Dawah, a Turkish-language pro-Islamic State group chat on Telegram – and employing feminist methodology, this article demonstrates how gendered online spaces influence women's ‘everyday practices’ within extremist movements. We argue that women-only online spaces not only facilitate gendered practices by allowing women to share everyday experiences, hold ideological discussions, and engage in debate, but also provide an important means to navigate these issues within the movement itself. In fact, women-only forums are actively used by women within extremist movements to exert greater agency in the face of otherwise constraining gendered ideological constructs. In turn, gendered everyday practices are reinforced by virtual communities that strengthen a sense of meaning – and purpose – in the movement, albeit being ideologically confined to the private sphere in many ways. This study sheds light not only on the differences in participation between women and men, but also on how such virtual communities can serve as spaces to frame and reinforce gendered practices in extremist movements. This has key implications for deradicalisation and disengagement strategies, which are at present overwhelmingly gender neutral. We provide evidence of how women navigate agency in these spaces, while challenging the stereotype that women in extremist movements are typically passive actors confined to traditional roles.
A Critical Reflection on James Kreines's Interpretation of Hegel's Account of ‘Mechanism’
Authors: Rokni Ahilleas
Published: December 2022

James Kreines's Reason in the World (2015) offers an engaging and thought-provoking examination of Hegel's ambitions in the Science of Logic. However, it has gone unnoticed that there are two fundamental misinterpretations in his account of ‘Mechanism’ from the Logic. First, Kreines interprets the chapter as beginning with a ‘pure mechanism’ hypothesis that investigates the coherence of a purely mechanistic explanation of the world that makes no appeal to the immanent concept of things. Thus, according to Kreines, the Concept is absent from the beginning of ‘Mechanism’ and only appears in the final section of the chapter, in ‘C. Absolute Mechanism’ in the subsection on the law, what Kreines conceptualizes as ‘reasonable mechanism’. Second, within his overall interpretation of ‘Mechanism’ as the development from the ‘pure mechanism’ hypothesis to ‘reasonable mechanism’ Kreines claims that there are logical moments that are explanatorily relevant and some that are not. Thus, Kreines will want to claim that Hegel's analysis of ‘pure mechanism’ reveals that ‘pure mechanism’ fails to be explanatorily relevant because, a) the logical moments do not have a concept immanent to them, and b) have ‘indifference’. It is only in the law that mechanistic explanations become explanatorily relevant because of the appearance of the Concept and the disappearance of ‘indifference’. I argue against both these positions. First, I think that there is no textual support for the idea that ‘Mechanism’ begins without the Concept immanent to it. Second, I think that Kreines is mistaken to equate ‘indifference’ with explanatory irrelevance and the absence of the Concept. My approach in this paper is to give my own analysis of the relevant passages from ‘Mechanism’ and, in doing so, to both show the misgivings of Kreines's interpretation and to offer an alternative way of reading the chapter.
Modern Scepticism, Metaphysics, and Absolute Knowing in Hegel's Science of Logic
Authors: Engelman Robert
Published: December 2022

While there are good reasons to think that Hegel would not engage with modern scepticism in the Science of Logic, this article argues that he nevertheless does so in a way that informs the text's conception of logic as the latter pertains to metaphysics. Hegel engages with modern scepticism's general concerns that philosophy should begin without unexamined presuppositions and should come to attain not only knowledge of truth, but corresponding second-order knowledge: knowledge of knowing truth. These concerns inform two needs that Hegel formulates for first philosophy, which logic—by unifying with metaphysics, which is traditionally synonymous with first philosophy—is to satisfy. However, logic, for the Logic, is unified with metaphysics as a science of absolute knowing, the form of thinking involved in traditional metaphysics. As such, logic, for the Logic, is neither anti-metaphysical nor reducible to metaphysics, but is rather a science of metaphysical thinking, which, for Hegel, includes metaphysics. The article emphasizes how Hegel's construal of logic as a science of absolute knowing avoids running into the ‘swimming problem’ that Hegel raises against, broadly, epistemological forms of first philosophy.
Between Chemism and Life: Is Hegel's Teleology Misplaced?
Authors: Ebeturk Emre
Published: December 2022

In this paper, I raise a question concerning the place of ‘Teleology’ in Hegel's system of logic and ask whether ‘Teleology’ as a logical category can and should come immediately before ‘Life’. I offer two main reasons to think that the category of ‘Teleology’ might be misplaced. The first and the indirect reason is inspired by a difference between the logical system and the Philosophy of Nature concerning the immediate precursors and the emergence of life as a logical category and real determinacy. In Hegel's Logic, ‘Teleology’ is interposed between ‘Chemism’ and ‘Life’, while in his Philosophy of Nature, ‘Organics’ immediately follows ‘The Chemical Process’. Although the systematic order of the natural determinacies laid out in the Philosophy of Nature has no authority over the sequence of logical determinacies, and although there does not have to be a one-to-one correspondence between the logical categories and natural determinacies of Hegel's system, I argue that the smooth transition from the chemical process to the self-sustaining totality of the geological organism in the Philosophy of Nature, is an incentive to consider a parallel transition in the logical exposition, which I show to be workable. The second and the direct reason is that Hegel's category of ‘Teleology’ cannot but make a crucial reference to the initial determinacy of the category of ‘Life,’ without which it is inconceivable. By explaining why this reference is untenable and how, by contrast, the initial determinacy of life is conceivable independently of the process in which some subjective end is realized in objectivity through external means, I conclude that the logic of ‘Life’ and internal teleology should precede the logic of external teleology, allowing for a direct passage from ‘Chemism’ to ‘Life’.
Drop impact on a sticky porous surface with gas discharge: transformation of drops into bubbles
Authors: Weimar Lukas , Hu Luyang , Baier Tobias , Hardt Steffen
Published: December 2022

The impact of drops on a porous surface with high contact-angle hysteresis and gas discharge is studied. Four different impact modes, ranging from complete repulsion to fast immobilization of a drop on the surface, are identified and mapped in a space spanned by the pressure difference of the gas across the porous surface and the impact Weber number of the drop. The most remarkable aspect of the dynamics is the transformation of a drop into a bubble, which occurs when a drop just overcomes the repulsion by the gas flow and wets the surface. The transition to the regime in which a drop is transformed to a bubble is well described by a simple scaling relationship based on a balance between inertia and the repulsive force due to the gas flow.
Explaining bilateral patterns of global wine trade, 1962–2019
Authors: Puga German , Sharafeyeva Alfinura , Anderson Kym
Published: December 2022

This study uses gravity models to explain bilateral patterns of global wine trade since 1962. This is, to our knowledge, the first study on global wine trade covering the second wave of globalization as a whole. The results suggest that the impact of distance, common language, and common colonizer post-1945 on wine trade was lower in the 1991–2019 period than in the 1962–1990 period. We also use gravity models to explain the impact on bilateral wine trade patterns of similarities across countries in the mix of winegrape varieties in their vineyards. Although our models do not allow us to identify causality, the results suggest that countries trade more wine with each other the closer their mix of winegrape varieties.
Optimizing the clipping frequency and nitrogen topdressing in a dual-purpose oat used for fodder and cover cropping
Authors: Janhi Kudzayi , Chiduza Cornelius , Mupangwa John , Muzangwa Lindah
Published: December 2022

Management strategies such as nitrogen (N) topdressing and clipping can be used to optimize a cover crop for the dual purpose of soil cover and forage. The present study tested oat (Avena sativa) for a holistic provision of soil cover and forage under various levels of clipping frequency and N topdressing. Effects on root and above-ground biomass, acid detergent fiber, neutral detergent fiber, and crude protein (CP) were evaluated. Clipping frequency had four levels, namely clipped only at termination (C1), clipped at 28 days after emergence (DAE) and termination (C2), clipped at 28, 42 DAE, and termination (C3), and clipped at 28, 42, 56 DAE, and termination (C4). Nitrogen topdressing had two levels, namely with (N1) and without (N0) the recommended N topdressing. Increasing clipping frequency reduced the root and aerial biomass and did not affect the forage quality harvested before termination. However, N topdressing increased biomass and CP content across the clipping frequencies. Results suggest clipping thrice combined with N topdressing (C4 + N1) provides the best option to satisfy both soil cover and livestock demands. The treatment (C4 + N1) gave > 2 t ha−1 of biomass during the growing period and 6 t ha−1 at termination which can be used for livestock forage and soil cover, respectively. Clipping thrice without N topdressing (C4 + N0) was the best option for resource-constrained farmers.
Judicializing Environmental Politics? China's Procurator-led Public Interest Litigation against the Government
Authors: Wang Yueduan , Xia Ying
Published: December 2022

Scholars consider deficient local accountability mechanisms a key shortcoming of China's response to environmental issues. Through empirical analysis of the new procurator-led public interest litigation (PIL) system, this study examines whether – and to what extent – this shortcoming can be remedied by empowering the juridical institutions. It concludes that thanks to the procuratorates’ political insider status, relative autonomy from local politics and extensive resources, procurators have generally found ways to maintain a delicate balance between holding executive agencies environmentally accountable and managing local governments’ resistance to the PIL system. However, reliance on top-down political support may ultimately hinder the expansion and stability of the procuratorial PIL system.
Should the Dutch Law on Euthanasia Be Expanded to Include Children?
Authors: Verhagen A.A.E (Eduard) , Buijsen Martin
Published: December 2022

The 2002 Dutch Euthanasia law applies to patients aged 12 years and older. Developments in end-of-life care and decision-making in the last decade have sparked the debate about usefulness and necessity to extend euthanasia to include children under 12 years of age. This paper describes two opposite positions: the affirmative position of a pediatrician and expert in pediatric palliative care and the negative position of a jurist and specialist in health law.
Pandemic Rule-Breakers, Moral Luck, and Blaming the Blameworthy
Authors: Hill Jesse
Published: December 2022

This paper takes under consideration a piece by Roger Crisp in which he questions what the problem of moral luck can teach us about COVID-19 lockdown rule-breakers. Taking the position that although such rule-breakers might seem to be new examples of moral luck, Crisp ends up denying the existence of moral luck and argues that moral luck is an outdated notion in so far as it relies on other questionable aspects of morality, that is, retributivist punishment and blame. Although the author agrees with Crisp that pandemic rule-breaker cases are putative examples of resultant moral luck, he proposes that Crisp has misconstrued what moral luck is and the paper examines in detail what he sees as the numerous problems with Crisp’s claims. The author concludes that Crisp’s analysis of pandemic rule-breaking does not shed any new light on the moral luck debate, and the difficult questions of luck, moral responsibility, and desert are not so easily resolved.
Reconsidering Capacity to Appoint a Healthcare Proxy
Authors: Appel Jacob M.
Published: December 2022

Clinicians are often called upon to assess the capacity of a patient to appoint a healthcare agent. Although a consensus has emerged that the standard for such assessment should differ from that for capacity to render specific healthcare decisions, exactly what standard should be employed remains unsettled and differs by jurisdiction. The current models in use draw heavily upon analogous methods used in clinical assessment, such as the “four skills” approach. This essay proposes an alternative model that relies upon categorization and sliding scale risk assessment that can be used to determine to how much scrutiny the proxy appointment should be subjected and how much certainty of accuracy should be required in order to maximize the patient’s autonomy and ensure that her underlying wishes are met.
The Stability of Political Compromise—Abortion Legislation in Denmark and Norway
Authors: Holm Søren
Published: December 2022

In the 1970s, both Denmark and Norway passed abortion legislation that is still the basis for the regulation of abortion in these countries. The legislation was fairly liberal with abortion on demand until 12 weeks of gestation and a permission system for later abortions. This article provides a brief history of the developments leading up to these political compromises and an analysis of the reasons why they have proved remarkably stable. It ends by looking at some factors that may now destabilize 50 years of stable compromise about abortion.
Transcatheter closure of large perimembranous ventricular septal defects with inlet to outlet extension with the Amplatzer Vascular Plug-II
Authors: Piccinelli Enrico , Bautista-Rodriguez Carles , Fraisse Alain
Published: December 2022

Transcatheter closure of perimembranous ventricular septal defect is an alternative to surgery in selected small to medium defects with a reasonable distance between the defect and the aortic or tricuspid valves. Surgical closure is generally preferred for large defects with an inlet to outlet extension, aortic malalignment, or deficient aortic rim. We report two successful cases of percutaneous closure of large perimembranous ventricular septal defects with inlet to outlet extension using an Amplatzer Vascular Plug-II via a retrograde approach. Transcatheter closure of large perimembranous ventricular septal defect with inlet to outlet extension is feasible and facilitated by the characteristics of the Amplatzer Vascular Plug-II device and the specific implantation technique.
Cosmopocalypse: From Prophetic Vision to Political Foresight in Romola
Authors: Reinken Brian
Published: December 2022

This article contends that George Eliot's higher critical approach to biblical prophecy led her to interpret prophetic knowledge about the future as a product of historical scholarship rather than supernatural revelation. This interpretation bore creative fruit in Eliot's 1862–63 novel Romola, a book that repeatedly condemns the irrational ethos of supernatural prophecy by rebuking mystical seers’ emotional volatility and their ignorance of history. As a rational alternative to supernaturalism, Romola upholds a serious, scholarly mode of prophecy whose power to predict the future derives from historical research. Recasting prophecy as a rational mode of historical scholarship enables Romola to deploy it as a method of intellectually responsible political analysis. In the process of conflating the prediction of the future with the study of history, the rational prophetic mode demands that political visionaries must temper utopian promises about a cosmopolitan future with sober-minded analyses of the intercultural violence that has plagued the past. By revealing cosmopolitan utopia's historical limitations, Eliot's prophetic mode ultimately promotes a “cosmopocalyptic” form of politics.
Neglecting Model Parametric Uncertainty Can Drastically Underestimate Flood Risks
Authors: Sharma Sanjib , Lee Benjamin Seiyon , Hosseini‐Shakib Iman , Haran Murali , Keller Klaus
Published: December 2022

Floods drive dynamic and deeply uncertain risks for people and infrastructures. Uncertainty characterization is a crucial step in improving the predictive understanding of multi‐sector dynamics and the design of risk‐management strategies. Current approaches to estimate flood hazards often sample only a relatively small subset of the known unknowns, for example, the uncertainties surrounding the model parameters. This approach neglects the impacts of key uncertainties on hazards and system dynamics. Here we mainstream a recently developed method for Bayesian inference to calibrate a computationally expensive distributed hydrologic model. We compare three different calibration approaches: (a) stepwise line search, (b) precalibration or screening, and (c) the Fast Model Calibrations (FaMoS) approach. FaMoS deploys a particle‐based approach that takes advantage of the massive parallelization afforded by modern high‐performance computing systems. We quantify how neglecting parametric uncertainty and data discrepancy can drastically underestimate extreme flood events and risks. Precalibration improves prediction skill score over a stepwise line search. The Bayesian calibration improves the uncertainty characterization of model parameters and flood risk projections.
USP36 facilitates esophageal squamous carcinoma progression via stabilizing YAP
Authors: Zhang Wenhao , Luo Junwen , Xiao Zhaohua , Zang Yifeng , Li Xin , Zhou Yougjia , Zhou Jie , Tian Zhongxian , Zhu Jian , Zhao Xiaogang
Published: December 2022

Esophageal squamous carcinoma (ESCC) is the major subtype of esophageal cancer in China, accounting for 90% of cases. Recent studies revealed that abnormalities in the Hippo/YAP axis are pervasive in ESCC and are recognized as the important driver of ESCC progression. Since the activity of Hippo signaling is controlled by phosphorylation cascade, it is a mystery why the major effector YAP is still over-activated when the cascade is inhibited. Several studies suggested that in addition to phosphorylation, other protein modifications such as ubiquitination also play important roles in manipulating Hippo/YAP signaling activity. Since YAP protein stability is controlled via an appropriate balance between E3 ubiquitin ligases and deubiquitinases, we performed deubiquitinase siRNA screening and identified USP36 as a deubiquitinase significantly related to Hippo/YAP signaling activity and ESCC progression. USP36 expression was elevated in ESCC samples and correlated with poor differentiation. USP36 expression was correlated with YAP protein levels in ESCC samples. Molecular studies demonstrated that USP36 associated with the YAP protein and enhanced YAP protein stability by blocking the K48-linked polyubiquitination of YAP. In conclusion, our study revealed a novel deubiquitinase in regulating Hippo signaling in ESCC, which could be an encouraging drug target for Hippo-driven ESCC.
Proteogenomic characterization of MiT family translocation renal cell carcinoma
Authors: Qu Yuanyuan , Wu Xiaohui , Anwaier Aihetaimujiang , Feng Jinwen , Xu Wenhao , Pei Xiaoru , Zhu Yu , Liu Yang , Bai Lin , Yang Guojian , Tian Xi , Su Jiaqi , Shi Guo-Hai , Cao Da-Long , Xu Fujiang , Wang Yue , Gan Hua-Lei , Ni Shujuan , Sun Meng-Hong , Zhao Jian-Yuan , Zhang Hailiang , Ye Dingwei , Ding Chen
Published: December 2022

Microphthalmia transcription factor (MiT) family translocation renal cell carcinoma (tRCC) is a rare type of kidney cancer, which is not well characterized. Here we show the comprehensive proteogenomic analysis of tRCC tumors and normal adjacent tissues to elucidate the molecular landscape of this disease. Our study reveals that defective DNA repair plays an important role in tRCC carcinogenesis and progression. Metabolic processes are markedly dysregulated at both the mRNA and protein levels. Proteomic and phosphoproteome data identify mTOR signaling pathway as a potential therapeutic target. Moreover, molecular subtyping and immune infiltration analysis characterize the inter-tumoral heterogeneity of tRCC. Multi-omic integration reveals the dysregulation of cellular processes affected by genomic alterations, including oxidative phosphorylation, autophagy, transcription factor activity, and proteasome function. This study represents a comprehensive proteogenomic analysis of tRCC, providing valuable insights into its biological mechanisms, disease diagnosis, and prognostication.
SepN is a septal junction component required for gated cell–cell communication in the filamentous cyanobacterium Nostoc
Authors: Kieninger Ann-Katrin , Tokarz Piotr , Janović Ana , Pilhofer Martin , Weiss Gregor L. , Maldener Iris
Published: December 2022

Multicellular organisms require controlled intercellular communication for their survival. Strains of the filamentous cyanobacterium Nostoc regulate cell–cell communication between sister cells via a conformational change in septal junctions. These multi-protein cell junctions consist of a septum spanning tube with a membrane-embedded plug at both ends, and a cap covering the plug on the cytoplasmic side. The identities of septal junction components are unknown, with exception of the protein FraD. Here, we identify and characterize a FraD-interacting protein, SepN, as the second component of septal junctions in Nostoc. We use cryo-electron tomography of cryo-focused ion beam-thinned cyanobacterial filaments to show that septal junctions in a sepN mutant lack a plug module and display an aberrant cap. The sepN mutant exhibits highly reduced cell–cell communication rates, as shown by fluorescence recovery after photobleaching experiments. Furthermore, the mutant is unable to gate molecule exchange through septal junctions and displays reduced filament survival after stress. Our data demonstrate the importance of controlling molecular diffusion between cells to ensure the survival of a multicellular organism.
Halogen-bonded shape memory polymers
Authors: Guo Hongshuang , Puttreddy Rakesh , Salminen Turkka , Lends Alons , Jaudzems Kristaps , Zeng Hao , Priimagi Arri
Published: December 2022

Halogen bonding (XB), a non-covalent interaction between an electron-deficient halogen atom and a Lewis base, is widely adopted in organic synthesis and supramolecular crystal engineering. However, the roadmap towards materials applications is hindered by the challenges in harnessing this relatively weak intermolecular interaction to devise human-commanded stimuli-responsive soft materials. Here, we report a liquid crystalline network comprising permanent covalent crosslinks and dynamic halogen bond crosslinks, which possess reversible thermo-responsive shape memory behaviour. Our findings suggest that I···N halogen bond, a paradigmatic motif in crystal engineering studies, enables temporary shape fixation at room temperature and subsequent shape recovery in response to human body temperature. We demonstrate versatile shape programming of the halogen-bonded polymer networks through human-hand operation and propose a micro-robotic injection model for complex 1D to 3D shape morphing in aqueous media at 37 °C. Through systematic structure-property-performance studies, we show the necessity of the I···N crosslinks in driving the shape memory effect. The halogen-bonded shape memory polymers expand the toolbox for the preparation of smart supramolecular constructs with tailored mechanical properties and thermoresponsive behaviour, for the needs of, e.g., future medical devices.
Perfluorodecalin-based oxygenated emulsion as a topical treatment for chemical burn to the eye
Authors: Li Sanming , Pang Kunpeng , Zhu Shuyan , Pate Kathryn , Yin Jia
Published: December 2022

Chemical injuries to the eye are emergencies with limited acute treatment options other than prompt irrigation and can cause permanent vision loss. We developed a perfluorodecalin-based supersaturated oxygen emulsion (SSOE) to topically deliver high concentration of oxygen to the eye. SSOE is manufactured in hyperbaric conditions and stored in a ready-to-use canister. Upon dispensation, SSOE rapidly raises partial oxygen pressure 3 times over atmospheric level. SSOE is biocompatible with human corneal cells and safe on mouse eyes in vivo. A single topical application of SSOE to the eye after alkali injury significantly promotes corneal epithelial wound healing, decreases anterior chamber exudation, and reduces optical opacity and cataract formation in mice. SSOE treatment reduces intraocular hypoxia, cell death, leukocyte infiltration, production of inflammatory mediators, and hypoxia-inducible factor 1-alpha signaling, thus hastening recovery of normal tissue integrity during the wound healing process. Here, we show that SSOE is an effective topical therapeutic in the acute treatment of ocular chemical injuries.
Cortical and subcortical morphological alterations in motor subtypes of Parkinson’s disease
Authors: Li Jianyu , Zhang Yuanchao , Huang Zitong , Jiang Yihan , Ren Zhanbing , Liu Daihong , Zhang Jiuquan , La Piana Roberta , Chen Yifan
Published: December 2022

Parkinson’s disease (PD) can be classified into an akinetic-rigid (AR) and a tremor-dominant (TD) subtype based on predominant motor symptoms. Patients with different motor subtypes often show divergent clinical manifestations; however, the underlying neural mechanisms remain unclear. This study aimed to characterize the cortical and subcortical morphological alterations in motor subtypes of PD. T1-weighted MRI images were obtained for 90 patients with PD (64 with the AR subtype and 26 with the TD subtype) and 56 healthy controls (HCs). Cortical surface area, sulcal depth (measured by Freesurfer’s Sulc index), and subcortical volume were computed to identify the cortical and subcortical morphological alterations in the two motor subtypes. Compared with HCs, we found widespread surface area reductions in the AR subtype yet sparse surface area reductions in the TD subtype. We found no significant Sulc change in the AR subtype yet increased Sulc in the right supramarginal gyrus in the TD subtype. The hippocampal volumes in both subtypes were lower than those of HCs. In PD patients, the surface area of left posterior cingulate cortex was positively correlated with Mini-Mental State Examination (MMSE) score, while the Sulc value of right middle frontal gyrus was positively correlated with severity of motor impairments. Additionally, the hippocampal volumes were positively correlated with MMSE and Montreal Cognitive Assessment scores and negatively correlated with severity of motor impairments and Hoehn & Yahr scores. Taken together, these findings may contribute to a better understanding of the neural substrates underlying the distinct symptom profiles in the two PD subtypes.
Synthetic anaplerotic modules for the direct synthesis of complex molecules from CO2
Authors: Diehl Christoph , Gerlinger Patrick D. , Paczia Nicole , Erb Tobias J.
Published: December 2022

Anaplerosis is an essential feature of metabolism that allows the continuous operation of natural metabolic networks, such as the citric acid cycle, by constantly replenishing drained intermediates. However, this concept has not been applied to synthetic in vitro metabolic networks, thus far. Here we used anaplerotic strategies to directly access the core sequence of the CETCH cycle, a new-to-nature in vitro CO2-fixation pathway that features several C3–C5 biosynthetic precursors. We drafted four different anaplerotic modules that use CO2 to replenish the CETCH cycle’s intermediates and validated our designs by producing 6-deoxyerythronolide B (6-DEB), the C21-macrolide backbone of erythromycin. Our best design allowed the carbon-positive synthesis of 6-DEB via 54 enzymatic reactions in vitro at yields comparable to those with isolated 6-DEB polyketide synthase (DEBS). Our work showcases how new-to-nature anaplerotic modules can be designed and tailored to enhance and expand the synthetic capabilities of complex catalytic in vitro reaction networks.
Polarity of the CRISPR roadblock to transcription
Authors: Hall Porter M. , Inman James T. , Fulbright Robert M. , Le Tung T. , Brewer Joshua J. , Lambert Guillaume , Darst Seth A. , Wang Michelle D.
Published: December 2022

CRISPR (clustered regularly interspaced short palindromic repeats) utility relies on a stable Cas effector complex binding to its target site. However, a Cas complex bound to DNA may be removed by motor proteins carrying out host processes and the mechanism governing this removal remains unclear. Intriguingly, during CRISPR interference, RNA polymerase (RNAP) progression is only fully blocked by a bound endonuclease-deficient Cas (dCas) from the protospacer adjacent motif (PAM)-proximal side. By mapping dCas-DNA interactions at high resolution, we discovered that the collapse of the dCas R-loop allows Escherichia coli RNAP read-through from the PAM-distal side for both Sp–dCas9 and As–dCas12a. This finding is not unique to RNAP and holds for the Mfd translocase. This mechanistic understanding allowed us to modulate the dCas R-loop stability by modifying the guide RNAs. This work highlights the importance of the R-loop in dCas-binding stability and provides valuable mechanistic insights for broad applications of CRISPR technology.
Vegetation assessments under the influence of environmental variables from the Yakhtangay Hill of the Hindu-Himalayan range, North Western Pakistan
Authors: Ullah Hameed , Khan Shujaul Mulk , jaremko Mariusz , Jahangir Sadia , Ullah Zahid , Ali Iftikhar , Ahmad Zeeshan , Badshah Hussain
Published: December 2022

Vegetation structures and dynamics are the result of interactions between abiotic and biotic factors in an ecosystem. The present study was designed to investigate vegetation structure and species diversity along various environmental variables in the Yakhtangay Hills of the Hindu-Himalayan Mountain Pakistan, by using multivariate statistical analysis. Quadrat quantitative method was used for the sampling of vegetation. PC-ORD version 5 software was used to classify the vegetation into different plants communities using cluster analysis. The results of regression analysis among various edaphic variables shows that soil organic matter, total dissolved solids, electrical conductivity, CaCO3and moisture contents shows a significant positive correlation with species abundance, while the soil pH has inverse relationship with plant species abundance. Similarly, species richness increases with increase in soil organic matter, CaCO3and moisture contents, while decrease with increase in soil pH, total dissolved solids and electrical conductivity (p< 0.05). The vegetation was classified into four major plant communities and their respective indicators were identified using indicator species analysis. Indicator species analysis reflects the indicators of the study area are mostly the indicators to the Himalayan or moist temperate ecosystem. These indicators could be considered for micro-habitat conservation and respective ecosystem management plans not only in the study area but also in other region with similar sort of environmental conditions.
Vaccine hesitancy prospectively predicts nocebo side-effects following COVID-19 vaccination
Authors: Hoffman Yaakov S. G. , Levin Yafit , Palgi Yuval , Goodwin Robin , Ben-Ezra Menachem , Greenblatt-Kimron Lee
Published: December 2022

The directionality between vaccine hesitancy and COVID-19 vaccine side-effects has not been hitherto examined. We hypothesized a nocebo effect, whereby vaccine hesitancy towards the second Pfizer vaccination dose predicts subsequent side-effects for a booster dose, beyond other effects. We expected these nocebo effects to be driven by (mis)information in males and prior experience in females. A representative sample of older adults (n = 756, mean age = 68.9 ± 3.43) were questioned in a typical cross-lagged design (wave 1 following a second Pfizer dose, wave 2 after their booster). As hypothesized, earlier vaccine hesitancy predicted subsequent booster side-effects for females (β = 0.10 p = 0.025, f 2 = 0.02) and males (β = 0.34, p < 0.001, f 2 = 0.16); effects were stronger in males (χ2Δ (1) = 4.34, p = 0.03). The (W1-to-W2) side-effect autoregression was stronger in females (β = .34, p < 0.001; males β = 0.18, p < 0.001), χ2Δ (1) = 26.86, p < 0.001. Results show that a quantifiable and meaningful portion of COVID-19 vaccine side-effects is predicted by vaccine hesitancy, demonstrating that side-effects comprise a psychosomatic nocebo component in vaccinated individuals. The data reveal distinct risk levels for future side-effects, suggesting the need to tailor public health messaging.
Electronic and optical properties of the buckled and puckered phases of phosphorene and arsenene
Authors: Galicia Hernandez Jose Mario , Fernandez-Escamilla H. N. , Guerrero Sanchez J. , Takeuchi Noboru
Published: December 2022

Using first-principles calculations, we have investigated the structural, electronic, and optical properties of phosphorene and arsenene, group V two-dimensional materials. They have attracted the scientific community’s interest due to their possible applications in electronics and optoelectronics. Since phosphorene and arsenene are not planar monolayers, two types of structures were considered for each system: puckered and buckled arrangements. Computations of band gap were performed within the GW approach to overcome the underestimation given by standard DFT and predict trustable band gap values in good agreement with experimental measurements. Our calculated electronic band gaps lie in the range from near-infrared to visible light, suggesting potential applications in optoelectronics devices. The computed electronic band gaps are 2.95 eV and 1.83 eV for blue and black phosphorene systems. On the other hand, the values for buckled and puckered arsenene are 2.56 eV and 1.51 eV, respectively. Moreover, the study of the optical properties has been dealt by computing the dielectric function imaginary part, which was obtained using the Bethe–Salpeter approach. The use of this technique allows the consideration of excitonic effects. Results indicate strong exciton binding energies of 830 meV for blue phosphorene, 540 meV for black phosphorene, 690 meV for buckled arsenene, and 484 meV for puckered arsenene. The results of our study suggest the possibility of using these materials in electronic and optoelectronic devices.