bluuebunny/crossref_metadata_2025 huggingface dataset:
The Role of Nutrition and Nutritional Supplements in the Prevention and Treatment of Malnutrition in Chronic Obstructive Pulmonary Disease: Current Approaches in Nutrition Therapy
Authors: Tuna Tuğba , Samur Gülhan
Published: January 2025

Purpose of Review

Malnutrition is a significant comorbidity in Chronic Obstructive Pulmonary Disease (COPD), contributing to disease progression and reduced quality of life. This narrative review examines the role of nutritional therapy in the prevention and management of malnutrition in COPD, emphasizing evidence-based approaches and their clinical implications.

Recent Findings

COPD patients face increased metabolic demands, systemic inflammation, and reduced dietary intake, resulting in muscle wasting, sarcopenia, and cachexia. Recent evidence highlights the efficacy of targeted nutritional strategies, including essential amino acid supplementation, omega-3 fatty acids, vitamin D, and antioxidants, in improving respiratory function, muscle strength, and patient well-being. Comprehensive nutritional assessments and personalized interventions are increasingly recognized as critical components of COPD care. However, long-term efficacy data remain limited.

Nutritional therapy plays a pivotal role in managing malnutrition and improving clinical outcomes in COPD. This review synthesizes the latest evidence, identifies gaps in current research, and proposes strategies for integrating personalized nutrition into COPD care. Future studies are needed to establish the long-term benefits of these interventions and to develop tailored nutritional guidelines for COPD patients.
Defining Hyperphagia for Improved Diagnosis and Management of MC4R Pathway–Associated Disease: A Roundtable Summary
Authors: Heymsfield Steven B. , Clément Karine , Dubern Beatrice , Goldstone Anthony P. , Haqq Andrea M. , Kühnen Peter , Richards Jesse , Roth Christian L. , Akker Erica L. T. van den , Wabitsch Martin , Yanovski Jack A.
Published: January 2025

Purpose of review

Hyperphagia is a condition associated with rare obesity-related diseases, presenting as a pathologic, insatiable hunger accompanied by abnormal food-seeking behaviors. In October 2023, a group of researchers and clinicians with expert knowledge on hyperphagia convened at the annual ObesityWeek meeting to discuss the need for a unified definition of hyperphagia and key items necessary to improve the identification, assessment, and treatment of hyperphagia in patients with melanocortin 4 receptor (MC4R) pathway–associated diseases.

Recent findings

The definition of hyperphagia proposed by this group is a pathologic, insatiable hunger accompanied by abnormal food-seeking behaviors. Suggested methods to accurately identify patients with hyperphagia include increased physician and parent/caregiver education and standardized efficient screening procedures for use in the clinic. The etiology of hyperphagia as related to abnormal MC4R signaling was also reviewed and proposed as a central cause of the condition across several underlying diseases.

Given this potential unified underlying pathology, the expert group recommends that patients with hyperphagia undergo genetic testing and that treatment include comprehensive weight-management strategies incorporating lifestyle and pharmacotherapies targeted at addressing hyperphagia.
Symplectic ACD codes over a non-commutative non-unitary ring
Authors: Manseri Sarra , Solé Patrick
Published: January 2025

We introduce a symplectic inner product on vectors over a non-unitary non commutative ring of order 4. Linear and additive codes over that ring are explored from the standpoint of self-duality and complementarity with their duals.
Evaluating the Effects of a Teacher-Implemented Mindfulness-Based Intervention on Teacher Stress and Student Prosocial Behavior
Authors: Phan Mary L. , Renshaw Tyler L. , Domenech Rodríguez Melanie M. , Brunson McClain Maryellen , Ler Moo Eh , Humphries Austin , Parker Breanna
Published: January 2025

This pilot study evaluated the effects of a mindfulness-based intervention (MBI) on teacher stress and coping as well as students’ prosocial classroom behavior. This study also explored the implementation fidelity and social validity of this MBI with teachers. This study used a single-case multiple baseline design across four elementary teachers. The MBI consisted of self-practice and a proactively culturally-adapted classroom-based intervention. We gathered data on teacher stress and coping as well as student prosocial behavior in the classroom for two weeks. Teachers received weekly in-person fidelity checks and performance feedback. MBI sustainability was monitored with two-week and one-month follow-up questionnaires post-intervention. MBI self-practice and classroom-based implementation were conducted with high fidelity and had strong social validity. The MBI decreased teacher stress for two of four teachers and improved coping abilities for two of four teachers. Further, three of four teachers reported the MBI had small yet desirable effects on students’ academic engagement, respectful behavior, and disruptive behavior in the classroom. Although results show potential promises in the short-term, follow-ups suggested the MBI had poor sustainability. This study provides proof of concept for the MBI’s potential to positively affect both teachers and students, but more research is needed to understand the mixed results. Results have practical implications for informing future research related to using MBI to reduce teacher stress and coping as well as for improving students’ classroom behavior. We hope this study encourages researchers to engage in MBIs to promote teacher and student well-being.
Basic Considerations for Data Pooling Strategy in Multi-Regional Clinical Trials (MRCTs)
Authors: Song Jiali , Ji Chen , Chen Meng , Dong Jun , Zhu Chao , Wu Haiyan , Zhang Wei , Zhang Kezhou , Yu Bing , Wang Yun , Zhang Hua , Jia Fan , Hou Yan
Published: January 2025

The National Medical Products Administration of China has been implementing ICH E17, which describes the general principles for planning and designing of multi-regional clinical trials (MRCTs), yet there are several ambiguities in the execution and conduct remains in China or East Asia. In specific, pooling strategy, effect modifiers (EMs), statistical analysis, sample size allocation and their impact in alignment with global trial remains a challenge. In this paper, we explore on the criteria mentioned above under the context of China. EMs need to be determined and identified from intrinsic and extrinsic factors which might have the impact to the drug on specific populations. If no EMs are found, we use pooling by regions to understand whether differences across East Asian population exists, and whether pooling by East Asian is necessary. Statistical models used in the analysis are also listed to estimate the drug effect in pooled populations. In summary, this paper outlines the details of the MRCTs practices in China and provides better insights in practice both domestically and internationally for any future improvements.
Examination of mechanical properties of 3D printed geopolymer mortar using the Taguchi method
Authors: Tanyildizi Harun , Coskun Ahmet , Seloglu Maksut , Durmaz Taner
Published: January 2025

This study examined the strength features of 3D printed fly ash-based geopolymer mortar with silica fume using the Taguchi and ANOVA methods. This study used the Taguchi L18(21 × 32) orthogonal array. Silica fume was used in the mixtures at 0% and 10% of the binder weight. 40 × 40 × 160 mm specimens were manufactured by a 3D printer. After the specimens were produced, they were cured at 80 °C for 24, 48, and 72 h. Then, these specimens were kept at 20 ± 2 °C for 3, 7, and 28 days. Lastly, the microstructural features, compressive strength, and flexural strength of the samples were determined. The ANOVA results found that the most affecting parameter for the strength properties of geopolymer mortars was found to be silica fume. Also, the Taguchi method found that optimum values of silica fume, curing time, and curing day for strength properties of geopolymer mortar were 10%, 48 h, and 28 days, respectively.
Unraveling the Distinct Roles of Snowmelt and Glacier‐Melt on Agricultural Water Availability: A Novel Indicator and Its Application in a Glacierized Basin of China’s Arid Region
Authors: Zha Hang , Zhang Fan , Zhang Hongbo , Tang Shizhen , Zhang Longhui , Luo Lun
Published: January 2025

Mountain runoff is a vital water source for irrigation in global arid regions. Investigating the roles of major mountain runoff components such as snowmelt and glacier‐melt, on downstream irrigation water availability is important for understanding water resource security. Snowmelt and glacier‐melt have different timing and availability. However, their potentially distinct impacts on water supplies for downstream irrigation have been seldom investigated previously. This study proposes a novel indicator, Irrigation Dependence on runoff Component (IDC), to assess the individual impact of different runoff components on irrigation water availability, considering water supply, water demand and their relationship. Applying IDC to the Yarkant River basin (YRB) in China’s arid region, mainly fed by mountain runoff from the northern Tibetan Plateau, reveals that, despite glacier‐melt runoff being the primary contributor to total runoff in the YRB, irrigation water availability is generally more reliant on snowmelt runoff due to seasonal variations in the water supply/demand relationship. Further sensitivity tests under 48 climate scenarios indicate that IDC of glacier‐melt runoff significantly increases under drier climates, while that of snowmelt runoff decreases as the climate warms, implying potentially increased importance of glacier‐melt in future, especially under drier conditions and during the transition season. Additionally, the crucial role of anthropogenic factors, including changes in planting area and irrigation water use efficiency, in influencing irrigation water demand is highlighted for improved estimation. This study provides important implications on how cryosphere changes impact water resources management and an efficient indicator for further studies in glacierized arid basins globally.
Treasure Bowl: PM2.5 Aggregation in the Eye of a Tropical Cyclone
Authors: Wang Ruiwen , Wang Hao , Zhang Chunlin , Gong Daocheng , Ma Fangyuan , He Congrong , Chen Duohong , Shen Jin , Zhou Yan , Ristovski Zoran , Liu Shaw Chen , Wang Boguang
Published: January 2025

A local tropical cyclone (TC) in South China Sea was observed making its first complete landfall on an island. Following the arrival of the TC eye, PM2.5 concentration rose from 4 µg/m³ to 44 µg/m³. Mass reconstruction results reveal that sea salt emerged as the primary source. The similar molar ratios of elements before and after landfall confirm that the source of PM2.5 is associated with the local terrigenous sediment. The ratio of Na+/Cl− in the TC eyewall is approximately 5:1 indicating the existence of chlorine depletion. Meanwhile, the concentration of Cl− and molar ratios like Si/Fe inside the TC eyewall show a rapid increase, and reach a peak in the TC eye, indicating that marine particulate matter invades and presents a treasure‐bowl‐like stepwise aggregation. Our findings provide statistical and theoretical foundations for understanding extreme air pollution events, offering direct evidence of sea‐land transport throughout the entire TC.
Monitoring and Modeling the Soil‐Plant System Toward Understanding Soil Health
Authors: Zeng Yijian , Verhoef Anne , Vereecken Harry , Ben‐Dor Eyal , Veldkamp Tom , Shaw Liz , Van Der Ploeg Martine , Wang Yunfei , Su Zhongbo
Published: January 2025

The soil health assessment has evolved from focusing primarily on agricultural productivity to an integrated evaluation of soil biota and biotic processes that impact soil properties. Consequently, soil health assessment has shifted from a predominantly physicochemical approach to incorporating ecological, biological and molecular microbiology indicators. This shift enables a comprehensive exploration of soil microbial community properties and their responses to environmental changes arising from climate change and anthropogenic disturbances. Despite the increasing availability of soil health indicators (physical, chemical, and biological) and data, a holistic mechanistic linkage has not yet been fully established between indicators and soil functions across multiple spatiotemporal scales. This article reviews the state‐of‐the‐art of soil health monitoring, focusing on understanding how soil‐microbiome‐plant processes contribute to feedback mechanisms and causes of changes in soil properties, as well as the impact these changes have on soil functions. Furthermore, we survey the opportunities afforded by the soil‐plant digital twin approach, an integrative framework that amalgamates process‐based models, Earth Observation data, data assimilation, and physics‐informed machine learning, to achieve a nuanced comprehension of soil health. This review delineates the prospective trajectory for monitoring soil health by embracing a digital twin approach to systematically observe and model the soil‐plant system. We further identify gaps and opportunities, and provide perspectives for future research for an enhanced understanding of the intricate interplay between soil properties, soil hydrological processes, soil‐plant hydraulics, soil microbiome, and landscape genomics.
Machine Learning Prediction of Tritium‐Helium Groundwater Ages in the Central Valley, California, USA
Authors: Azhar Abdullah , Chakraborty Indrasis , Visser Ate , Liu Yang , Lerback Jory Chapin , Oerter Erik
Published: January 2025

Groundwater ages provides insight into recharge rates, flow velocities, and vulnerability to contaminants. The ability to predict groundwater ages based on more accessible parameters via Machine Learning (ML) would advance our ability to guide sustainable management of groundwater resources. In this study, ML models were trained and tested on a large data set of tritium concentrations and tritium‐helium groundwater ages from the California Central Valley, a large groundwater basin with complex land use, irrigation, and water management practices. The ML models were trained on 63 features, including location, well construction information, landscape characteristics, and climate variables, water chemistry, and stable isotopes. The Bagging regressor method can accurately classify (F1‐score = 0.91) groundwater samples as either modern or pre‐modern whereas the accuracy of the ML prediction of continuous tritium‐helium groundwater ages is limited and explains only of the variability in this data set. In general, ML groundwater age prediction relies mostly on features related to (a) the source of groundwater recharge, (b) contaminant history, (c) aquifer materials, (d) well construction, and (e) geochemical reactions along flow paths.
Dissociating social reward learning and behavior in alcohol use disorder
Authors: Jangard Simon , Lindström Björn , Khemiri Lotfi , Jayaram-Lindström Nitya , Olsson Andreas
Published: January 2025

Background

Alcohol use disorder (AUD) is associated with deficits in social cognition and behavior, but why these deficits are acquired is unknown. We hypothesized that a reduced association between actions and outcomes for others, i.e., social reward learning, would explain prevalent social deficiencies in AUD.

Methods

We conducted one laboratory study (n = 234) and one confirmatory online study (n = 258), comparing young adults with AUD to age-, gender-, and education-matched healthy controls on a standardized reward learning task. In the task, participants learned to maximize reward for another person and for oneself. To elucidate the potential relation between reward learning and social behavior in AUD, we administered two measures: a dictator game task and a self-report measure. Finally, we applied reinforcement learning models to examine the computational properties of learning.

Results

Social and individual learning, expressed in choice behavior, were comparable in individuals with AUD and healthy controls. Individual differences in learning were not associated with reduced social behavior in AUD. Computational modeling suggested that the learning mechanisms are comparable in AUD and healthy controls and indifferent to whether learning maximizes reward for another person or oneself.

Conclusions

Individuals with AUD demonstrated preserved reward learning abilities that do not vary with social behavior. Together, these results indicate that reward processes may not be relevant for understanding compromised social behavior in AUD.
Autophagic flux-lipid droplet biogenesis cascade sustains mitochondrial fitness in colorectal cancer cells adapted to acidosis
Authors: Liu Xiaojie , Sun Xue , Mu Wenqing , Li Yanan , Bu Wenqing , Yang Tingting , Zhang Jia , Liu Rui , Ren Jiayu , Zhou Jin , Li Peishan , Shi Yufang , Shao Changshun
Published: January 2025

Cancer development is associated with adaptation to various stressful conditions, such as extracellular acidosis. The adverse tumor microenvironment also selects for increased malignancy. Mitochondria are integral in stress sensing to allow for tumor cells to adapt to stressful conditions. Here, we show that colorectal cancer cells adapted to acidic microenvironment (CRC-AA) are more reliant on oxidative phosphorylation than their parental cells, and the acetyl-CoA in CRC-AA cells are generated from fatty acids and glutamine, but not from glucose. Consistently, CRC-AA cells exhibit increased mitochondrial mass and fitness that depends on an upregulated autophagic flux-lipid droplet axis. Lipid droplets (LDs) function as a buffering system to store the fatty acids derived from autophagy and to protect mitochondria from lipotoxicity in CRC-AA cells. Blockade of LD biogenesis causes mitochondrial dysfunction that can be rescued by inhibiting carnitine palmitoyltransferase 1 α (CPT1α). High level of mitochondrial superoxide is essential for the AMPK activation, resistance to apoptosis, high autophagic flux and mitochondrial function in CRC-AA cells. Thus, our results demonstrate that the cascade of autophagic flux and LD formation plays an essential role in sustaining mitochondrial fitness to promote cancer cell survival under chronic acidosis. Our findings provide insight into the pro-survival metabolic plasticity in cancer cells under microenvironmental or therapeutic stress and imply that this pro-survival cascade may potentially be targeted in cancer therapy.
Rapid iPSC-derived neuromuscular junction model uncovers motor neuron dominance in amyotrophic lateral sclerosis cytopathy
Authors: Ting Hsiao-Chien , Guo Yun-Ting , Su Hong-Lin , Chen Yu-Shuan , Lin Shinn-Zong , Harn Horng-Jyh , Chang Chia-Yu
Published: January 2025

The neuromuscular junction (NMJ) is essential for transmitting signals from motor neurons (MNs) to skeletal muscles (SKMs), and its dysfunction can lead to severe motor disorders. However, our understanding of the NMJ is limited by the absence of accurate human models. Although human induced pluripotent stem cell (iPSC)-derived models have advanced NMJ research, their application is constrained by challenges such as limited differentiation efficiency, lengthy generation times, and cryopreservation difficulties. To overcome these limitations, we developed a rapid human NMJ model using cryopreserved MNs and SKMs derived from iPSCs. Within 12 days of coculture, we successfully recreated NMJ-specific connectivity that closely mirrors in vivo synapse formation. Using this model, we investigated amyotrophic lateral sclerosis (ALS) and replicated ALS-specific NMJ cytopathies with SOD1 mutant and corrected isogenic iPSC lines. Quantitative analysis of 3D confocal microscopy images revealed a critical role of MNs in initiating ALS-related NMJ cytopathies, characterized by alterations in the volume, number, intensity, and distribution of acetylcholine receptors, ultimately leading to impaired muscle contractions. Our rapid and precise in vitro NMJ model offers significant potential for advancing research on NMJ physiology and pathology, as well as for developing treatments for NMJ-related diseases.
Anthracyclines disaggregate and restore mutant p63 function: a potential therapeutic approach for AEC syndrome
Authors: Boncimino Fabiana , D’Auria Ludovica , Todorova Kristina , van der Zanden Sabina Y. , Neefjes Jacques , Mandinova Anna , Missero Caterina , Sol Stefano
Published: January 2025

Ankyloblepharon-Ectodermal Defects-Cleft Lip/Palate (AEC) syndrome is a rare genetic disorder caused by mutations in the TP63 gene, which encodes a transcription factor essential for epidermal gene expression. A key feature of AEC syndrome is chronic skin erosion, for which no effective treatment currently exists. Our previous studies demonstrated that mutations associated with AEC syndrome lead to p63 protein misfolding and aggregation, exerting a dominant-negative effect. By performing a high-throughput screening of epigenetic and FDA-approved compounds in a co-transfection model of wild-type and mutant p63, we found that two compounds, Doxorubicin and Epirubicin, alleviate protein aggregation and restore p63 transactivation function. Moreover, treatment with these compounds reduced protein aggregation and restored the expression of keratinocyte-specific p63 target genes in primary keratinocytes derived from a conditional ΔNp63αL514F knock-in AEC mouse model, which mimics the ectodermal defects and skin erosions characteristic of AEC syndrome. A chemical analog of Doxorubicin, diMe-Doxorubicin, which exhibits lower tissue and organ toxicity, was also found to be effective in promoting the disaggregation of mutant p63 and rescuing its transcriptional activity. Our findings identify compounds that can partially resolve mutant p63 aggregation, increase its monomeric isoform, and reactivate its transcriptional function. These results suggest potential therapeutic efficacy for treating skin erosions in AEC syndrome.
Epigenetic variation in light of population genetic practice
Authors: Mueller Sarah A. , Merondun Justin , Lečić Sonja , Wolf Jochen B. W.
Published: January 2025

The evolutionary impact of epigenetic variation depends on its transgenerational stability and source - whether genetically determined, environmentally induced, or due to spontaneous, genotype-independent mutations. Here, we evaluate current approaches for investigating an independent role of epigenetics in evolution, pinpointing methodological challenges. We further identify opportunities arising from integrating epigenetic data with population genetic analyses in natural populations. Efforts to advance data quality, study design, and statistical treatment are encouraged to consolidate our understanding of the source of heritable epigenetic variation, quantify its autonomous potential for evolution, and enrich population genetic analyses with an additional layer of information.
Diversity-oriented synthesis of stereodefined tetrasubstituted alkenes via a modular alkyne gem-addition strategy
Authors: Di Xuan , Zhou Sitian , Qin Yali , Li Wenjun , Zhang Yue , Zhang Jie , Shen Xu , Han Jie , Xie Jin , Jin Hongming
Published: January 2025

Stereocontrolled construction of tetrasubstituted olefins has been an attractive issue yet remains challenging for synthetic chemists. In this manuscript, alkynyl selenides, when treated with ArBCl2, are subject to an exclusive 1,1-carboboration, affording tetrasubstituted alkenes with excellent levels of E-selectivity. Detailed mechanistic studies, supported by DFT calculations, elucidates the role of selenium in this 1,1-addition process. Coupled with subsequent C-B and C-Se bond transformations, this 1,1-addition protocol constitutes a modular access to stereodefined all-carbon tetrasubstituted alkenes. The merit of this approach is demonstrated by programmed assembly of diverse functionalized multi-arylated alkenes, especially enabling the stereospecific synthesis of all six possible stereoisomers of tetraarylethene (TAE) derived from the random permutation of four distinct aryl substituents around the double bond. The diversity-oriented synthesis is further utilized to explore different TAE luminogenic properties and potential Se-containing antitumor lead compounds.
The α-globin super-enhancer acts in an orientation-dependent manner
Authors: Kassouf Mira T. , Francis Helena S. , Gosden Matthew , Suciu Maria C. , Downes Damien J. , Harrold Caroline , Larke Martin , Oudelaar Marieke , Cornell Lucy , Blayney Joseph , Telenius Jelena , Xella Barbara , Shen Yuki , Sousos Nikolaos , Sharpe Jacqueline A. , Sloane-Stanley Jacqueline , Smith Andrew J. H. , Babbs Christian , Hughes Jim R. , Higgs Douglas R.
Published: January 2025

Individual enhancers are defined as short genomic regulatory elements, bound by transcription factors, and able to activate cell-specific gene expression at a distance, in an orientation-independent manner. Within mammalian genomes, enhancer-like elements may be found individually or within clusters referred to as locus control regions or super-enhancers (SEs). While these behave similarly to individual enhancers with respect to cell specificity, distribution and distance, their orientation-dependence has not been formally tested. Here, using the α-globin locus as a model, we show that while an individual enhancer works in an orientation-independent manner, the direction of activity of a SE changes with its orientation. When the SE is inverted within its normal chromosomal context, expression of its normal targets, the α-globin genes, is severely reduced and the normally silent genes lying upstream of the α-globin locus are upregulated. These findings add to our understanding of enhancer-promoter specificity that precisely activate transcription.
The effect of avatar identity on spontaneous perspective-taking in patients with schizophrenia
Authors: Xie Pei , Huang ChaoZheng , Wang XiaoQuan , Sang HanBin , Zhou AiBao
Published: January 2025

Controversy exists regarding whether the spontaneity of altercentric intrusion is impaired in patients with schizophrenia during implicit visual perspective-taking tasks. This study explored the characteristics of spontaneous visual perspective-taking in patients with schizophrenia and the effect of an avatar identity on their perspective-taking. We recruited 65 patients with schizophrenia and 65 healthy participants to complete 4 visual perspective-taking experiments for uncued other-avatar and self-avatar tasks and cued other-avatar and self-avatar tasks. In uncued other-avatar experiments, healthy controls showed a significant reduction in accuracy and an increase in response latency when the number of visible discs differed from that seen by the other-avatar (inconsistent condition), indicating altercentric intrusion. However, patients with schizophrenia did not exhibit this effect. In uncued self-avatar experiments, when the avatar was defined as the participant themselves, patients with schizophrenia did not show spontaneous perspective-taking. However, in cued other-avatar experiments, they showed altercentric intrusion in response latency, and in cued self-avatar experiments, they showed altercentric intrusion in accuracy and response latency. These results suggest that patients with schizophrenia have the tendency to spontaneously adopt the perspective of others, which is predicated on their awareness of the existence of perspectives. In addition, the avatar’s identity as a stranger hinders the spontaneous perspective-taking processes in patients with schizophrenia.
DeepExtremeCubes: Earth system spatio-temporal data for assessing compound heatwave and drought impacts
Authors: Ji Chaonan , Fincke Tonio , Benson Vitus , Camps-Valls Gustau , Fernández-Torres Miguel-Ángel , Gans Fabian , Kraemer Guido , Martinuzzi Francesco , Montero David , Mora Karin , Pellicer-Valero Oscar J. , Robin Claire , Söchting Maximilian , Weynants Mélanie , Mahecha Miguel D.
Published: January 2025

With climate extremes’ rising frequency and intensity, robust analytical tools are crucial to predict their impacts on terrestrial ecosystems. Machine learning techniques show promise but require well-structured, high-quality, and curated analysis-ready datasets. Earth observation datasets comprehensively monitor ecosystem dynamics and responses to climatic extremes, yet the data complexity can challenge the effectiveness of machine learning models. Despite recent progress in deep learning to ecosystem monitoring, there is a need for datasets specifically designed to analyse compound heatwave and drought extreme impact. Here, we introduce the DeepExtremeCubes database, tailored to map around these extremes, focusing on persistent natural vegetation. It comprises over 40,000 globally sampled small data cubes (i.e. minicubes), with a spatial coverage of 2.5 by 2.5 km. Each minicube includes (i) Sentinel-2 L2A images, (ii) ERA5-Land variables and generated extreme event cube covering 2016 to 2022, and (iii) ancillary land cover and topography maps. The paper aims to (1) streamline data accessibility, structuring, pre-processing, and enhance scientific reproducibility, and (2) facilitate biosphere dynamics forecasting in response to compound extremes.
Diversity and composition of vegetation and soil seed banks after sand dune restoration by oil mulching and plantations
Authors: Jalilian Banafsheh , Rostami Noredin , Heydari Mehdi , Kohzadian Mehrdad , Valkó Orsolya , Omidipour Reza
Published: January 2025

Soil seed bank (SSB) is valuable reserves of seeds hidden in the soil and are especially important for the preservation and establishment of vegetation under adverse environmental conditions. However, there is a lack of knowledge on the effects of restoration measures on SSB, especially in arid ecosystems. Here, we assess the impacts of oil mulching (1 and 3 years after mulching) and plantations (15-year-old) on the diversity and composition of SSB and aboveground vegetation (AGV) in comparison with those in non-restored areas (i.e., control). Based on the results, species richness was poor in the studied area (36 species belonging to 16 families), with a lower contribution of SSB than of AGV (11 and 34 species, respectively). The largest number of exclusive species was observed in the planted treatment for both SSB and AGV (4 and 5 species, respectively), while the lowest was found in the 1-yr mulching treatment. The mean comparison of the diversity indices revealed that the highest values occurred in the plantation and 3-yr-mulching plots. The seed density in the plantation area was significantly greater (4145 ± 694 seeds/m2) than that in the other areas (3-yr-mulching > 1-yr-mulching > control treatments (145 ± 53, 65 ± 28, and 43 ± 22, respectively). The results of the DCA showed that the plantation treatment was completely separated from the other treatments in terms of the plant composition of the AGV, and the treatment closest to that area was 3-yr mulching, which indicates the positive effect of time since mulching on plant composition. The results of this study suggest that there is a trade-off between the short-term and medium-term effects of oil mulching, such that in the early years, oil mulching has a negative effect on the AGV and SSB, but its positive effects increase with time since mulching. It can be concluded that mulching, along with afforestation, creates a favorable microclimate and improves the diversity and composition of AGV and SSB.
Atmospheric air plasma pre-activation and customizable covalent functionalization of PVDF-membranes of microtiter filter plates
Authors: Ádám Bálint Árpád , Spátay Sára , Jávor Bálint , László Szabolcs , Illés Levente , Fürjes Péter , Tóth Tünde , Huszthy Péter , Golcs Ádám
Published: January 2025

Microtiter-plate-based systems are unified platforms of high-throughput experimentation (HTE). These polymeric devices are used worldwide on a daily basis—mainly in the pharmaceutical industry—for parallel syntheses, reaction optimization, various preclinical studies and high-throughput screening methods. Accordingly, laboratory automation today aims to handle these commercially available multiwell plates, making developments focused on their modifications a priority area of modern applied research. We performed the covalent functionalization of the porous PVDF-membrane of microtiter filter plates as the essence of conventional and common sandwich plate systems by introducing a generalizable method. After surface-activation of the indifferent membrane polymer, customizable functionalization becomes feasible by covalently attached monofunctional molecular linkers. The study was designed with future adaptability, and thus, industrially widespread atmospheric plasma and two different chemical treatments were investigated and compared in terms of practical implementation, polarization effects, extent of labeling, effects on morphology and porosity as well as on permeability. For critical comparison, contact angle measurements, surface ATR-FTIR, 1H-NMR, 19F-NMR, UV–Vis spectroscopy, scanning electron microscopy and permeability tests were used.
Biocompatibility of variable thicknesses of a novel directly printed aligner in orthodontics
Authors: Bleilöb Maximilian , Welte-Jzyk Claudia , Knode Vanessa , Ludwig Björn , Erbe Christina
Published: January 2025

Direct printed aligners (DPAs) offer benefits like the ability to vary layer thickness within a single DPA and to 3D print custom-made removable orthodontic appliances. The biocompatibility of appliances made from Tera Harz TA-28 (Graphy Inc., Seoul, South Korea) depends on strict adherence to a standardized production and post-production protocol, including UV curing. Our aim was to evaluate whether design modifications that increase layer thickness require a longer UV curing time to ensure biocompatibility. Specimens with varying layer thickness were printed to high accuracy using Tera Harz TA-28 and the Asiga MAX 3D printer (Asiga SPS ™ technology, Sydney, Australia). UV curing durations were set at 20, 30 and 60 min. Cytotoxicity was evaluated using the AlamarBlue assay on human gingival fibroblasts. Cell viability decreased with increasing specimen thickness (significant for 2 mm [p < 0.001], 4 mm [p < 0.0001], and 6 mm [p < 0.01]) under the manufacturer-recommended 20-min UV curing. Extending the curing time did not improve cell viability. However, cell viability never decreased by more than 30%, meeting EN ISO 10993-5 standards for non-cytotoxicity. The standard 20-minute UV curing protocol ensures the biocompatibility and patient safety of Tera Harz TA-28 for material thicknesses up to 6 mm.
Optimization of metal polymer friction pair composition for hydrogen wear reduction through thermal stabilization analysis
Authors: Volchenko Dmytro , Kernytskyy Ivan , Royko Yuriy , Ostashuk Mykola , Fidrovska Nataliia , Skrypnyk Vasyl , Zhuravlev Dmytro , Klochko Nataliia , Rys Vasyl , Berezovetska Oksana , Dixit Saurav , Stefańska Anna , Koda Eugeniusz , Singh Subhav , Sharma Kamal , Mahadeva Rajesh
Published: January 2025

The composition of the metal-polymer friction pair is carefully considered for interacting with water and hydrogen, ensuring the metals electrode process potential remains below waters in a neutral medium. Simultaneously, adherence to defined chemical composition ratios for the metal-polymer materials is crucial. This analysis is conducted under conditions of thermal stabilization, characterized by a minimal temperature gradient across the rim thickness within an equivalent thermal field. Using the quasi-chemical approximation, the paper derives a concentration-dependent diffusion coefficient of hydrogen (H) in iron (Fe) across a broad spectrum. This derivation includes electronic and vibrational contributions to the chemical potential. The research establishes a correlation between the equivalent diffusion coefficient and the concentration of diffusing hydrogen atoms from the metal, such as the pulley or drum rim. These findings offer novel insights into optimizing hydrogen wear behaviour in brake friction couples, contributing to advancements in materials and design considerations in the automotive field.
Enhancing lane detection in autonomous vehicles with multi-armed bandit ensemble learning
Authors: Pandian J. Arun , Thirunavukarasu Ramkumar , Mariappan L. Thanga
Published: January 2025

This study introduces a novel ensemble learning technique namely Multi-Armed Bandit Ensemble (MAB-Ensemble), designed for lane detection in road images intended for autonomous vehicles. The foundation of the proposed MAB-Ensemble technique is inspired in terms of Multi-Armed bandit optimization to facilitate efficient model selection for lane segmentation. The benchmarking dataset namely TuSimple is used for training, validating and testing the proposed and existing lane detection techniques. Convolutional Neural Networks (CNNs) architecture which includes ENet, PINet, ResNet-50, ResNet-101, SqueezeNet, and VGG16Net are employed in lane detection problems to construct segmentation models and demonstrate proficiency in distinct road conditions. However, the proposed MAB-Ensemble technique overcomes the limitations of individual models by dynamically selecting the most suitable CNN model based on prevailing environmental factors. The proposed technique optimizes the segmentation accuracy and treats the attained accuracy as a reward signal in the context of reinforcement learning by interacting with the environment through CNN model selection. The MAB-Ensemble achieved an overall accuracy of 90.28% in different road conditions. The results overcome the performance of the individual CNN models and state-of-the-art ensemble techniques. Also, it demonstrates superior performance which includes daytime, night-time, and abnormal road conditions. The MAB-Ensemble technique offers a promising solution for robust lane detection by harnessing the collective strengths of diverse CNN models.
Multi-objective design of multi-material truss lattices utilizing graph neural networks
Authors: Frey Ramón , Tucker Michael R. , Afrasiabi Mohamadreza , Bambach Markus
Published: January 2025

The rapid advancements in additive manufacturing (AM) across different scales and material classes have enabled the creation of architected materials with highly tailored properties. Beyond geometric flexibility, multi-material AM further expands design possibilities by combining materials with distinct characteristics. While machine learning has recently shown great potential for the fast inverse design of lattice structures, its application has largely been limited to single-material systems. In this work, we propose a novel approach that incorporates material properties as edge features within the graph representation of multi-material truss lattices, utilizing graph neural networks (GNNs) to develop a fast and efficient inverse design framework. We validate this framework by designing lattices with tunable thermal expansion and stiffness properties, showcasing its ability to explore a broad and flexible design space. We showcase the framework’s inverse design capabilities for both single and multi-objective optimization tasks and assess its limitations. Additionally, we demonstrate the superior capacity of GNNs in capturing structure-property relationships for multi-material systems. We anticipate that the continued advancement of GNN-assisted inverse design will play a key role in unlocking the full potential of multi-material truss lattices.
Characterizing the omics landscape based on 10,000+ datasets
Authors: Brombacher Eva , Schilling Oliver , Kreutz Clemens
Published: January 2025

The characteristics of data produced by omics technologies are pivotal, as they critically influence the feasibility and effectiveness of computational methods applied in downstream analyses, such as data harmonization and differential abundance analyses. Furthermore, variability in these data characteristics across datasets plays a crucial role, leading to diverging outcomes in benchmarking studies, which are essential for guiding the selection of appropriate analysis methods in all omics fields. Additionally, downstream analysis tools are often developed and applied within specific omics communities due to the presumed differences in data characteristics attributed to each omics technology. In this study, we investigate over ten thousand datasets to understand how proteomics, metabolomics, lipidomics, transcriptomics, and microbiome data vary in specific data characteristics. We were able to show patterns of data characteristics specific to the investigated omics types and provide a tool that enables researchers to assess how representative a given omics dataset is for its respective discipline. Moreover, we illustrate how data characteristics can impact analyses at the example of normalization in the presence of sample-dependent proportions of missing values. Given the variability of omics data characteristics, we encourage the systematic inspection of these characteristics in benchmark studies and for downstream analyses to prevent suboptimal method selection and unintended bias.
Plant root carbon inputs drive methane production in tropical peatlands
Authors: Girkin N. T. , Siegenthaler A. , Lopez O. , Stott A. , Ostle N. , Gauci V. , Sjögersten S.
Published: January 2025

Tropical peatlands are carbon-dense ecosystems that are significant sources of atmospheric methane (CH4). Recent work has demonstrated the importance of trees as an emission pathway for CH4 from the peat to the atmosphere. However, there remain questions over the processes of CH4 production in these systems and how they relate to substrate supply. Principally, these questions relate to the relative contribution of recent photosynthetically fixed carbon, released as root exudates, versus carbon substrate supply from the slowly decomposing peat matrix to CH4 emissions within these ecosystems. Here, we examined the role of root inputs in regulating CH4 production inferred from soil emissions using a combination of in situ tree girdling, in situ13C natural abundance labelling via stem injections, and a 13CO2 labelling of transplanted plants of two contrasting plant functional types, a broadleaved evergreen tree, and a canopy palm. Girdling of broadleaved evergreen trees reduced CH4 fluxes by up to 67%. Stem injections of trees and palms with a natural abundance label resulted in significant isotopic enrichment of CH4 fluxes, reinforcing the link between root carbon inputs and peat CH4 fluxes. Ex situ
13CO2 labelling of plants resulted in significant 13C enrichment of peat CH4 fluxes. Taken together, our results demonstrate for the first time that plant root exudates make a substantial contribution to CH4 production in tropical peatlands.
Temporal transcriptional profiling of host cells infected by a veterinary alphaherpesvirus using nanopore sequencing
Authors: Tombácz Dóra , Maróti Zoltán , Oláh Péter , Dörmő Ákos , Gulyás Gábor , Kalmár Tibor , Csabai Zsolt , Boldogkői Zsolt
Published: January 2025

In our research, we performed temporal transcriptomic profiling of host cells infected with Equid alphaherpesvirus 1 (EHV-1) by utilizing direct cDNA sequencing based on nanopore MinION technology. The sequencing reads were harnessed for transcript quantification at various time points. Viral infection-induced differential gene expression was identified through the edgeR package. The identified genes were segmented into six groups based on their kinetic characteristics. The initial three clusters encompass immediate-early response genes, typically transcription factors and elements of antiviral signaling pathways. These genes were either upregulated (cluster 1) or downregulated (clusters 2 and 3) during the early infection phase. The remaining three clusters include late response genes. In these categories, it is challenging to determine whether changes in gene expression are directly connected to the viral infection or merely side effects of the infection. A study of gene associations using the STRINGDB software revealed several gene networks that might be directly impacted by the virus. We also explored whether gene co-expression could be a result of their collective regulation by upstream transcription factors using the Gene Regulatory Network database. Finally, our differential transcript usage (DTU) analysis identified a number of genes that exhibited altered proportions of transcript isoforms in comparison to non-infected cells. Thus, our analysis revealed that EHV-1 infection not only alters host gene expression but also leads to differential use of transcript isoforms, particularly splice variants.
Personality traits of women with hereditary risk for breast/ovarian cancer versus obstetric history and cancer preventive behaviors
Authors: Żurawska Joanna , Pięta Beata , Wilczak Maciej , Wojciechowska Małgorzata , Rzymski Paweł , Pieczykolan Agnieszka , Krysa Justyna , Bień Agnieszka
Published: January 2025

The aim of the study is to analyze the relationship between personality traits of women with hereditary predisposition to breast/ovarian cancer and their obstetric history and cancer-preventive behaviors. A total of 357 women, participants of ‘The National Program for Families With Genetic/Familial High Risk for Cancer’, were included in the study. The Neo Five-Factor Inventory (NEO-FFI) and a standardized original questionnaire designed for the purpose of the study were used. Breast ultrasound examination at a younger age was associated with Extraversion. Openness to Experience was linked with lower number of children, more frequent use of hormonal contraceptives, and younger age at first breast ultrasound examination. Women with higher Agreeableness scores were less likely to use contraceptives and underwent their first breast ultrasound later in life. Conscientiousness was associated with more frequent use of hormonal contraceptives and younger age at first breast ultrasound examination. Women at increased risk for developing breast/ovarian cancer who used hormonal contraceptives underwent breast ultrasound examinations earlier in life, while those who had breastfed their children chose to have their first mammogram earlier in life. Personality traits affect health-related behaviors and should be taken into account when designing theoretical models as well as interventions regarding health habits.
Ultrasonic emulsification of Cananga odorata nanoemulsion formulation for enhancement of herbicidal potential
Authors: Laosinwattana Chamroon , Somala Naphat , Dimak Jantra , Teerarak Montinee , Chotsaeng Nawasit
Published: January 2025

A nanoemulsion was fabricated from Cananga odorata essential oil (EO) and stabilized by incorporation of Tween 80 using ultrasonication. The major constituents of the EO were benzyl benzoate, linalool, and phenylmethyl ester. Differing sonication amplitude (20–60%) and time (2–10 min) were assessed for effects on nanoemulsion droplet size and polydispersity index (PI). The smallest droplet size of 43.98 nm (PI 0.222) was obtained using 40% amplitude for 8 min; this nanoemulsion was evaluated for its droplet characteristics and pre-emergence herbicidal activities on Amaranthus tricolor. FT-IR confirmed ultrasonic emulsification to not affect the EO components. Regarding stability, storage at 4 °C was determined appropriate, with droplet size changing slightly after five weeks. Assays of herbicidal potential showed the coarse emulsion and nanoemulsion to both reduce A. tricolor germination and growth, with the nanoemulsion being more effective at a given concentration and the difference in effectivity correlating to droplet size. Remarkably, treatment with 250 ppm nanoemulsion and coarse emulsion respectively resulted in 100% and 63.75% germination inhibition. Both emulsions decreased seed imbibition and alpha-amylase activity. The highest relative electrolyte leakage was achieved in seed treated with the nanoemulsion. Therefore, this ultrasonic-based nanoemulsion may have utility as bioherbicide alternative.