bluuebunny/crossref_metadata_2025 huggingface dataset:
Associations of health literacy with self-management behaviours and health outcomes in chronic kidney disease: a systematic review
Authors: Billany Roseanne E. , Thopte Ashnee , Adenwalla Sherna F. , March Daniel S. , Burton James O. , Graham-Brown Matthew P. M.
Published: January 2023

Introduction

Low health literacy is widely reported in people with chronic kidney disease (CKD) and has been associated with reduced disease self-management, poor health outcomes, increased mortality and poorer quality of life. However, these associations are still not well understood.

Methods

Electronic-based systematic searches were performed to identify studies examining associations between health literacy and self-management behaviours and/or health outcomes in patients with CKD. A tabular and narrative synthesis of the data was performed. Meta-analysis was not appropriate due to the heterogeneity of study designs and methods.

Results

Searches identified 48 studies that met the inclusion criteria. A total of 41 published articles, six conference abstracts, and one thesis were included. Of the 48 studies, 11 were cohort and 37 were cross-sectional. In total there were 25,671 patients; 16,952 from cohort studies. Median study sample size was 159 (IQR 92–275). Study quality was high (5), moderate (24) and poor (19). Thirteen measures of health literacy were used. Despite the limitations of the available evidence, there appear to be consistent relationships between higher health literacy and favourable self-management behaviours for patients with CKD. Definitive relationships between health literacy and patient outcomes are far less clear and remain incompletely understood.

Discussion

Conclusive evidence describing a causal link between health literacy and patient outcomes remains limited, but for many outcomes, a consistent association is described. In addition to associations with mortality, hospitalisation and clinical events, there were consistent associations between health literacy and favourable self-management behaviours which could support the development of patient education aimed at improving health literacy.

Graphical abstract
Development of statistical downscaling model based on Volterra series realization, principal components and ridge regression
Authors: Singh Pooja , Shamseldin Asaad Y. , Melville Bruce W. , Wotherspoon Liam
Published: January 2023

Impacts of the global climate change in hydrology and water resources are accessed by downscaling of local daily rainfall from large-scale climate variables. This study developed a statistical downscaling model based on the Volterra series, principal components and ridge regression. This model is known, hereafter as SDCRR. The proposed model is applied at four different stations of the Manawatu River basin, in the North Island of New Zealand to downscale daily rainfall. The large-scale climate variables from the National Centers for Environmental Predictions (NCEP) reanalysis data are used in the present study to obtain with the wide range (WR) and the restricted range (RR) of predictors. The developed SDCRR model incorporated the climate change signals sufficiently by working with WR predictors. Further, principal component analysis (PC) was applied to the set of WR predictors, which were also used as the orthogonal filter in the ridge regression model to deal with the multi-collinearity. The ridge regression coefficients determined were less sensitive to random errors, and were capable of reducing the mean square error between the observed and the simulated daily precipitation data. Thus, the combined application of principal component analysis (PCA) and ridge regression improved the performance of the model. This combination is steady enough to capture appropriate information from predictors of the region. The performance of the SDCRR model is compared with that of the widely used statistical downscaling model (SDSM). The results of the study show the SDCRR model has better performance than the SDSM.
O-minimal de Rham Cohomology
Authors: Figueiredo Rodrigo
Published: January 2023

O-minimal geometry generalizes both semialgebraic and subanalytic geometries, and has been very successful in solving special cases of some problems in arithmetic geometry, such as André–Oort conjecture. Among the many tools developed in an o-minimal setting are cohomology theories for abstract-definable continuous manifolds such as singular cohomology, sheaf cohomology and Čech cohomology, which have been used for instance to prove Pillay’s conjecture concerning definably compact groups. In the present thesis we elaborate an o-minimal de Rham cohomology theory for abstract-definable
$C^{\infty }$
manifolds in an o-minimal expansion of the real field which admits smooth cell decomposition and defines the exponential function. We can specify the o-minimal cohomology groups and attain some properties such as the existence of Mayer–Vietoris sequence and the invariance under abstract-definable
$C^{\infty }$
diffeomorphisms. However, in order to obtain the invariance of our o-minimal cohomology under abstract-definable homotopy we must work in a tame context that defines sufficiently many primitives and assume the validity of a statement related to Bröcker’s question.

Abstract prepared by Rodrigo Figueiredo.

E-mail: rodrigo@ime.usp.br

URL: https://doi.org/10.11606/T.45.2019.tde-28042019-181150
Independence Relations in Abstract Elementary Categories
Authors: Kamsma Mark
Published: January 2023

In model theory, a branch of mathematical logic, we can classify mathematical structures based on their logical complexity. This yields the so-called stability hierarchy. Independence relations play an important role in this stability hierarchy. An independence relation tells us which subsets of a structure contain information about each other, for example, linear independence in vector spaces yields such a relation.

Some important classes in the stability hierarchy are stable, simple, and NSOP
$_1$
, each being contained in the next. For each of these classes there exists a so-called Kim-Pillay style theorem. Such a theorem describes the interaction between independence relations and the stability hierarchy. For example, simplicity is equivalent to admitting a certain independence relation, which must then be unique.

All of the above classically takes place in full first-order logic. Parts of it have already been generalised to other frameworks, such as continuous logic, positive logic, and even a very general category-theoretic framework. In this thesis we continue this work.

We introduce the framework of AECats, which are a specific kind of accessible category. We prove that there can be at most one stable, simple, or NSOP
$_1$
-like independence relation in an AECat. We thus recover (part of) the original stability hierarchy. For this we introduce the notions of long dividing, isi-dividing, and long Kim-dividing, which are based on the classical notions of dividing and Kim-dividing but are such that they work well without compactness.

Switching frameworks, we generalise Kim-dividing in NSOP
$_1$
theories to positive logic. We prove that Kim-dividing over existentially closed models has all the nice properties that it is known to have in full first-order logic. We also provide a full Kim-Pillay style theorem: a positive theory is NSOP
$_1$
if and only if there is a nice enough independence relation, which then must be given by Kim-dividing.

Abstract prepared by Mark Kamsma.

E-mail:mark@markkamsma.nl.

URL:https://markkamsma.nl/phd-thesis.
Boolean-Valued Models and Their Applications
Authors: Wu Xinhe
Published: January 2023

Boolean-valued models generalize classical two-valued models by allowing arbitrary complete Boolean algebras as value ranges. The goal of my dissertation is to study Boolean-valued models and explore their philosophical and mathematical applications.

In Chapter 1, I build a robust theory of first-order Boolean-valued models that parallels the existing theory of two-valued models. I develop essential model-theoretic notions like “Boolean-valuation,” “diagram,” and “elementary diagram,” and prove a series of theorems on Boolean-valued models, including the (strengthened) Soundness and Completeness Theorem, the Löwenheim–Skolem Theorems, the Elementary Chain Theorem, and many more.

Chapter 2 gives an example of a philosophical application of Boolean-valued models. I apply Boolean-valued models to the language of mereology to model indeterminacy in the parthood relation. I argue that Boolean-valued semantics is the best degree-theoretic semantics for the language of mereology. In particular, it trumps the well-known alternative—fuzzy-valued semantics. I also show that, contrary to what many have argued, indeterminacy in parthood entails neither indeterminacy in existence nor indeterminacy in identity, though being compatible with both.

Chapter 3 (joint work with Bokai Yao) gives an example of a mathematical application of Boolean-valued models. Scott and Solovay famously used Boolean-valued models on set theory to obtain relative consistency results. In Chapter 3, I investigate two ways of extending the Scott–Solovay construction to set theory with urelements. I argue that the standard way of extending the construction faces a serious problem, and offer a new way that is free from the problem.

Abstract prepared by Xinhe Wu.

E-mail: xinhewu@mit.edu
DL4DS—Deep learning for empirical downscaling
Authors: Gomez Gonzalez Carlos Alberto
Published: January 2023

A common task in Earth Sciences is to infer climate information at local and regional scales from global climate models. Dynamical downscaling requires running expensive numerical models at high resolution, which can be prohibitive due to long model runtimes. On the other hand, statistical downscaling techniques present an alternative approach for learning links between the large- and local-scale climate in a more efficient way. A large number of deep neural network-based approaches for statistical downscaling have been proposed in recent years, mostly based on convolutional architectures developed for computer vision and super-resolution tasks. This paper presents deep learning for empirical downscaling (DL4DS), a python library that implements a wide variety of state-of-the-art and novel algorithms for downscaling gridded Earth Science data with deep neural networks. DL4DS has been designed with the goal of providing a general framework for training convolutional neural networks with configurable architectures and learning strategies to facilitate the conduction of comparative and ablation studies in a robust way. We showcase the capabilities of DL4DS on air quality Copernicus Atmosphere Monitoring Service (CAMS) data over the western Mediterranean area. The DL4DS library can be found in this repository: https://github.com/carlos-gg/dl4ds
Connected sums of codimension two locally flat submanifolds
Authors: Livingston Charles
Published: January 2023

Let$X$and$Y$be oriented topological manifolds of dimension$n\!+\!2$, and let$K\! \subset \! X$and$J \! \subset \! Y$be connected, locally-flat, oriented,$n$–dimensional submanifolds. We show that up to orientation preserving homeomorphism there is a well-defined connected sum$(X,K)\! \mathbin {\#}\! (Y,J)$. For$n = 1$, the proof is classical, relying on results of Rado and Moise. For dimensions$n=3$and$n \ge 6$, results of Edwards-Kirby, Kirby, and Kirby-Siebenmann concerning higher dimensional topological manifolds are required. For$n = 2, 4,$and$5$, Freedman and Quinn's work on topological four-manifolds is required along with the higher dimensional theory.
NEW HUMAN BONE RADIOCARBON DATES FROM THE ROMAN PERIOD–MIGRATION PERIOD LITHUANIAN CEMETERIES
Authors: Kurila Laurynas , Piličiauskienė Giedrė , Simčenka Edvardas , Miliauskienė Žydrūnė , Ežerinskis Žilvinas , Šapolaitė Justina , Garbaras Andrius
Published: January 2023

A set (n = 37) of new human bone radiocarbon accelerator mass spectrometry (14C AMS) dates from 11 Lithuanian Late Roman Period–Migration Period cemeteries is presented and discussed in the light of the established schemes of archaeological chronology. The focus of the paper is on the burials of the military and social elite, which indicate the emergence of new cultural traditions in E–S and W–Central Lithuania or the immigration that took place during this time. The 14C dates allow us to suggest corrections to the dominant chronological pattern of cultural development in the region.
Associations between dietary variety, portion size and body weight: prospective evidence from UK Biobank participants
Authors: Embling Rochelle , Price Menna J. , Lee Michelle D. , Jones Alex , Wilkinson Laura L.
Published: January 2023

‘Dietary variety’ has been identified as a factor associated with food intake. Whilst this relationship may have longer-term benefits for body weight management when eating low-energy, nutrient-dense foods, it may increase the risk of overconsumption (and body adiposity) when foods are high energy density. This study sought to further explore pathways underpinning the relationship between dietary variety and body weight, by considering energy density as a moderating factor and portion size as a mediating factor in this relationship. Using prospective data from the UK Biobank, dietary variety scores (DVS), cumulative portion size and energy density were derived from 24-h dietary recall questionnaires at baseline and follow-up. BMI, whole-body fat percentage and fat-free mass were included as outcomes. Contrary to predictions, linear multiple regression models found some evidence of a negative, direct association between DVS and body weight outcomes at baseline (b= –0·13). Though dietary variety was significantly associated with larger portions across time points (b= 41·86–82·64), a moderated mediation effect was not supported at baseline or follow-up (Index ≤ 0·035). Taken together, these findings provide population-level evidence to support a positive association between variety and food intake, which in turn has potential implications for body weight management, both in terms of moderating food intake and benefitting diet quality.
Sb–Au-bearing chalcedonies in hot geothermal systems: insights from the jasperoids of Poggio Peloso (southern Tuscany, Italy)
Authors: Gliozzo Elisabetta , Brogi Andrea , Ruggieri Giovanni , Langone Antonio
Published: January 2023

Detailed characterization was performed on the chalcedonies from the jasperoids of the Pietratonda–Poggio Peloso Sb–Au deposit (southern Tuscany, Italy). The main purpose was to retrieve information on the geothermal fluids that formed the chalcedonies and the source of antimony concentrations. Investigations were performed using optical microscopy, laser ablation inductively coupled plasma mass spectroscopy and X-ray diffraction on both the chalcedonies and the lithotypes cropping out in the area. The results obtained allow the chalcedonies of Pietratonda–Poggio Peloso to be described as aunicum, based on the very high contents of Sb that do not find a comparison in the literature. The textures showed multiple generations of silica that agree well with an environment characterized by multiple injections of mineralizing solutions, bearing variable physicochemical characteristics. The transport likely took place in an alkaline environment, while the acidification of the water may have favoured the precipitation at varying temperatures but not higher than 225 °C. The rocks from which the constituents may have been leached are the hosting carbonates and the surrounding metamorphic rocks. Among the examined rocks, the metamorphic rocks showed the most numerous and significant correspondences with the chalcedonies and were the only ones in which discrete amounts of gold contents were found.
RELEVANT MOMENT SELECTION UNDER MIXED IDENTIFICATION STRENGTH
Authors: Dovonon Prosper , Doko Tchatoka Firmin , Aguessy Michael
Published: January 2023

This paper proposes a robust moment selection method aiming to pick the best model even if this is a moment condition model with mixed identification strength, that is, moment conditions including moment functions that are local to zero uniformly over the parameter set. We show that the relevant moment selection procedure of Hall et al. (2007, Journal of Econometrics 138, 488–512) is inconsistent in this setting as it does not explicitly account for the rate of convergence of parameter estimation of the candidate models which may vary. We introduce a new moment selection procedure based on a criterion that automatically accounts for both the convergence rate of the candidate model’s parameter estimate and the entropy of the estimator’s asymptotic distribution. The benchmark estimator that we consider is the two-step efficient generalized method of moments estimator, which is known to be efficient in this framework as well. A family of penalization functions is introduced that guarantees the consistency of the selection procedure. The finite-sample performance of the proposed method is assessed through Monte Carlo simulations.
The Bryson synthesis: The forging of climate change narratives during the World Food Crisis
Authors: Naylor Robert L.
Published: January 2023

Argument

During the first half of the 1970s, climate research gained a new significance and began to be perceived within political and academic circles as being worthy of public support. Conventional explanations for this increased status include a series of climate anomalies that generated awareness and heightened concern over the potentially devastating effects of climate change. Controversial climatologist Reid Bryson was one of the first to publicly promote what he saw as a definitive link between these climate anomalies and unidirectional climate change in the fall of 1973, and rising food prices in the same year gave him a platform on which to air his views to receptive senior members of the US Congress. Bryson’s testimony before a US Senate subcommittee offers a unique glimpse into how he was able to successfully resonate his agenda with that of senior politicians in a time of crisis, as well as the immediate responses of those senior US politicians upon first hearing climate change arguments. Bryson was one of the most prominent US climatologists to break a taboo against making bold climatological predictions and de-facto policy recommendations in public. As a result, although Bryson was criticized by many in the climatological community, his actions instigated the involvement of other scientists in the public arena, leading to an important elevation in US public climate discourse.
National trends and disparities in retail food environments in the USA between 1990 and 2014
Authors: Hirsch Jana A , Zhao Yuzhe , Melly Steven , Moore Kari A , Berger Nicolas , Quinn James , Rundle Andrew , Lovasi Gina S
Published: January 2023

Objective:

To describe national disparities in retail food environments by neighbourhood composition (race/ethnicity and socio-economic status) across time and space.

Design:

We examined built food environments (retail outlets) between 1990 and 2014 for census tracts in the contiguous USA (n71 547). We measured retail food environment as counts of all food stores, all unhealthy food sources (including fast food, convenience stores, bakeries and ice cream) and healthy food stores (including supermarkets, fruit and vegetable markets) from National Establishment Time Series business data. Changes in food environment were mapped to display spatial patterns. Multi-level Poisson models, clustered by tract, estimated time trends in counts of food stores with a land area offset and independent variables population density, racial composition (categorised as predominantly one race/ethnicity (>60 %) or mixed), and inflation-adjusted income tertile.

Setting:

The contiguous USA between 1990 and 2014.

Participants:

All census tracts (n71 547).

Results:

All food stores and unhealthy food sources increased, while the subcategory healthy food remained relatively stable. In models adjusting for population density, predominantly non-Hispanic Black, Hispanic, Asian and mixed tracts had significantly more destinations of all food categories than predominantly non-Hispanic White tracts. This disparity increased over time, predominantly driven by larger increases in unhealthy food sources for tracts which were not predominantly non-Hispanic White. Income and food store access were inversely related, although disparities narrowed over time.

Conclusions:

Our findings illustrate a national food landscape with both persistent and shifting spatial patterns in the availability of establishments across neighbourhoods with different racial/ethnic and socio-economic compositions.
Where lies the bundle of sticks? A comment on Bart Wilson's ‘The Primacy of Property’
Authors: Thurman Walter
Published: January 2023

‘The Primacy of Property’ is a deep discussion of property as an evolved institution and should stimulate useful discussion of how property rights and transaction costs economists should ply their trade.
Political and Social Discussion Network Survey Items Are Not Interchangeable
Authors: Reilly Jack Lyons , Belk Jack K.
Published: January 2023

Experimentalists and survey researchers regularly measure the makeup and size of respondent personal discussion networks to learn about the social context in which citizens make political choices. When measuring these personal networks, some scholars use question prompts that specifically ask respondents about whom they discuss “politics” with, while others use more general prompts that ask respondents about whom they discuss “important matters” with. Prior research suggests that “political” discussion network prompts create self-reported networks that are substantively similar to “important matters” prompts. We conduct a nationally representative survey experiment to re-evaluate this question. Our results suggest that, although the size of networks generated by the two questions may be similar on average, the two questions generate different response distributions overall. In particular, respondents interested in politics report larger political discussion networks than general discussion networks, and respondents uninterested in politics report smaller political discussion networks than general discussion networks.
Früherkennung seelischer Belastung in der onkologischen Versorgungspraxis
Authors: Labouvie Hildegard , Dietz Thilo , Schiewer Vera , Kusch Michael
Published: January 2023

Zusammenfassung: Die Distress-Skala (DS) bildet ein Single-Item-Instrument in Form einer zehnstufigen Likertskala in 2 Varianten zur Identifikation psychosozialer Belastungen zum Krankheitsbeginn (Screening-Variante) sowie im Krankheitsverlauf (Verlaufsvariante). Die DS wurde an einer Stichprobe onkologisch erkrankter Patientinnen und Patienten mit einer Größe von N = 661 nahe am Diagnosezeitpunkt validiert. Bei N = 92 der Stichprobe lagen insgesamt 3 Erhebungszeitpunkte vor, anhand dessen die Validierung der Verlaufsvariante erfolgte. Unter Verwendung des HADS-Gesamtsummenscore-Schwellenwerts > 14 als externes Kriterium wurde für die Screening-Variante der DS ein Schwellenwert > 7 mit einer Sensitivität von 81 % bzw. 78 % und einer Spezifität von 71 % bzw. 75 % ermittelt. Die Verlaufsvariante der DS erzielte bei einem Schwellenwert von > 5 eine Sensitivität zu T2 von 77 % und zu T3 von 70 % und eine Spezifität zu T2 von 67 % und zu T3 von 78 %. Die Ergebnisse weisen eine gute Diskriminierungsfähigkeit auf und empfehlen den Einsatz der DS zu Beginn der Krebserkrankung bzw. im Krankheitsverlauf.
Intratumoral microbiota: roles in cancer initiation, development and therapeutic efficacy
Authors: Yang Li , Li Aitian , Wang Ying , Zhang Yi
Published: January 2023

Microorganisms, including bacteria, viruses, fungi, and other eukaryotes, play critical roles in human health. An altered microbiome can be associated with complex diseases. Intratumoral microbial components are found in multiple tumor tissues and are closely correlated with cancer initiation and development and therapy efficacy. The intratumoral microbiota may contribute to promotion of the initiation and progression of cancers by DNA mutations, activating carcinogenic pathways, promoting chronic inflammation, complement system, and initiating metastasis. Moreover, the intratumoral microbiota may not only enhance antitumor immunity via mechanisms including STING signaling activation, T and NK cell activation, TLS production, and intratumoral microbiota-derived antigen presenting, but also decrease antitumor immune responses and promote cancer progression through pathways including upregulation of ROS, promoting an anti-inflammatory environment, T cell inactivation, and immunosuppression. The effect of intratumoral microbiota on antitumor immunity is dependent on microbiota composition, crosstalk between microbiota and the cancer, and status of cancers. The intratumoral microbiota may regulate cancer cell physiology and the immune response by different signaling pathways, including ROS, β-catenin, TLR, ERK, NF-κB, and STING, among others. These viewpoints may help identify the microbiota as diagnosis or prognosis evaluation of cancers, and as new therapeutic strategy and potential therapeutic targets for cancer therapy.
Technology used in activity based therapy for individuals living with spinal cord injury across Canada
Authors: Gauthier Cindy , Walden Kristen , Jervis-Rademeyer Hope , Musselman Kristin E. , Kaiser Anita , Wolfe Dalton L. , Noonan Vanessa K. , Donkers Sarah J.
Published: January 2023

Study design

Cross-sectional equipment inventory.

Objectives

The objective of this study was to describe the equipment used in activity-based therapy (ABT) programs for individuals with spinal cord injury or disorder (SCI/D) across Canada.

Settings

Publicly funded and private SCI/D care settings.

Methods

A survey on equipment available for ABT for different therapeutic goals was answered by Canadian sites providing SCI/D rehabilitation. Information about the setting and type of client were also collected. The survey results were compiled into an inventory of the reported types and use of ABT related equipment, with equipment grouped into varying levels of technology. Descriptive statistics and qualitative descriptive analysis were used to answer the questions: (1) ‘who’ used the equipment, (2) ‘what’ types of equipment are used, (3) ‘why’ (i.e., for which therapeutic goals), and (4) ‘how’ it is used.

Results

Twenty-two sites from eight Canadian provinces completed the survey. Reported equipment was classified into 5 categories (from low to high-tech). Most equipment reported was used to train balance. The high-tech equipment reported as available, was mostly used for walking training and strengthening of the lower limbs. Low-tech equipment was reported as being used most frequently, while high-tech devices, although available, were reported as infrequently or rarely used.

Conclusions

A large spectrum of equipment with varying levels of technology were reported as available, but were inconsistently used to provide ABT interventions across sites. In order to increase the clinical use of available equipment for ABT, education tools such as protocols regarding ABT principles and implementation are needed.
Simultaneous blockade of VEGF-B and IL-17A ameliorated diabetic kidney disease by reducing ectopic lipid deposition and alleviating inflammation response
Authors: Cao Zhonglian , Zhao Hui , Fan Jiajun , Shen Yilan , Han Lei , Jing Guangjun , Zeng Xian , Jin Xin , Zhu Zeguo , Bian Qi , Nan Yanyang , Hu Xiaozhi , Mei Xiaobin , Ju Dianwen , Yang Ping
Published: January 2023

The pathogenesis of diabetic kidney disease (DKD) is complicated. Current clinical treatments fail to achieve satisfactory efficacy in the prevention of DKD progression, it urgently needs novel and effective treatment for DKD. In this study, we firstly demonstrated that renal lipid metabolism abnormality and inflammation significantly changed in DKD conditions by mining public transcriptomic data of DKD patient samples. KEGG analysis further exhibited the critical role of vascular endothelial growth factor B (VEGF-B) and interleukin 17A (IL-17A) signal pathways in DKD progression, indicating that VEGF-B and IL-17A might be the promising targets for DKD treatment. Then the potential of a novel combination therapy, anti-VEGF-B plus anti-IL-17A antibody, was evaluated for DKD treatment. Our results demonstrated that simultaneous blockade of VEGF-B and IL-17A signaling with their neutralizing antibodies alleviated renal damage and ameliorated renal function. The therapeutic effectiveness was not only related to the reduced lipid deposition especially the neutral lipids in kidney but also associated with the decreased inflammation response. Moreover, the therapy alleviated renal fibrosis by reducing collagen deposition and the expression of fibronectin and α-SMA in kidney tissues. RNA-seq analysis indicated that differential expression genes (DEGs) in db/db mice were significantly clustered into lipid metabolism, inflammation, fibrosis and DKD pathology-related pathways, and 181 of those DEGs were significantly reversed by the combinatory treatment, suggesting the underlying mechanism of administration of anti-VEGF-B and anti-IL-17A antibodies in DKD treatment. Taken together, this study identified that renal lipid metabolism abnormality and inflammation were critically involved in the progression of DKD, and simultaneous blockade of VEGF-B and IL-17A signaling represents a potential DKD therapeutic strategy.
Comparative analysis of genome-scale, base-resolution DNA methylation profiles across 580 animal species
Authors: Klughammer Johanna , Romanovskaia Daria , Nemc Amelie , Posautz Annika , Seid Charlotte A. , Schuster Linda C. , Keinath Melissa C. , Lugo Ramos Juan Sebastian , Kosack Lindsay , Evankow Ann , Printz Dieter , Kirchberger Stefanie , Ergüner Bekir , Datlinger Paul , Fortelny Nikolaus , Schmidl Christian , Farlik Matthias , Skjærven Kaja , Bergthaler Andreas , Liedvogel Miriam , Thaller Denise , Burger Pamela A. , Hermann Marcela , Distel Martin , Distel Daniel L. , Kübber-Heiss Anna , Bock Christoph
Published: January 2023

Methylation of cytosines is a prototypic epigenetic modification of the DNA. It has been implicated in various regulatory mechanisms across the animal kingdom and particularly in vertebrates. We mapped DNA methylation in 580 animal species (535 vertebrates, 45 invertebrates), resulting in 2443 genome-scale DNA methylation profiles of multiple organs. Bioinformatic analysis of this large dataset quantified the association of DNA methylation with the underlying genomic DNA sequence throughout vertebrate evolution. We observed a broadly conserved link with two major transitions—once in the first vertebrates and again with the emergence of reptiles. Cross-species comparisons focusing on individual organs supported a deeply conserved association of DNA methylation with tissue type, and cross-mapping analysis of DNA methylation at gene promoters revealed evolutionary changes for orthologous genes. In summary, this study establishes a large resource of vertebrate and invertebrate DNA methylomes, it showcases the power of reference-free epigenome analysis in species for which no reference genomes are available, and it contributes an epigenetic perspective to the study of vertebrate evolution.
Scalable high yield exfoliation for monolayer nanosheets
Authors: Wang Zhuyuan , Yan Xue , Hou Qinfu , Liu Yue , Zeng Xiangkang , Kang Yuan , Zhao Wang , Li Xuefeng , Yuan Shi , Qiu Ruosang , Uddin Md Hemayet , Wang Ruoxin , Xia Yun , Jian Meipeng , Kang Yan , Gao Li , Liang Songmiao , Liu Jefferson Zhe , Wang Huanting , Zhang Xiwang
Published: January 2023

Although two-dimensional (2D) materials have grown into an extended family that accommodates hundreds of members and have demonstrated promising advantages in many fields, their practical applications are still hindered by the lack of scalable high-yield production of monolayer products. Here, we show that scalable production of monolayer nanosheets can be achieved by a facile ball-milling exfoliation method with the assistance of viscous polyethyleneimine (PEI) liquid. As a demonstration, graphite is effectively exfoliated into graphene nanosheets, achieving a high monolayer percentage of 97.9% at a yield of 78.3%. The universality of this technique is also proven by successfully exfoliating other types of representative layered materials with different structures, such as carbon nitride, covalent organic framework, zeolitic imidazolate framework and hexagonal boron nitride. This scalable exfoliation technique for monolayer nanosheets could catalyze the synthesis and industrialization of 2D nanosheet materials.
Rapidly shifting immunologic landscape and severity of SARS-CoV-2 in the Omicron era in South Africa
Authors: Sun Kaiyuan , Tempia Stefano , Kleynhans Jackie , von Gottberg Anne , McMorrow Meredith L. , Wolter Nicole , Bhiman Jinal N. , Moyes Jocelyn , Carrim Maimuna , Martinson Neil A. , Kahn Kathleen , Lebina Limakatso , du Toit Jacques D. , Mkhencele Thulisa , Viboud Cécile , Cohen Cheryl ,   the PHIRST-C group, Buys Amelia , de Gouveia Linda , du Plessis Mignon , Gómez-Olivé Francesc Xavier , Kgasago Kgaugelo Patricia , Kotane Retshidisitswe , Moloantoa Tumelo , Tollman Stephen , Wafawanaka Floidy
Published: January 2023

South Africa was among the first countries to detect the SARS-CoV-2 Omicron variant. However, the size of its Omicron BA.1 and BA.2 subvariants (BA.1/2) wave remains poorly understood. We analyzed sequential serum samples collected through a prospective cohort study before, during, and after the Omicron BA.1/2 wave to infer infection rates and monitor changes in the immune histories of participants over time. We found that the Omicron BA.1/2 wave infected more than half of the cohort population, with reinfections and vaccine breakthroughs accounting for > 60% of all infections in both rural and urban sites. After the Omicron BA.1/2 wave, we found few (< 6%) remained naïve to SARS-CoV-2 and the population immunologic landscape is fragmented with diverse infection/immunization histories. Prior infection with the ancestral strain, Beta, and Delta variants provided 13%, 34%, and 51% protection against Omicron BA.1/2 infection, respectively. Hybrid immunity and repeated prior infections reduced the risks of Omicron BA.1/2 infection by 60% and 85% respectively. Our study sheds light on a rapidly shifting landscape of population immunity in the Omicron era and provides context for anticipating the long-term circulation of SARS-CoV-2 in populations no longer naïve to the virus.
The metabolite alpha-ketobutyrate extends lifespan by promoting peroxisomal function in C. elegans
Authors: Wu Nan , Ma Yi-Cheng , Gong Xin-Qian , Zhao Pei-Ji , Jia Yong-Jian , Zhao Qiu , Duan Jia-Hong , Zou Cheng-Gang
Published: January 2023

Metabolism is intimately linked to aging. There is a growing number of studies showing that endogenous metabolites may delay aging and improve healthspan. Through the analysis of existing transcriptome data, we discover a link between activation of the transsulfuration pathway and a transcriptional program involved in peroxisome function and biogenesis in long-lived glp-1(e2141ts) mutant Caenorhabditis elegans worms. Subsequently, we show that supplementation with α-ketobutyrate, an intermediate of the transsulfuration pathway, extends lifespan in wild-type worms. Alpha-ketobutyrate augments the production of NAD+ via the lactate dehydrogenase LDH-1, leading to SIR-2.1/SIRT1-mediated enhanced peroxisome function and biogenesis, along with a concomitant increase in the expression of acox-1.2/ACOX1 in the peroxisomal fatty acid β-oxidation pathway. ACOX-1.2/ACOX1 promotes H2O2 formation, thereby resulting in activation of SKN-1/NRF2. This transcription factor in turn extends the lifespan of worms by driving expression of autophagic and lysosomal genes. Finally, we show that α-ketobutyrate also delays the cellular senescence in fibroblast cells through the SIRT1-ACOX1-H2O2-NRF2 pathway. This finding uncovers a previously unknown role for α-ketobutyrate in organismal lifespan and healthspan by coordinating the NAD+-SIRT1 signaling and peroxisomal function.
3D printing of thermosets with diverse rheological and functional applicabilities
Authors: Sun Yuxuan , Wang Liu , Ni Yangyang , Zhang Huajian , Cui Xiang , Li Jiahao , Zhu Yinbo , Liu Ji , Zhang Shiwu , Chen Yong , Li Mujun
Published: January 2023

Thermosets such as silicone are ubiquitous. However, existing manufacturing of thermosets involves either a prolonged manufacturing cycle (e.g., reaction injection molding), low geometric complexity (e.g., casting), or limited processable materials (e.g., frontal polymerization). Here, we report an in situ dual heating (ISDH) strategy for the rapid 3D printing of thermosets with complex structures and diverse rheological properties by incorporating direct ink writing (DIW) technique and a heating-accelerated in situ gelation mechanism. Enabled by an integrated Joule heater at the printhead, extruded thermosetting inks can quickly cure in situ, allowing for DIW of various thermosets with viscosities spanning five orders of magnitude, printed height over 100 mm, and high resolution of 50 μm. We further demonstrate DIW of a set of heterogenous thermosets using multiple functional materials and present a hybrid printing of a multilayer soft electronic circuit. Our ISDH strategy paves the way for fast manufacturing of thermosets for various emerging fields.
Development of a BIM-based bridge maintenance system (BMS) for managing defect data
Authors: Li Sai , Zhang Zhongjian , Lin Daming , Zhang Tongrui , Han Lu
Published: January 2023

Bridges might experience many defects during use, such as pavement cracks and reinforcement corrosion, which easily produce an accumulated impact that threatens bridge safety. Thus, there is a need for the regular inspection and maintenance of bridges. This paper presents a bridge maintenance system (BMS) based on building information modelling (BIM), which is utilized in bridge defect information management using a digitalization method. A bridge defect three-dimensional BIM (BIM3D) library is established and combined with a bridge model to visualize bridge defect conditions. Based on bridge inspection data, bridge defect information is digitally classified and encoded according to the international framework for dictionaries (IFD) standard and used to establish a database. An evaluation of bridge technical conditions is performed, and the results are graded and displayed in different colours, reflecting the visualization function of BIM technology. Maintenance suggestions are provided according to the range of bridge technical condition scores, reflecting the informatization function of BIM technology. With the Xinjiang Cocodala Bridge in China as a case study, a bridge BIM3D model and inspection data are imported into the BMS to utilize the functions of ‘visualization of bridge defect conditions’, ‘evaluation of bridge technical conditions’ and ‘recommendations of bridge maintenance methods'.
Predictors for metamorphopsia in eyes undergoing macular hole surgery
Authors: Takeyama Asuka , Imamura Yutaka , Fujimoto Taichi , Iida Toshiya , Komiya Yuko , Shibata Masaki , Ishida Masahiro
Published: January 2023

Metamorphopsia is an important visual symptom of macular disease. We determined predictors for metamorphopsia investigating the relationships of macular hole (MH) diameter and retinal layer thicknesses with metamorphopsia after MH surgery. Forty-two eyes of 42 consecutive patients undergoing MH surgery were retrospectively studied. Metamorphopsia was measured with M-CHARTS. Inner nuclear layer (INL) and outer retinal layer (OR) thicknesses were measured 1000 μm away from central fovea at using Spectralis. Preoperative M-CHARTS scores correlated with MH diameters (P = 0.007–0.031) and changes of temporal OR thickness (P = 0.008–0.010). Postoperative M-CHARTS score at 3 months correlated with preoperative nasal and inferior OR thicknesses (P = 0.003 and 0.016) and with changes of superior INL at 3 and 6 months (P = 0.011 and 0.025), and score at 1 month with change of temporal OR at 6 months (P = 0.033). Postoperative improvement of M-CHARTS scores correlated with changes of temporal INL and superior OR (P = 0.026 and 0.002). Multiple regression analysis revealed that MH diameter was a significant predictor for metamorphopsia. Photoreceptor displacement and inner retinal change may generate metamorphopsia in MH undergoing surgery, however MH diameter is the most powerful predictor.
The putative transporter MtUMAMIT14 participates in nodule formation in Medicago truncatula
Authors: Garcia Kevin , Cloghessy Kaylee , Cooney Danielle R. , Shelley Brett , Chakraborty Sanhita , Kafle Arjun , Busidan Aymeric , Sonawala Unnati , Collier Ray , Jayaraman Dhileepkumar , Ané Jean-Michel , Pilot Guillaume
Published: January 2023

Transport systems are crucial in many plant processes, including plant–microbe interactions. Nodule formation and function in legumes involve the expression and regulation of multiple transport proteins, and many are still uncharacterized, particularly for nitrogen transport. Amino acids originating from the nitrogen-fixing process are an essential form of nitrogen for legumes. This work evaluates the role of MtN21 (henceforth MtUMAMIT14), a putative transport system from the MtN21/EamA-like/UMAMIT family, in nodule formation and nitrogen fixation in Medicago truncatula. To dissect this transporter’s role, we assessed the expression of MtUMAMIT14 using GUS staining, localized the corresponding protein in M. truncatula root and tobacco leaf cells, and investigated two independent MtUMAMIT14 mutant lines. Our results indicate that MtUMAMIT14 is localized in endosomal structures and is expressed in both the infection zone and interzone of nodules. Comparison of mutant and wild-type M. truncatula indicates MtUMAMIT14, the expression of which is dependent on the presence of NIN, DNF1, and DNF2, plays a role in nodule formation and nitrogen-fixation. While the function of the transporter is still unclear, our results connect root nodule nitrogen fixation in legumes with the UMAMIT family.
Geometric deep learning reveals the spatiotemporal features of microscopic motion
Authors: Pineda Jesús , Midtvedt Benjamin , Bachimanchi Harshith , Noé Sergio , Midtvedt Daniel , Volpe Giovanni , Manzo Carlo
Published: January 2023

The characterization of dynamical processes in living systems provides important clues for their mechanistic interpretation and link to biological functions. Owing to recent advances in microscopy techniques, it is now possible to routinely record the motion of cells, organelles and individual molecules at multiple spatiotemporal scales in physiological conditions. However, the automated analysis of dynamics occurring in crowded and complex environments still lags behind the acquisition of microscopic image sequences. Here we present a framework based on geometric deep learning that achieves the accurate estimation of dynamical properties in various biologically relevant scenarios. This deep-learning approach relies on a graph neural network enhanced by attention-based components. By processing object features with geometric priors, the network is capable of performing multiple tasks, from linking coordinates into trajectories to inferring local and global dynamic properties. We demonstrate the flexibility and reliability of this approach by applying it to real and simulated data corresponding to a broad range of biological experiments.
Surfaceome mapping of primary human heart cells with CellSurfer uncovers cardiomyocyte surface protein LSMEM2 and proteome dynamics in failing hearts
Authors: Berg Luecke Linda , Waas Matthew , Littrell Jack , Wojtkiewicz Melinda , Castro Chase , Burkovetskaya Maria , Schuette Erin N. , Buchberger Amanda Rae , Churko Jared M. , Chalise Upendra , Waknitz Michelle , Konfrst Shelby , Teuben Roald , Morrissette-McAlmon Justin , Mahr Claudius , Anderson Daniel R. , Boheler Kenneth R. , Gundry Rebekah L.
Published: January 2023

Cardiac cell surface proteins are drug targets and useful biomarkers for discriminating among cellular phenotypes and disease states. Here we developed an analytical platform, CellSurfer, that enables quantitative cell surface proteome (surfaceome) profiling of cells present in limited quantities, and we apply it to isolated primary human heart cells. We report experimental evidence of surface localization and extracellular domains for 1,144 N-glycoproteins, including cell-type-restricted and region-restricted glycoproteins. We identified a surface protein specific for healthy cardiomyocytes, LSMEM2, and validated an anti-LSMEM2 monoclonal antibody for flow cytometry and imaging. Surfaceome comparisons among pluripotent stem cell derivatives and their primary counterparts highlighted important differences with direct implications for drug screening and disease modeling. Finally, 20% of cell surface proteins, including LSMEM2, were differentially abundant between failing and non-failing cardiomyocytes. These results represent a rich resource to advance development of cell type and organ-specific targets for drug delivery, disease modeling, immunophenotyping and in vivo imaging
Correction: An optically reversible room-temperature solid-state cobalt(iii) photoswitch based on nitro-to-nitrito linkage isomerism
Authors: Deresz Krystyna A. , Kamiński Radosław , Kutniewska Sylwia E. , Krówczyński Adam , Schaniel Dominik , Jarzembska Katarzyna N.
Published: January 2023

Correction for ‘An optically reversible room-temperature solid-state cobalt(iii) photoswitch based on nitro-to-nitrito linkage isomerism’ by Krystyna A. Deresz et al., Chem. Commun., 2022, 58, 13439–13442, https://doi.org/10.1039/d2cc05134f.
Tuning primary and secondary coordination spheres of ruthenium complexes for the homogeneous water oxidation reaction: a perspective from catalytic activity and overpotential
Authors: Ma Hao-Chen , Hsiao Shun-Chien , Wang Yu-Heng
Published: January 2023

The impact of primary and secondary coordination spheres on Ru-based water oxidation catalysts is analyzed from kinetics (turnover frequency, TOF) and thermodynamics (overpotential,η) perspectives.
Microbiome and hydraulic performance changes of drinking water biofilters during disruptive events-media replacement, lake diatom bloom, and chlorination
Authors: Abkar Leili , Taylor Anita , Stoddart Amina , Gagnon Graham
Published: January 2023

Little is known about filter media microbiome and characteristics during disruptive events and drastic hydraulic performance decline in drinking water biofilters.
β(2 → 1)-β(2 → 6) branched graminan-type fructans and β(2 → 1) linear fructans impact mucus-related and endoplasmic reticulum stress-related genes in goblet cells and attenuate inflammatory responses in a fructan dependent fashion
Authors: Fernández-Lainez Cynthia , aan de Stegge Myrthe , Silva-Lagos Luis Alfredo , López-Velázquez Gabriel , de Vos Paul
Published: January 2023

Dietary fibers such as fructans beneficially impact the expression of mucus- and ER stress-related genes in goblet cells (GCs) and attenuate inflammatory responses, which contributes to the knowledge of the effects of fructans on intestinal health.
Identification of yeast α-glucosidase inhibitors from Pueraria lobata by ligand fishing based on magnetic mesoporous silicon combined with knock-out/knock-in technology
Authors: Xu Jinfang , Fan Zhiyu , Yang Gangqiang , Yang Yanan , Wu Xinjie , Li Tongtong , Wang Qili , Gao Jianping
Published: January 2023

Ligand fishing combined with knock-out/knock-in chromatography to efficiently screen components with α-glucosidase inhibitory activities from Pueraria lobata and evaluate holistic activities and interactions between these constituents.
Capsaicin ameliorates diet-induced disturbances of glucose homeostasis and gut microbiota in mice associated with the circadian clock
Authors: Liang Wanxia , Ho Chi-Tang , Lan Yaqi , Xiao Jie , Huang Qingrong , Cao Yong , Lu Muwen
Published: January 2023

Capsaicin ameliorates diet-induced disturbances of glucose homeostasis and gut microbiota in mice associating with the circadian clock.