bluuebunny/crossref_metadata_2025 huggingface dataset:
Entity alignment via graph neural networks: a component-level study
Authors: Shu Yanfeng , Zhang Ji , Huang Guangyan , Chi Chi-Hung , He Jing
Published: November 2023

Entity alignment plays an essential role in the integration of knowledge graphs (KGs) as it seeks to identify entities that refer to the same real-world objects across different KGs. Recent research has primarily centred on embedding-based approaches. Among these approaches, there is a growing interest in graph neural networks (GNNs) due to their ability to capture complex relationships and incorporate node attributes within KGs. Despite the presence of several surveys in this area, they often lack comprehensive investigations specifically targeting GNN-based approaches. Moreover, they tend to evaluate overall performance without analysing the impact of individual components and methods. To bridge these gaps, this paper presents a framework for GNN-based entity alignment that captures the key characteristics of these approaches. We conduct a fine-grained analysis of individual components and assess their influences on alignment results. Our findings highlight specific module options that significantly affect the alignment outcomes. By carefully selecting suitable methods for combination, even basic GNN networks can achieve competitive alignment results.
A global and regional assessment of the timing of birth registration using DHS and MICS survey data
Authors: Adair Tim , Li Hang
Published: November 2023

Registration of birth within the first year of life is important to ensure children receive its full benefits and that fertility statistics derived from these data are informative for policy. This study provides an up-to-date global and regional assessment of the timing of birth registration by using all available birth registration data of children aged less than five years reported in Demographic and Health Surveys and Multiple Indicator Cluster Surveys from 2010 onwards. We calculated adjusted age-specific birth registration completeness by converting period age-specific completeness data into a hypothetical cohort. Timing of birth registration was analysed using ratios of adjusted age-specific completeness, with differentials by region, over time, and level of completeness assessed using bivariate and multivariate analyses. Almost 20% of registered births in countries with incomplete birth registration (less than 95%) were not registered until after 12 months, and this has not improved since 2010. In several countries this figure is greater than 50%, particularly in South Asia. There remains considerable scope to improve the timeliness of birth registration, particularly in countries where the overall level of completeness is lower. Strengthening and enforcing legislation for the mandatory registration of births before age 12 months and greater involvement of the health sector in registration processes are two ways which will improve birth registration timing.
Predicting academic success: machine learning analysis of student, parental, and school efforts
Authors: Jin Xin
Published: November 2023

Understanding what predicts students’ educational outcomes is crucial to promoting quality education and implementing effective policies. This study proposes that the efforts of students, parents, and schools are interrelated and collectively contribute to determining academic achievements. Using data from the China Education Panel Survey conducted between 2013 and 2015, this study employs four widely used machine learning techniques, namely, Lasso, Random Forest, AdaBoost, and Support Vector Regression, which are effective for prediction tasks—to explore the predictive power of individual predictors and variable categories. The effort exerted by each group has varying impacts on academic exam results, with parents’ demanding requirements being the most significant individual predictor of academic performance; the category of school effort has a greater impact than parental and student effort when controlling for various social-origin-based characteristics; and significant gender differences among junior high students in China, with school effort exhibiting a greater impact on academic achievement for girls than for boys, and parental effort showing a greater impact for boys than for girls. This study advances the understanding of the role of effort as an independent factor in the learning process, theoretically and empirically. The findings have substantial implications for education policies aimed at enhancing school effort, emphasizing the need for gender-specific interventions to improve academic performance for all students.
Deciphering the roles of triiodothyronine (T3) and thyroid-stimulating hormone (TSH) on cardiac electrical remodeling in clinical and experimental hypothyroidism
Authors: Casis Oscar , Echeazarra Leire , Sáenz-Díez Beatriz , Gallego Mónica
Published: November 2023

Hypothyroidism is the most frequent endocrine pathology. Although clinical or overt hypothyroidism has been traditionally associated to low T3 / T4 and high thyrotropin (TSH) circulating levels, other forms exist such as subclinical hypothyroidism, characterized by normal blood T3 / T4 and high TSH. In its different forms is estimated to affect approximately 10% of the population, especially women, in a 5:1 ratio with respect to men. Among its consequences are alterations in cardiac electrical activity, especially in the repolarization phase, which is accompanied by an increased susceptibility to cardiac arrhythmias. Although these alterations have traditionally been attributed to thyroid hormone deficiency, recent studies, both clinical trials and experimental models, demonstrate a fundamental role of TSH in cardiac electrical remodeling. Thus, both metabolic thyroid hormones and TSH regulate cardiac ion channel expression in many and varied ways. This means that the different combinations of hormones that predominate in different types of hypothyroidism (overt, subclinic, primary, central) can generate different forms of cardiac electrical remodeling. These new findings are raising the relevant question of whether serum TSH reference ranges should be redefined.
Characterization of blaOXA-48-carrying plasmids and small non-AMR-coding plasmids collected from Ukrainian patients
Authors: van Almsick Vincent F. , Sobkowiak Annika , Scherff Natalie , Schuler Franziska , Mellmann Alexander , Schwierzeck Vera
Published: November 2023

Purpose

Carbapenemase-producing Enterobacterales (CPE) pose a serious threat for healthcare facilities worldwide, yet the mode of transmission is often unclear. Recently, we recorded an increase of blaOXA-48-harboring isolates at our hospital associated with patients with previous medical treatment in the Ukraine. We used long-read whole genome sequencing (lrWGS) to characterize these isolates including their plasmids.

Methods

Samples were collected as part of clinical routine diagnostic or screening of multi-drug resistance bacteria (MDRB). Antimicrobial susceptibility testing was performed and all MDRB (n = 10) were sequenced by lrWGS for genotyping, identification of antimicrobial resistance (AMR) genes, and characterization of plasmids.

Results

While routine analysis of core genome multilocus sequence typing (cgMLST) did not show any genetic similarities between isolates, we found an unexpected high similarity in the plasmid diversity of different Enterobacterales in patients with previous medical treatment in the Ukraine. This included an IncL/M plasmid carrying blaOXA-48 and additional small non-AMR-coding plasmids.

Conclusion

Our results show that lrWGS can be used in the routine setting to uncover similarities in plasmids and may give further information about potential epidemiologic associations. In the future, analysis of both AMR and non-AMR plasmids may provide an additional layer of information for molecular surveillance of CPE.
Acute kidney injury in multiple myeloma patients undergoing autologous hematopoietic stem cell transplant: a cohort study
Authors: Rodrigues Natacha , Costa Claudia , Branco Carolina , Martins Carlos , Lopes José António
Published: November 2023

Background

Autologous hematopoietic stem cell transplant plays an important role in multiple myeloma (MM) treatment. Increasing incidence of MM and growing awareness of acute kidney injury (AKI) as a complication of hematopoietic stem cell transplant results in the need to better understand AKI in these patients. We aimed to evaluate incidence, risk factors and 5-year prognostic impact of AKI in MM patients undergoing autologous hematopoietic stem cell transplant.

Methods

Retrospective cohort study. AKI was defined by the KDIGO classification using creatinine and urinary output criteria. We used survival analysis methods considering competing events for risk factors and disease-free survival, Cox proportional regression for overall survival and stepwise regression methods for multivariable models.

Results

We analyzed data regarding 143 patients. The cumulative incidence of AKI and moderate-to-severe AKI was 49.7% and 14.1%, respectively. Factors with independent impact on AKI were obesity (HR: 1.83, 95% CI 1.07–3.11; p = 0.026), Hematopoietic cell transplantation—specific comorbidity index (HCT-CI) ≥ 2 (HR: 1.85, 95% CI 1.08–3.17), chronic kidney disease (CKD) (HR: 2.06, 95% CI 1.05–4.04), amyloidosis (HR: 2.25, 95% CI 1.25–4.06), mucositis grade 3–4 (HR: 2.19, 95% CI 1.25–3.86) and exposure to nephrotoxic drugs (HR: 2.0856, 95% CI 1.04–4.19). Moderate-to-severe AKI had an impact (HR: 1.62, 95% CI 1.15–2.31) on 5-year overall survival.

Conclusion

Acute kidney injury affects almost half of MM patients undergoing autologous hematopoietic stem cell transplantation, and reduction in urinary output allows early diagnosis in almost a quarter of the patients. Obesity, HCT-CI ≥ 2, CKD, amyloidosis, mucositis grade 3–4 and exposure to nephrotoxic drugs are significant risk factors. Moderate-to-severe AKI is associated with lower 5-year overall survival.

Graphical abstract
Ready or Not
Authors: Morgan Rachel
Published: November 2023

Debates about the best means of preparing archaeologists continue. This article reviews data from 674 archaeological job postings to assess in-demand archaeological knowledge, skills, and abilities. The needs assessment reveals American archaeology's demand for dynamic, highly skilled professionals capable of identifying, preserving, and protecting the past. The skills demanded in archaeology job postings are the skills necessary to not only succeed as an archaeologist in any sector but also meet the challenges faced by the discipline more generally.
Thermal management system design for a series hybrid-electric propulsion architecture
Authors: Potamiti M. , Gkoutzamanis V.G. , Kalfas A.I.
Published: November 2023

The current paper is focused on the conceptual design of a thermal management system with a liquid working medium for a commuter hybrid-electric aircraft, featuring a series propulsion configuration. Regarding the system’s architecture, parametric analyses are conducted, by altering the number of heat exchangers. To clarify, a centralised and a decentralised thermal management system architecture are examined. Furthermore, a computational model calculates the temperatures during the system’s operation and the required coolant mass flows to sufficiently cool all the compartments. Subsequently, the required heat exchanger surface is determined and the weight of each compartment that comprises the thermal management system can be calculated. It is worth noting, that the compartments’ cold plate weight is integrated. The results indicate that the decentralised configuration results in lower temperature fields for all components compared to the centralised configuration. However, the latter weighs 32.2% lower at 158.22kg while the decentralised configuration weighs 233.48kg.
Transition From Primary to Secondary School From the Perspectives of Students With Autism Spectrum Disorder and Concomitant Intellectual Giftedness
Authors: Minnie Carolyn Anne
Published: November 2023

Transition from primary to secondary school is an often challenging milestone in the lives of all students. Although existing research provides insight into transition for students with autism spectrum disorder (ASD), research that considers transition from the perspective of students with ASD and concomitant intellectual giftedness (IG) appears scant. This paper contributes to narrowing this gap by providing insight into the experiences of 21 students with ASD and concomitant IG who had already transitioned to secondary school. Data gathered from focus group discussions revealed that this particular cohort of students experienced difficulties in gaining social acceptance by same-age peers and were unequipped to meet the expectations of secondary school teachers and an increased workload, which intensified their transition experience. These findings highlight that this cohort of students requires specific preparation and support to transition to secondary school, which was not occurring.
GENUS CURVES WITH BAD REDUCTION AT ONE ODD PRIME
Authors: DĄBROWSKI ANDRZEJ , SADEK MOHAMMAD
Published: November 2023

The problem of classifying elliptic curves over
$\mathbb Q$
with a given discriminant has received much attention. The analogous problem for genus
$2$
curves has only been tackled when the absolute discriminant is a power of
$2$
. In this article, we classify genus
$2$
curves C defined over
${\mathbb Q}$
with at least two rational Weierstrass points and whose absolute discriminant is an odd prime. In fact, we show that such a curve C must be isomorphic to a specialization of one of finitely many
$1$
-parameter families of genus
$2$
curves. In particular, we provide genus
$2$
analogues to Neumann–Setzer families of elliptic curves over the rationals.
Fallow weed application alters rice yield by changing nitrogen uptake
Authors: Chen Ge , Kang Yuling , Cao Fangbo , Chen Jiana , Huang Min
Published: November 2023

Fallow weeds can be abundant in rice paddies without any inputs and provide ecosystem services like those of cover crops, such as reducing nitrogen (N) leaching and capturing carbon. Therefore, allowing fallow weeds to grow is a potential alternative to cover crops in rice cropping systems. To evaluate the feasibility of this strategy, the effect of fallow weeds on grain yield in rice needs to be clarified. In this study, 2-year field experiments were conducted to compare N uptake, biomass production, yield components, and grain yield in rice with and without application of fallow weeds (500 g m−2, sun-dried). Results showed that the application of fallow weeds reduced aboveground N uptake and biomass production by 21–30% during the early growth period (from transplanting to mid-tillering) in rice. However, these reductions did not lead to reduced grain yield because they were compensated for or even exceeded by increased aboveground N uptake and biomass production during the middle and late growth periods (from panicle initiation to maturity). In addition, the application of fallow weeds increased spikelets per panicle in rice by 6–7%. These results provide preliminary evidence that fallow weeds may alter yield formation in rice and highlight the need for further investigations of the ecophysiological mechanism underlying the effect of fallow weeds on N uptake in rice.
How (not) to talk about plant-based foods: using language to support the transition to sustainable diets
Authors: Papies Esther K. , Davis Tess , Farrar Stephanie , Sinclair Maddie , Wehbe Lara H.
Published: November 2023

Reducing meat consumption is essential to curb further climate change and limit the catastrophic environmental degradation resulting from the current global food system. However, consumers in industrialised countries are hesitant to reduce their meat intake, often because they find plant-based foods less appealing. Despite the climate emergency, eating meat is still perceived as the norm, and recommended in most national dietary guidelines. To support the transition to more sustainable diets by providing insights for increasing the appeal of plant-based foods to mainstream consumers, this review presents recent research findings on how people think and communicate about meat-based and plant-based foods. The key findings we review include: (1) while vegans think about plant-based foods in terms of enjoyable eating experiences, omnivores think about plant-based foods in terms of health, vegan identity and other abstract information that does not motivate consumption in the moment. (2) Packages of ready-meals and social media posts on Instagram present plant-based foods with fewer references to enjoyable eating experiences than meat-based foods. (3) Presenting plant-based foods with language that references enjoyable eating experiences increases their appeal, especially for habitual meat eaters. This language includes words about sensory features of the food (e.g., crunchy, creamy), eating context (e.g. pub; with family) and immediate positive consequences of eating (e.g. comforting, delicious). In contrast, the term ‘vegan’ is strongly associated with negative stereotypes. Hence, rather than referring to being vegan, meat-free or healthy, the language used for plant-based foods should refer to sensory appeal, attractive eating situations and enjoyment.
High genetic diversity of Echinococcus canadensis G10 in northeastern Asia: is it the region of origin?
Authors: Wassermann Marion , Addy Francis , Kokolova Ludmila , Okhlopkov Innokentiy , Leibrock Sarah , Oberle Jenny , Oksanen Antti , Romig Thomas
Published: November 2023

Echinococcus canadensis consists of 4 genotypes: G6, G7, G8 and G10. While the first 2 predominantly infect domestic animals, the latter are sylvatic in nature involving mainly wolves and cervids as hosts and can be found in the northern temperate to Arctic latitudes. This circumstance makes the acquisition of sample material difficult, and little information is known about their genetic structure. The majority of specimens analysed to date have been from the European region, comparatively few from northeast Asia and Alaska. In the current study, Echinococcus spp. from wolves and intermediate hosts from the Republic of Sakha in eastern Russia were examined. Echinococcus canadensis G10 was identified in 15 wolves and 4 cervid intermediate hosts. Complete mitochondrial cytochrome c oxidase subunit 1 (cox1) sequences were obtained from 42 worm and cyst specimens from Sakha and, for comparison, from an additional 13 G10 cysts from Finland. For comparative analyses of the genetic diversity of G10 of European and Asian origin, all available cox1 sequences from GenBank were included, increasing the number of sequences to 99. The diversity found in northeast Asia was by far higher than in Europe, suggesting that the geographic origin of E. canadensis (at least of G10) might be northeast Asia.
Ethnic differences in intergenerational housing mobility in England and Wales
Authors: Buscha Franz , Gorman Emma , Sturgis Patrick , Zhang Min
Published: November 2023

Home ownership is the largest component of wealth for most households and its intergenerational transmission underpins the production and reproduction of economic inequalities across generations. Yet, little is currently known about ethnic differences in the intergenerational transmission of housing tenure. In this paper, we use linked Census data covering 1971–2011 to document rates of intergenerational housing tenure mobility across ethnic groups in England and Wales. We find that while home ownership declined across all ethnic groups during this period, there were substantial differences between them. Black, Pakistani, and Bangladeshi households experienced the strongest intergenerational link between parent and child housing tenure, and Black individuals had the highest rates of downward housing mobility. In contrast, those of Indian origin had homeownership rates similar to White British families, and a weaker link between parent and child housing tenure. These patterns are likely to exacerbate existing gradients in other dimensions of ethnicity-based inequality, now and in the future.
An extreme case of cor triatriatum mimicking hypoplastic left heart syndrome and combined pulmonary vein stenosis
Authors: Hong Hee Ju , Kwon Hye Won , Kwak Jae Gun , Lee Sang Yun , Lee Yoon Seong
Published: November 2023

A 65-day-old girl presented to the emergency room with lethargy, requiring emergency venoarterial extracorporeal membrane oxygenation for refractory cardiogenic shock. Initially, hypoplastic left heart syndrome was suspected. However, cor triatriatum with a pinpoint opening on the membrane was diagnosed based on a detailed echocardiographic examination. After membrane resection, the left heart size was restored. However, follow-up echocardiography performed 4 months later showed occlusion of both upper pulmonary veins and stenosis in both lower pulmonary veins. Hybrid balloon angioplasty was performed in all pulmonary veins, and stents were inserted into the right upper and lower pulmonary veins. Despite repeated balloon angioplasty, all pulmonary vein stenosis progressed over 6 months and the patient expired while waiting for a heart-lung transplant. Even after successful repair of cor triatriatum, short-term close follow-up is required for detecting the development of pulmonary vein stenosis.
Does information disclosure mitigate air pollution? Evidence from China
Authors: Yu Sitian , Liang Yinhe , Wang Hongyu
Published: November 2023

From 2013 to 2015, China gradually established nationwide air quality monitoring stations and began to release real-time air pollution information to the public. We exploit step-by-step environmental regulations across cities to identify the effects of information disclosure on air pollution. We find that information disclosure significantly decreases the concentrations of PM2.5 and PM10. Through mechanism analysis, we find that information disclosure raises the level of government awareness, increases the amount of investments in air pollution prevention and control, stimulates green innovation, and forces heavily polluting enterprises to shut down. Additionally, we find evidence that the effectiveness of information disclosure varies across cities.
The Present Participle with Wērden and Wēsen in Middle Low German: A Corpus-Based Analysis of Structure and Meaning
Authors: Ihden Sarah
Published: November 2023

A comprehensive description of the combination of the finite auxiliary verbs wērden ‘become’/wēsen ‘be’ and a present participle in Middle Low German is still a strong desideratum. This study presents a corpus-based analysis of the aforementioned phenomenon with a special focus on its grammatical structure and its different meanings. In particular, it focuses on a wide range of temporal and aspectual meanings, depending on the auxiliary verb, its tense and mood. Moreover, the relationship between the semantics of the main verb and the meaning of the whole construction is investigated. Finally, the competition with alternative verbal complex constructions expressing the same meaning is also explored. The analysis is carried out on the basis of Middle Low German texts from different times, language areas, and genres.
Weathering of Rocks Can Release Carbon Dioxide
Authors: Crowell Rachel
Published: November 2023

New research upends the notion that the weathering of rocks mainly removes CO2 from the atmosphere. Rocks can also be carbon sources, releasing as much CO2 as Earth’s volcanoes.
NO Radiative Cooling and Ionospheric Response to the HILDCAA Events Following Geomagnetic Storms
Authors: Ranjan Alok Kumar , Sunil Krishna M. V. , Kumar Akash , Sarkhel Sumanta , Chakrabarty D. , Reeves G. D.
Published: November 2023

Nitric oxide infrared (5.3 µm) radiative cooling plays an important role in Earth's upper atmospheric energy balance during space weather events. Its behavior during a HILDCAA event following a geomagnetic storm can be more complicated than what is observed in an isolated geomagnetic storm (without HILDCAA). In order to understand this contrast, two moderate (SYM‐Hmin −80 nT; April 2005 (event‐1) and −65 nT; December 2006 (event‐2)), and an intense (Dstmin −150 nT; May 2000 (event‐3)) geomagnetic storms followed by HILDCAA events are considered for this study. It is found that, despite the larger solar wind‐magnetospheric energy coupling during the main phases of event‐1 and event‐2, the NO radiative cooling (NORC) and energetic electron precipitation (EEP) rates are larger during the HILDCAA phase. TIE‐GCM simulations indicate that the NORC pattern can be mainly attributed to variation in temperature, [O], and [NO] during HILDCAA. A larger rates of EEP due to the continuous substorm activity contributed to an additional ionization in D‐region and E‐region of the northern polar ionosphere during HILDCAA period of event‐2. This work is the first attempt to understand the NORC and EEP fluctuations during HILDCAA events preceded by geomagnetic events like event‐1 and event‐2. This study presents a comprehensive investigation of NORC and energetic electron (>27.93 keV) precipitation rate during HILDCAA event preceded by a moderate geomagnetic storm. An atmospheric chemistry‐based NORC emission model is used to understand the variation of NORC during intense geomagnetic storm (event‐3).
Arabidopsis telomerase takes off by uncoupling enzyme activity from telomere length maintenance in space
Authors: Barcenilla Borja Barbero , Meyers Alexander D. , Castillo-González Claudia , Young Pierce , Min Ji-Hee , Song Jiarui , Phadke Chinmay , Land Eric , Canaday Emma , Perera Imara Y. , Bailey Susan M. , Aquilano Roberto , Wyatt Sarah E. , Shippen Dorothy E.
Published: November 2023

Spaceflight-induced changes in astronaut telomeres have garnered significant attention in recent years. While plants represent an essential component of future long-duration space travel, the impacts of spaceflight on plant telomeres and telomerase have not been examined. Here we report on the telomere dynamics of Arabidopsis thaliana grown aboard the International Space Station. We observe no changes in telomere length in space-flown Arabidopsis seedlings, despite a dramatic increase in telomerase activity (up to 150-fold in roots), as well as elevated genome oxidation. Ground-based follow up studies provide further evidence that telomerase is induced by different environmental stressors, but its activity is uncoupled from telomere length. Supporting this conclusion, genetically engineered super-telomerase lines with enhanced telomerase activity maintain wildtype telomere length. Finally, genome oxidation is inversely correlated with telomerase activity levels. We propose a redox protective capacity for Arabidopsis telomerase that may promote survivability in harsh environments.
Enhancement of short/medium-range order and thermal conductivity in ultrahard sp3 amorphous carbon by C70 precursor
Authors: Shang Yuchen , Yao Mingguang , Liu Zhaodong , Fu Rong , Yan Longbiao , Yang Long , Zhang Zhongyin , Dong Jiajun , Zhai Chunguang , Hou Xuyuan , Fei Liting , Zhang GuanJie , Ji Jianfeng , Zhu Jie , Lin He , Sundqvist Bertil , Liu Bingbing
Published: November 2023

As an advanced amorphous material, sp3 amorphous carbon exhibits exceptional mechanical, thermal and optical properties, but it cannot be synthesized by using traditional processes such as fast cooling liquid carbon and an efficient strategy to tune its structure and properties is thus lacking. Here we show that the structures and physical properties of sp3 amorphous carbon can be modified by changing the concentration of carbon pentagons and hexagons in the fullerene precursor from the topological transition point of view. A highly transparent, nearly pure sp3−hybridized bulk amorphous carbon, which inherits more hexagonal-diamond structural feature, was synthesized from C70 at high pressure and high temperature. This amorphous carbon shows more hexagonal-diamond-like clusters, stronger short/medium-range structural order, and significantly enhanced thermal conductivity (36.3 ± 2.2 W m−1 K−1) and higher hardness (109.8 ± 5.6 GPa) compared to that synthesized from C60. Our work thus provides a valid strategy to modify the microstructure of amorphous solids for desirable properties.
Introspective inference counteracts perceptual distortion
Authors: Mihali Andra , Broeker Marianne , Ragalmuto Florian D. M. , Horga Guillermo
Published: November 2023

Introspective agents can recognize the extent to which their internal perceptual experiences deviate from the actual states of the external world. This ability, also known as insight, is critically required for reality testing and is impaired in psychosis, yet little is known about its cognitive underpinnings. We develop a Bayesian modeling framework and a psychophysics paradigm to quantitatively characterize this type of insight while people experience a motion after-effect illusion. People can incorporate knowledge about the illusion into their decisions when judging the actual direction of a motion stimulus, compensating for the illusion (and often overcompensating). Furthermore, confidence, reaction-time, and pupil-dilation data all show signatures consistent with inferential adjustments in the Bayesian insight model. Our results suggest that people can question the veracity of what they see by making insightful inferences that incorporate introspective knowledge about internal distortions.
Discovery of ultrafast spontaneous spin switching in an antiferromagnet by femtosecond noise correlation spectroscopy
Authors: Weiss M. A. , Herbst A. , Schlegel J. , Dannegger T. , Evers M. , Donges A. , Nakajima M. , Leitenstorfer A. , Goennenwein S. T. B. , Nowak U. , Kurihara T.
Published: November 2023

Owing to their high magnon frequencies, antiferromagnets are key materials for future high-speed spintronics. Picosecond switching of antiferromagnetic spin systems has been viewed a milestone for decades and pursued only by using ultrafast external perturbations. Here, we show that picosecond spin switching occurs spontaneously due to thermal fluctuations in the antiferromagnetic orthoferrite Sm0.7Er0.3FeO3. By analysing the correlation between the pulse-to-pulse polarisation fluctuations of two femtosecond optical probes, we extract the autocorrelation of incoherent magnon fluctuations. We observe a strong enhancement of the magnon fluctuation amplitude and the coherence time around the critical temperature of the spin reorientation transition. The spectrum shows two distinct features, one corresponding to the quasi-ferromagnetic mode and another one which has not been previously reported in pump-probe experiments. Comparison to a stochastic spin dynamics simulation reveals this new mode as smoking gun of ultrafast spontaneous spin switching within the double-well anisotropy potential.
Resurrecting ancestral antibiotics: unveiling the origins of modern lipid II targeting glycopeptides
Authors: Hansen Mathias H. , Adamek Martina , Iftime Dumitrita , Petras Daniel , Schuseil Frauke , Grond Stephanie , Stegmann Evi , Cryle Max J. , Ziemert Nadine
Published: November 2023

Antibiotics are central to modern medicine, and yet they are mainly the products of intra and inter-kingdom evolutionary warfare. To understand how nature evolves antibiotics around a common mechanism of action, we investigated the origins of an extremely valuable class of compounds, lipid II targeting glycopeptide antibiotics (GPAs, exemplified by teicoplanin and vancomycin), which are used as last resort for the treatment of antibiotic resistant bacterial infections. Using a molecule-centred approach and computational techniques, we first predicted the nonribosomal peptide synthetase assembly line of paleomycin, the ancestral parent of lipid II targeting GPAs. Subsequently, we employed synthetic biology techniques to produce the predicted peptide and validated its antibiotic activity. We revealed the structure of paleomycin, which enabled us to address how nature morphs a peptide antibiotic scaffold through evolution. In doing so, we obtained temporal snapshots of key selection domains in nonribosomal peptide synthesis during the biosynthetic journey from ancestral, teicoplanin-like GPAs to modern GPAs such as vancomycin. Our study demonstrates the synergy of computational techniques and synthetic biology approaches enabling us to journey back in time, trace the temporal evolution of antibiotics, and revive these ancestral molecules. It also reveals the optimisation strategies nature has applied to evolve modern GPAs, laying the foundation for future efforts to engineer this important class of antimicrobial agents.
ZeroBind: a protein-specific zero-shot predictor with subgraph matching for drug-target interactions
Authors: Wang Yuxuan , Xia Ying , Yan Junchi , Yuan Ye , Shen Hong-Bin , Pan Xiaoyong
Published: November 2023

Existing drug-target interaction (DTI) prediction methods generally fail to generalize well to novel (unseen) proteins and drugs. In this study, we propose a protein-specific meta-learning framework ZeroBind with subgraph matching for predicting protein-drug interactions from their structures. During the meta-training process, ZeroBind formulates training a protein-specific model, which is also considered a learning task, and each task uses graph neural networks (GNNs) to learn the protein graph embedding and the molecular graph embedding. Inspired by the fact that molecules bind to a binding pocket in proteins instead of the whole protein, ZeroBind introduces a weakly supervised subgraph information bottleneck (SIB) module to recognize the maximally informative and compressive subgraphs in protein graphs as potential binding pockets. In addition, ZeroBind trains the models of individual proteins as multiple tasks, whose importance is automatically learned with a task adaptive self-attention module to make final predictions. The results show that ZeroBind achieves superior performance on DTI prediction over existing methods, especially for those unseen proteins and drugs, and performs well after fine-tuning for those proteins or drugs with a few known binding partners.
A polymer tethering strategy to achieve high metal loading on catalysts for Fenton reactions
Authors: Wang Lixin , Rao Longjun , Ran Maoxi , Shentu Qikai , Wu Zenglong , Song Wenkai , Zhang Ziwei , Li Hao , Yao Yuyuan , Lv Weiyang , Xing Mingyang
Published: November 2023

The development of heterogenous catalysts based on the synthesis of 2D carbon-supported metal nanocatalysts with high metal loading and dispersion is important. However, such practices remain challenging to develop. Here, we report a self-polymerization confinement strategy to fabricate a series of ultrafine metal embedded N-doped carbon nanosheets (M@N-C) with loadings of up to 30 wt%. Systematic investigation confirms that abundant catechol groups for anchoring metal ions and entangled polymer networks with the stable coordinate environment are essential for realizing high-loading M@N-C catalysts. As a demonstration, Fe@N-C exhibits the dual high-efficiency performance in Fenton reaction with both impressive catalytic activity (0.818 min−1) and H2O2 utilization efficiency (84.1%) using sulfamethoxazole as the probe, which has not yet been achieved simultaneously. Theoretical calculations reveal that the abundant Fe nanocrystals increase the electron density of the N-doped carbon frameworks, thereby facilitating the continuous generation of long-lasting surface-bound •OH through lowering the energy barrier for H2O2 activation. This facile and universal strategy paves the way for the fabrication of diverse high-loading heterogeneous catalysts for broad applications.
Atomic-level polarization in electric fields of defects for electrocatalysis
Authors: Xu Jie , Xue Xiong-Xiong , Shao Gonglei , Jing Changfei , Dai Sheng , He Kun , Jia Peipei , Wang Shun , Yuan Yifei , Luo Jun , Lu Jun
Published: November 2023

The thriving field of atomic defect engineering towards advanced electrocatalysis relies on the critical role of electric field polarization at the atomic scale. While this is proposed theoretically, the spatial configuration, orientation, and correlation with specific catalytic properties of materials are yet to be understood. Here, by targeting monolayer MoS2 rich in atomic defects, we pioneer the direct visualization of electric field polarization of such atomic defects by combining advanced electron microscopy with differential phase contrast technology. It is revealed that the asymmetric charge distribution caused by the polarization facilitates the adsorption of H*, which originally activates the atomic defect sites for catalytic hydrogen evolution reaction (HER). Then, it has been experimentally proven that atomic-level polarization in electric fields can enhance catalytic HER activity. This work bridges the long-existing gap between the atomic defects and advanced electrocatalysis by directly revealing the angstrom-scale electric field polarization and correlating it with the as-tuned catalytic properties of materials; the methodology proposed here could also inspire future studies focusing on catalytic mechanism understanding and structure-property-performance relationship.
Unraveling the synergistic effects of Cu-Ag tandem catalysts during electrochemical CO2 reduction using nanofocused X-ray probes
Authors: Frisch Marvin L. , Wu Longfei , Atlan Clément , Ren Zhe , Han Madeleine , Tucoulou Rémi , Liang Liang , Lu Jiasheng , Guo An , Nong Hong Nhan , Arinchtein Aleks , Sprung Michael , Villanova Julie , Richard Marie-Ingrid , Strasser Peter
Published: November 2023

Controlling the selectivity of the electrocatalytic reduction of carbon dioxide into value-added chemicals continues to be a major challenge. Bulk and surface lattice strain in nanostructured electrocatalysts affect catalytic activity and selectivity. Here, we unravel the complex dynamics of synergistic lattice strain and stability effects of Cu-Ag tandem catalysts through a previously unexplored combination of in situ nanofocused X-ray absorption spectroscopy and Bragg coherent diffraction imaging. Three-dimensional strain maps reveal the lattice dynamics inside individual nanoparticles as a function of applied potential and product yields. Dynamic relations between strain, redox state, catalytic activity and selectivity are derived. Moderate Ag contents effectively reduce the competing evolution of H2 and, concomitantly, lead to an enhanced corrosion stability. Findings from this study evidence the power of advanced nanofocused spectroscopy techniques to provide new insights into the chemistry and structure of nanostructured catalysts.
Ending extreme poverty has a negligible impact on global greenhouse gas emissions
Authors: Wollburg Philip , Hallegatte Stephane , Mahler Daniel Gerszon
Published: November 2023

Growing consumption is both necessary to end extreme poverty1and one of the main drivers of greenhouse gas emissions2, creating a potential tension between alleviating poverty and limiting global warming. Most poverty reduction has historically occurred because of economic growth3–6, which means that reducing poverty entails increasing not only the consumption of people living in poverty but also the consumption of people with a higher income. Here we estimate the emissions associated with the economic growth needed to alleviate extreme poverty using the international poverty line of US $2.15 per day (ref. 7). Even with historical energy- and carbon-intensity patterns, the global emissions increase associated with alleviating extreme poverty is modest, at 2.37 gigatonnes of carbon dioxide equivalent per year or 4.9% of 2019 global emissions. Lower inequality, higher energy efficiency and decarbonization of energy can ease this tension further: assuming the best historical performance, the emissions for poverty alleviation in 2050 will be reduced by 90%. More ambitious poverty lines require more economic growth in more countries, which leads to notably higher emissions. The challenge to align the development and climate objectives of the world is not in reconciling extreme poverty alleviation with climate objectives but in providing sustainable middle-income standards of living.
Evaluation of the safety and feasibility of electrochemotherapy with intravenous bleomycin as local treatment of bladder cancer in dogs
Authors: Rangel Marcelo Monte Mor , Linhares Laís Calazans Menescal , de Oliveira Krishna Duro , Suzuki Daniela Ota Hisayasu , Maglietti Felipe Horacio , de Nardi Andrigo Barboza
Published: November 2023

Local treatment of canine urothelial carcinoma (UC) of the bladder is a challenge. More than 90% of the cases invade the muscular layer, more than 50% develop on bladder sites with a difficult surgical approach and often requiring radical surgical procedures. This study aims to evaluate the safety and feasibility of electrochemotherapy (ECT) with intravenous bleomycin (BLM) as a local therapy for bladder UC. This prospective study included 21 dogs with spontaneous bladder UC. Regional/distant metastases and neoplastic infiltration of the serosa was considered the main exclusion criteria. We had no deaths during ECT or in the immediate postoperative period, and no suture dehiscence. Most dogs (19/21) developed mild adverse effects, whereas two dogs developed ureteral stenosis. Complete response (CR) was achieved in 62% of the cases (13/21), while partial response (PR) was achieved in 24% (5/21). The median survival and disease-free survival times were 284 and 270 days, respectively. Overall survival was significantly better in the dogs who achieved a CR. In conclusion, ECT was well-tolerated in dogs with UC, demonstrating its safety and feasibility. These data pave the way for new studies aimed at evaluating the effectiveness of ECT in canine bladder UC as a translational model for human disease.
Using network analysis to identify leverage points based on causal loop diagrams leads to false inference
Authors: Crielaard Loes , Quax Rick , Sawyer Alexia D. M. , Vasconcelos Vítor V. , Nicolaou Mary , Stronks Karien , Sloot Peter M. A.
Published: November 2023

Network analysis is gaining momentum as an accepted practice to identify which factors in causal loop diagrams (CLDs)—mental models that graphically represent causal relationships between a system’s factors—are most likely to shift system-level behaviour, known as leverage points. This application of network analysis, employed to quantitatively identify leverage points without having to use computational modelling approaches that translate CLDs into sets of mathematical equations, has however not been duly reflected upon. We evaluate whether using commonly applied network analysis metrics to identify leverage points is justified, focusing on betweenness- and closeness centrality. First, we assess whether the metrics identify the same leverage points based on CLDs that represent the same system but differ in inferred causal structure—finding that they provide unreliable results. Second, we consider conflicts between assumptions underlying the metrics and CLDs. We recognise six conflicts suggesting that the metrics are not equipped to take key information captured in CLDs into account. In conclusion, using betweenness- and closeness centrality to identify leverage points based on CLDs is at best premature and at worst incorrect—possibly causing erroneous identification of leverage points. This is problematic as, in current practice, the results can inform policy recommendations. Other quantitative or qualitative approaches that better correspond with the system dynamics perspective must be explored.
Integration of fluorescence in situ hybridization and chromosome-length genome assemblies revealed synteny map for guinea pig, naked mole-rat, and human
Authors: Romanenko Svetlana A. , Kliver Sergei F. , Serdyukova Natalia A. , Perelman Polina L. , Trifonov Vladimir A. , Seluanov Andrei , Gorbunova Vera , Azpurua Jorge , Pereira Jorge C. , Ferguson-Smith Malcolm A. , Graphodatsky Alexander S.
Published: November 2023

Descriptions of karyotypes of many animal species are currently available. In addition, there has been a significant increase in the number of sequenced genomes and an ever-improving quality of genome assembly. To close the gap between genomic and cytogenetic data we applied fluorescent in situ hybridization (FISH) and Hi-C technology to make the first full chromosome-level genome comparison of the guinea pig (Cavia porcellus), naked mole-rat (Heterocephalus glaber), and human. Comparative chromosome maps obtained by FISH with chromosome-specific probes link genomic scaffolds to individual chromosomes and orient them relative to centromeres and heterochromatic blocks. Hi-C assembly made it possible to close all gaps on the comparative maps and to reveal additional rearrangements that distinguish the karyotypes of the three species. As a result, we integrated the bioinformatic and cytogenetic data and adjusted the previous comparative maps and genome assemblies of the guinea pig, naked mole-rat, and human. Syntenic associations in the two hystricomorphs indicate features of their putative ancestral karyotype. We postulate that the two approaches applied in this study complement one another and provide complete information about the organization of these genomes at the chromosome level.
Using trials of caloric restriction and bariatric surgery to explore the effects of body mass index on the circulating proteome
Authors: Goudswaard Lucy J. , Smith Madeleine L. , Hughes David A. , Taylor Roy , Lean Michael , Sattar Naveed , Welsh Paul , McConnachie Alex , Blazeby Jane M. , Rogers Chris A. , Suhre Karsten , Zaghlool Shaza B. , Hers Ingeborg , Timpson Nicholas J. , Corbin Laura J.
Published: November 2023

Thousands of proteins circulate in the bloodstream; identifying those which associate with weight and intervention-induced weight loss may help explain mechanisms of diseases associated with adiposity. We aimed to identify consistent protein signatures of weight loss across independent studies capturing changes in body mass index (BMI). We analysed proteomic data from studies implementing caloric restriction (Diabetes Remission Clinical trial) and bariatric surgery (By-Band-Sleeve), using SomaLogic and Olink Explore1536 technologies, respectively. Linear mixed models were used to estimate the effect of the interventions on circulating proteins. Twenty-three proteins were altered in a consistent direction after both bariatric surgery and caloric restriction, suggesting that these proteins are modulated by weight change, independent of intervention type. We also integrated Mendelian randomisation (MR) estimates of the effect of BMI on proteins measured by SomaLogic from a UK blood donor cohort as a third line of causal evidence. These MR estimates provided further corroborative evidence for a role of BMI in regulating the levels of six proteins including alcohol dehydrogenase-4, nogo receptor and interleukin-1 receptor antagonist protein. These results indicate the importance of triangulation in interrogating causal relationships; further study into the role of proteins modulated by weight in disease is now warranted.