bluuebunny/crossref_metadata_2025 huggingface dataset:
Hemostasis and complement in allogeneic hematopoietic stem cell transplantation: clinical significance of two interactive systems
Authors: Tsakiris Dimitrios A. , Gavriilaki Eleni , Chanou Ioanna , Meyer Sara C.
Published: July 2024

Hematopoietic stem cell transplantation (HCT) represents a curative treatment option for certain malignant and nonmalignant hematological diseases. Conditioning regimens before HCT, the development of graft-versus-host disease (GVHD) in the allogeneic setting, and delayed immune reconstitution contribute to early and late complications by inducing tissue damage or humoral alterations. Hemostasis and/or the complement system are biological regulatory defense systems involving humoral and cellular reactions and are variably involved in these complications after allogeneic HCT. The hemostasis and complement systems have multiple interactions, which have been described both under physiological and pathological conditions. They share common tissue targets, such as the endothelium, which suggests interactions in the pathogenesis of several serious complications in the early or late phase after HCT. Complications in which both systems interfere with each other and thus contribute to disease pathogenesis include transplant-associated thrombotic microangiopathy (HSCT-TMA), sinusoidal obstruction syndrome/veno-occlusive disease (SOS/VOD), and GVHD. Here, we review the current knowledge on changes in hemostasis and complement after allogeneic HCT and how these changes may define clinical impact.
Evolving scientific discovery by unifying data and background knowledge with AI Hilbert
Authors: Cory-Wright Ryan , Cornelio Cristina , Dash Sanjeeb , El Khadir Bachir , Horesh Lior
Published: July 2024

The discovery of scientific formulae that parsimoniously explain natural phenomena and align with existing background theory is a key goal in science. Historically, scientists have derived natural laws by manipulating equations based on existing knowledge, forming new equations, and verifying them experimentally. However, this does not include experimental data within the discovery process, which may be inefficient. We propose a solution to this problem when all axioms and scientific laws are expressible as polynomials and argue our approach is widely applicable. We model notions of minimal complexity using binary variables and logical constraints, solve polynomial optimization problems via mixed-integer linear or semidefinite optimization, and prove the validity of our scientific discoveries in a principled manner using Positivstellensatz certificates. We demonstrate that some famous scientific laws, including Kepler’s Law of Planetary Motion and the Radiated Gravitational Wave Power equation, can be derived in a principled manner from axioms and experimental data.
Exceptional figure of merit achieved in boron-dispersed GeTe-based thermoelectric composites
Authors: Jiang Yilin , Su Bin , Yu Jincheng , Han Zhanran , Hu Haihua , Zhuang Hua-Lu , Li Hezhang , Dong Jinfeng , Li Jing-Wei , Wang Chao , Ge Zhen-Hua , Feng Jing , Sun Fu-Hua , Li Jing-Feng
Published: July 2024

GeTe is a promising p-type material with increasingly enhanced thermoelectric properties reported in recent years, demonstrating its superiority for mid-temperature applications. In this work, the thermoelectric performance of GeTe is improved by a facile composite approach. We find that incorporating a small amount of boron particles into the Bi-doped GeTe leads to significant enhancement in power factor and simultaneous reduction in thermal conductivity, through which the synergistic modulation of electrical and thermal transport properties is realized. The thermal mismatch between the boron particles and the matrix induces high-density dislocations that effectively scatter the mid-frequency phonons, accounting for a minimum lattice thermal conductivity of 0.43 Wm−1K−1 at 613 K. Furthermore, the presence of boron/GeTe interfaces modifies the interfacial potential barriers, resulting in increased Seebeck coefficient and hence enhanced power factor (25.4 μWcm−1K−2 at 300 K). Consequently, we obtain a maximum figure of merit Zmax of 4.0 × 10−3 K−1 at 613 K in the GeTe-based composites, which is the record-high value in GeTe-based thermoelectric materials and also superior to most of thermoelectric systems for mid-temperature applications. This work provides an effective way to further enhance the performance of GeTe-based thermoelectrics.
Evaporate-casting of curvature gradient graphene superstructures for ultra-high strength structural materials
Authors: Lu Bing , Yu Li , Hu Yajie , Wang Ying , Zhao Fei , Zhao Yang , Liu Feng , Cheng Huhu , Qu Liangti
Published: July 2024

In contemporary manufacturing, the processing of structural materials plays a pivotal role in enabling the creation of robust, tailor-made, and precise components suitable for diverse industrial applications. Nonetheless, current material forming technologies face challenges due to internal stress and defects, resulting in a substantial decline in both mechanical properties and processing precision. We herein develop a processing strategy toward graphene superstructure with a curvature gradient, which allows us to fabricate robust structural materials with meticulously designed functional shapes. The structure consists of an arc-shaped assembly of graphene nanosheets positioned at co-axial curvature centers. During the dehydration-based evaporate-casting process, the assembly is tightened via capillary effect, inducing local bending. By precisely tuning the axis-center distance and tilt angle, we achieve accurate control over the shape of obtained structure. Notably, internal stress is harnessed to reinforce a designed mortise and tenon structure, resulting in a high joining strength of up to ~200 MPa. This innovative approach addresses the challenges faced by current material forming technologies and opens up more possibilities for the manufacturing of robust and precisely shaped components.
B3galt5 functions as a PXR target gene and regulates obesity and insulin resistance by maintaining intestinal integrity
Authors: Zhang Jinhang , Huang Ya , Li Hong , Xu Pengfei , Liu Qinhui , Sun Yang , Zhang Zijing , Wu Tong , Tang Qin , Jia Qingyi , Xia Yan , Xu Ying , Jing Xiandan , Li Jiahui , Mo Li , Xie Wen , Qu Aijuan , He Jinhan , Li Yanping
Published: July 2024

Pregnane X receptor (PXR) has been reported to regulate glycolipid metabolism. The dysfunction of intestinal barrier contributes to metabolic disorders. However, the role of intestinal PXR in metabolic diseases remains largely unknown. Here, we show that activation of PXR by tributyl citrate (TBC), an intestinal-selective PXR agonist, improves high fat diet (HFD)-induced obesity. The metabolic benefit of intestinal PXR activation is associated with upregulation of β-1,3 galactosyltransferase 5 (B3galt5). Our results reveal that B3galt5 mainly expresses in the intestine and is a direct PXR transcriptional target. B3galt5 knockout exacerbates HFD-induced obesity, insulin resistance and inflammation. Mechanistically, B3galt5 is essential to maintain the integrity of intestinal mucus barrier. B3galt5 ablation impairs the O-glycosylation of mucin2, destabilizes the mucus layer, and increases intestinal permeability. Furthermore, B3galt5 deficiency abolishes the beneficial effect of intestinal PXR activation on metabolic disorders. Our results suggest the intestinal-selective PXR activation regulates B3galt5 expression and maintains metabolic homeostasis, making it a potential therapeutic strategy in obesity.
FlhE functions as a chaperone to prevent formation of periplasmic flagella in Gram-negative bacteria
Authors: Halte Manuel , Andrianova Ekaterina P. , Goosmann Christian , Chevance Fabienne F. V. , Hughes Kelly T. , Zhulin Igor B. , Erhardt Marc
Published: July 2024

The bacterial flagellum, which facilitates motility, is composed of ~20 structural proteins organized into a long extracellular filament connected to a cytoplasmic rotor-stator complex via a periplasmic rod. Flagellum assembly is regulated by multiple checkpoints that ensure an ordered gene expression pattern coupled to the assembly of the various building blocks. Here, we use epifluorescence, super-resolution, and transmission electron microscopy to show that the absence of a periplasmic protein (FlhE) prevents proper flagellar morphogenesis and results in the formation of periplasmic flagella in Salmonella enterica. The periplasmic flagella disrupt cell wall synthesis, leading to a loss of normal cell morphology resulting in cell lysis. We propose that FlhE functions as a periplasmic chaperone to control assembly of the periplasmic rod, thus preventing formation of periplasmic flagella.
Transfer learning enables the rapid design of single crystal superalloys with superior creep resistances at ultrahigh temperature
Authors: Yang Fan , Zhao Wenyue , Ru Yi , Lin Siyuan , Huang Jiapeng , Du Boxuan , Pei Yanling , Li Shusuo , Gong Shengkai , Xu Huibin
Published: July 2024

Accelerating the design of Ni-based single crystal (SX) superalloys with superior creep resistance at ultrahigh temperatures is a desirable goal but extremely challenging task. In the present work, a deep transfer learning neural network with physical constraints for creep rupture life prediction at ultrahigh temperatures is constructed. Transfer learning enables deep learning model breaks through the generalization performance barrier in the extrapolation space of ultrahigh temperature creep properties in the case of a very small dataset, which is the key to achieving the above design goal. Transfer learning is demonstrated to be effective in utilizing the prior compositional sensitivities information contained in the pre-trained model, and motivates the fine-tuned model to capture the particular relationship between composition and creep rupture life at ultrahigh temperature. Aiming to find advanced SX superalloys applied at 1200 °C, the proposed transfer learning-based model guides us to design a superalloy with a verified creep rupture life of ~170 h at 80 MPa, which exceeds the state-of-art value by 30%. The improved γ/γ′ interface strengthening, which is effectively regulated by the Mo/Ta ratio to form γ′ rafting with longer, flatter interfaces and achieve stronger interfacial bonding, is revealed as the dominant mechanism behind combining experiments and first-principles calculations. Moreover, the excellent extrapolation ability of the proposed model is further confirmed to enhance the efficiency of active learning by reducing its dependence on the initial dataset size. This study provides a pioneering AI-driven approach for the rapid development of Ni-based SX superalloys applied in advanced aero-engine blades.
Terahertz near-field microscopy of metallic circular split ring resonators with graphene in the gap
Authors: Schiattarella Chiara , Di Gaspare Alessandra , Viti Leonardo , Justo Guerrero M. Alejandro , Li Lianhe H. , Salih Mohammed , Davies A. Giles , Linfield Edmund H. , Zhang Jincan , Ramezani Hamideh , Ferrari Andrea C. , Vitiello Miriam S.
Published: July 2024

Optical resonators are fundamental building blocks of photonic systems, enabling meta-surfaces, sensors, and transmission filters to be developed for a range of applications. Sub-wavelength size (< λ/10) resonators, including planar split-ring resonators, are at the forefront of research owing to their potential for light manipulation, sensing applications and for exploring fundamental light-matter coupling phenomena. Near-field microscopy has emerged as a valuable tool for mode imaging in sub-wavelength size terahertz (THz) frequency resonators, essential for emerging THz devices (e.g. negative index materials, magnetic mirrors, filters) and enhanced light-matter interaction phenomena. Here, we probe coherently the localized field supported by circular split ring resonators with single layer graphene (SLG) embedded in the resonator gap, by means of scattering-type scanning near-field optical microscopy (s-SNOM), using either a single-mode or a frequency comb THz quantum cascade laser (QCL), in a detectorless configuration, via self-mixing interferometry. We demonstrate deep sub-wavelength mapping of the field distribution associated with in-plane resonator modes resolving both amplitude and phase of the supported modes, and unveiling resonant electric field enhancement in SLG, key for high harmonic generation.
Analysis of a CRDI diesel engine powered by ternary fuel blends (diesel, biodiesel, and pentanol) doped with alumina nano-additives
Authors: Sudarsanam Mark , Jayaprabakar Jayaraman , Kumar J. Aravind , T R Praveenkumar , Rajasimman M.
Published: July 2024

Environmental constraints associated with fossil fuels have driven researchers to find a novel, potential and environmentally benign alternative fuel. Biodiesel, vegetable oil, and alcohol have gained rapid momentum thanks to their renewable nature and comparable energy contents in recent years. Accordingly, a Ternary fuel blend is prepared comprising three fuels namely diesel, biodiesel, and pentanol. Waste cooking oil was identified as the source for biodiesel and Pentanol was chosen among various alcohol alternatives due to improved energy density, reduced toxicity. These are endorsed to the enhancement in surface area-volume ratio of nano additives which boosts the catalytic combustion activity and also causing lesser fuel to take part in combustion for maintaining a constant engine speed. The experimentation is done with ternaryfuel blends with varying pentanol and biodiesel concentrations of diesel, biodiesel and pentanol). Upon experimentation, it was observed that, ternary fuel blend ‘TF’ comprising 70% diesel, 20% biodiesel and 10% pentanol, yielded best performance and was used for doping of Alumina oxide (Al2O3) nano additives. The Al2O3 nanoparticles were doped with ternary blends at fractions of 10 ppm, 20 ppm, and 30 ppm. It was observed that 20 ppm Al2O3 nanoparticle blended TF blend improved BTE and lowered BSFC by about 12.01% and 22.57% respectively. The performance tremendously along with lowered the CO emission by 49.21%, HC emission by 18.91% and smoke opacity by 9.02%.
Compact stars with non-uniform relativistic polytrope
Authors: Nouh Mohamed I. , Foda Mona M. , Aboueisha Mohamed S.
Published: July 2024

This paper presents new relativistic composite polytropic models for compact stars by simultaneously solving Einstein field equations with the polytropic state equation to simulate the spherically symmetric, static matter distribution. Using a non-uniform polytropic index, we get the Tolman–Oppenheimer–Volkoff equation for the relativistic composite polytrope (CTOV). To analyze the star's structure, we numerically solve the CTOV equation and compute the Emden and mass functions for various relativistic parameters and polytropic indices appropriate for neutron stars. The calculation results show that, as the relativistic parameter approaches zero, we recover the well-known Lane-Emden equation from the Newtonian theory of polytropic stars; thus, testing the computational code by comparing composite Newtonian models to those in the literature yields good agreement. We compute composite relativistic models for the neutron star candidates Cen X-3, SAXJ1808.4-3658, and PSR J1614-22304. We compare the findings with various existing models in the literature. Based on the accepted models for PSR J1614-22304 and Cen X-3, the star's core radius is predicted to be between 50 and 60% percent of its total radius, while we found that the radius of the core of star SAXJ1808.4-3658 is around 30% of the total radius. Our findings show that the neutron star structure may be approximated by a composite relativistic polytrope, resulting in masses and radii that are quite consistent with observation.
Circulating adrenal and gonadal steroid hormones heterogeneity in active young males and the contribution of 11-oxy androgens
Authors: Swart Amanda C. , van Rooyen Desmaré , du Toit Therina , Heyns Bianca , Molphy John , Wilson Mathew , Leahy Roisin , Atkin Stephen L.
Published: July 2024

The classical androgens, testosterone and dihydrotestosterone, together with dehydroepiandrosterone, the precusrsor to all androgens, are generally included in diagnostic steroid evaluations of androgen excess and deficiency disorders and monitored in androgen replacement and androgen suppressive therapies. The C11-oxy androgens also contribute to androgen excess disorders and are still often excluded from clinical and research-based steroids analysis. The contribution of the C11-oxy androgens to the androgen pool has not been considered in androgen deficiency. An exploratory investigation into circulating adrenal and gonadal steroid hormones in men was undertaken as neither the classical androgens nor the C11-oxy androgens have been evaluated in the context of concurrent measurement of all adrenal steroid hormones. Serum androgens, mineralocorticoids, glucocorticoids, progesterones and androgens were assessed in 70 healthy young men using ultra high performance supercritical fluid chromatography and tandem mass spectrometry. Testosterone, 24.5 nmol/L was the most prominent androgen detected in all participants while dihydrotestosterone, 1.23 nmol/L, was only detected in 25% of the participants. The 11-oxy androgens were present in most of the participants with 11-hydroxyandrostenedione, 3.37 nmol, in 98.5%, 11-ketoandrostenedione 0.764 in 77%, 11-hydroxytestosterone, 0.567 in 96% and 11-ketotestosterone: 0.440 in 63%. A third of the participants with normal testosterone and comparable 11-ketotestosterone, had significantly lower dehydroepiandrosterone (p < 0.001). In these males 11-hydroxyandrostenedione (p < 0.001), 11-ketoandrostenedione (p < 0.01) and 11-hydroxytestosterone (p < 0.006) were decreased. Glucocorticoids were also lower: cortisol (p < 0.001), corticosterone (p < 0.001), cortisone (p < 0.006) 11-dehydrocorticosterone (p < 0.001) as well as cortisol:cortisone (p < 0.001). The presence of dehydroepiandrosterone was associated with 16-hydroxyprogesterone (p < 0.001), which was also significantly lower. Adrenal and gonadal steroid analysis showed unexpected steroid heterogeneity in normal young men. Testosterone constitutes 78% of the circulating free androgens with the 11-oxy androgens abundantly present in all participants significantly contributing 22%. In addition, a subset of men were identified with low circulating dehydroepiandrosterone who showed altered adrenal steroids with decreased glucocorticoids and decreased C11-oxy androgens. Analysis of the classical and 11-oxy androgens with the additional measurement of dehydroepiandrosterone and 16-hydroxyprogesterone may allow better diagnostic accuracy in androgen excess or deficiency.
Detection of ChatGPT fake science with the xFakeSci learning algorithm
Authors: Hamed Ahmed Abdeen , Wu Xindong
Published: July 2024

Generative AI tools exemplified by ChatGPT are becoming a new reality. This study is motivated by the premise that “AI generated content may exhibit a distinctive behavior that can be separated from scientific articles”. In this study, we show how articles can be generated using means of prompt engineering for various diseases and conditions. We then show how we tested this premise in two phases and prove its validity. Subsequently, we introduce xFakeSci, a novel learning algorithm, that is capable of distinguishing ChatGPT-generated articles from publications produced by scientists. The algorithm is trained using network models driven from both sources. To mitigate overfitting issues, we incorporated a calibration step that is built upon data-driven heuristics, including proximity and ratios. Specifically, from a total of a 3952 fake articles for three different medical conditions, the algorithm was trained using only 100 articles, but calibrated using folds of 100 articles. As for the classification step, it was performed using 300 articles per condition. The actual label steps took place against an equal mix of 50 generated articles and 50 authentic PubMed abstracts. The testing also spanned publication periods from 2010 to 2024 and encompassed research on three distinct diseases: cancer, depression, and Alzheimer’s. Further, we evaluated the accuracy of the xFakeSci algorithm against some of the classical data mining algorithms (e.g., Support Vector Machines, Regression, and Naive Bayes). The xFakeSci algorithm achieved F1 scores ranging from 80 to 94%, outperforming common data mining algorithms, which scored F1 values between 38 and 52%. We attribute the noticeable difference to the introduction of calibration and a proximity distance heuristic, which underscores this promising performance. Indeed, the prediction of fake science generated by ChatGPT presents a considerable challenge. Nonetheless, the introduction of the xFakeSci algorithm is a significant step on the way to combating fake science.
Mediating role of social disengagement and loneliness in the nexus between functional health and mental well-being in older individuals
Authors: Barman Papai , Rahut Dil Bahadur , Mishra Rakesh
Published: July 2024

Few studies have focused sufficiently on the intricate link between functional health and depression among older people aged 60 and above in India. Therefore, the current study investigates the association between functional health and depression among older Indian adults through the mediating role of social disengagement and loneliness and the moderating role of living arrangements using recent data from the Longitudinal Aging Study in India (LASI: 2017–2018). Composite International Diagnostic Interview-Short Form (CIDI-SF) for depression, the Activities of Daily Living (ADL) and Instrumental Activities of Daily Living (IADL) for functional health, and the indoor/outdoor activities, visits, and religious events for social disengagement were used. The feelings of loneliness and living arrangements were measured using single-item questions and surveys/interviews of household members. Bivariate analysis, logistic regression, and a Partial Least Squares-Structural Equation Model were adopted. The results show that older persons with functional health had 1.85 times higher odds of depression; similarly, those not engaging in social activities and experiencing loneliness were more likely to feel depressed. Living with someone was negatively linked to depression. A significant moderation by living arrangements in the functional health-depression relationship was also observed. The results also indicate significant mediating roles of social disengagement and loneliness, with 22.0% and 3.08% mediation effects, respectively. Therefore, this study recommends the provision of housing and social interaction among older people.
Impact of ZnO NPs on photosynthesis in rice leaves plants grown in saline-sodic soil
Authors: Dang Kun , Wang Yuxin , Tian Hao , Bai Jingjing , Cheng Xiyuan , Guo Liying , Zhang Qiang , Geng Yanqiu , Shao Xiwen
Published: July 2024

Saline-sodic stress restricts the absorption of zinc by rice, consequently impacting the photosynthesis process of rice plants. In this experiment, Landrace 9 was selected as the test material and the potting method was employed to investigate the influence of ZnO nanoparticles (ZnO NPs) on zinc absorption and chlorophyll fluorescence in rice grown in saline-sodic land. The research findings demonstrate that the application of ZnO NPs proves to be more advantageous for the growth of rice in saline-sodic soil. Notably, the application of ZnO NPs significantly decreases the levels of Na+ and MDA in rice leaves in saline-sodic soil, while increasing the levels of K+ and Zn2+. Additionally, ZnO NPs enhances the content of chloroplast pigments, specific energy flux, quantum yield, and the performance of active PSII reaction center (PIABS) in rice leaves under saline-sodic stress. Furthermore, the relative variable fluorescence (WK and VJ) and quantum energy dissipation rate (φDo) of rice are also reduced. Therefore, the addition of ZnO NPs enhances the transfer of electrons and energy within the rice photosystem when subjected to saline-sodic stress. This promotes photosynthesis in rice plants growing in saline-sodic land, increasing their resistance to saline-sodic stress and ultimately facilitating their growth and development.
JACQLQ subjective symptom questionnaire score and clinical test results for patients with allergic conjunctival disease
Authors: Yamana Yasuo , Yamana Satoshi , Uchio Eiichi
Published: July 2024

We investigated the relationship between subjective symptoms and objective findings in patients with allergic conjunctival diseases (ACD) and test results for tear total IgE (t-tIgE), conjunctival eosinophils (c-Eo), serum total IgE (s-tIgE), serum-antigen specific IgE (s-sIgE), and serum eosinophils (s-Eo). Subjective symptoms and objective findings of patients with ACD were evaluated using Japanese Allergic Conjunctival Disease Quality of Life Questionnaire (JACQLQ), which described disability score and emotional score written by patient and clinical findings score written by ophthalmologist. We investigated the relationship between questionnaire scores and laboratory data for t-tIgE, c-Eo, s-tIgE, s-sIgE, and s-Eo. Scores of impediments to life and of moods were highest in vernal keratoconjunctivitis among ACD. Cases with positive pollen-sIgE showed significantly more nasal symptom score than those with negative pollen-sIgE (P < 0.05). Cases with positive t-tIgE or c-Eo showed significantly more objective symptoms’ JACQLQ score than those with negative t-tIgE or c-Eo (P < 0.05), respectively. Cases positive for house dust/mite-sIgE, showed significantly more objective symptoms’ JACQLQ score than those without for house dust/mite-sIgE (P < 0.05). These results indicate that ACD could be analyzed more accurately by the combination of JACQLQ and laboratory data.
Evidence of contact-induced variability in industrially-fabricated highly-scaled MoS2 FETs
Authors: Panarella Luca , Kaczer Ben , Smets Quentin , Tyaginov Stanislav , Saraza Canflanca Pablo , Vici Andrea , Verreck Devin , Schram Tom , Lin Dennis , Knobloch Theresia , Grasser Tibor , Lockhart de la Rosa César , Kar Gouri S. , Afanas’ev Valeri
Published: July 2024

Evidence of microscopic inhomogeneities of the side source/drain contacts in 300 mm wafer integrated MoS2 field-effect transistors is presented. In particular, the presence of a limited number of low Schottky barrier spots through which channel carriers are predominantly injected is demonstrated by the dramatic current changes induced by individual charge traps located near the source contact. Two distinct types of “contact-impacting traps” are identified. Type-1 trap is adjacent to the contact interface and exchanges carriers with the metal. Its impact is only observable when the adjacent contact is the reverse-biased FET source and limits the channel current. Type-2 trap is located in the AlOx gate oxide interlayer, near the source contact, and exchanges carriers with the channel. Its capture/emission time constants exhibit both a gate and drain bias dependence due to the high sensitivity of the contact regions to the applied lateral and vertical fields. Unlike typical channel-impacting oxide traps, both types of reported defects affect the Schottky barrier height and width rather than the threshold voltage and result in giant random telegraph noise (RTN). These observations indicate that the contact quality and geometry play a fundamental role in the ultimate scaling of 2D FETs.
Measurement of the depth-dependent local dynamics in thin polymer films through rejuvenation of ultrastable glasses
Authors: Karimi Saba , Yin Junjie , Salez Thomas , Forrest James A.
Published: July 2024

The depth dependence of structural relaxation dynamics is a key part of understanding thin glassy films. Despite this importance and decades of research, a method to provide this information has proved elusive. We measure the isothermal rejuvenation of stable glass films of poly(styrene), and demonstrate that the propagation of the front responsible for the transformation to a supercooled-liquid state serves as a highly localized probe of the local dynamics of the supercooled liquid. We use this connection to probe the depth-dependent relaxation rate with nanometric precision for a series of polystyrene films over a range of temperatures near the bulk glass transition temperature. The analysis shows the spatial extent of enhanced surface mobility and reveals the existence of an unexpected large dynamical length scale in the system. The results are compared with the cooperative-string model for glassy dynamics. The data reveals that the film-thickness dependence of whole film properties arises mainly from the volume fraction of the near-surface region. While the dynamics farthest from the free surface shows the expected bulk-like temperature dependence, the dynamics in the near-surface region shows very little dependence on temperature. This technique can be used in a broad range of thin film materials to gain previously unattainable information about localized structural relaxation.
Atmosphere circulation patterns synchronize pan-Arctic glacier melt and permafrost thaw
Authors: Sasgen Ingo , Steinhoefel Grit , Kasprzyk Caroline , Matthes Heidrun , Westermann Sebastian , Boike Julia , Grosse Guido
Published: July 2024

The Arctic is changing rapidly due to the amplification of global temperature trends, causing profound impacts on the ice sheet in Greenland, glaciers, frozen ground, ecosystems, and societies. Here, we focus on impacts that atmospheric circulation causes in addition to the climate warming trends. We combine time series of glacier mass balance from temporal satellite gravimetry measurements (GRACE/GRACE-FO; 2002–2023), active layer thickness in permafrost areas from ESA’s Climate Change Initiative remote sensing and modelling product (2003–2019), and field measurements of the Circumpolar Active Layer Monitoring Network (2002–2023). Despite regional and system-related complexities, we identify robust covariations between these observations, which vary asynchronously between neighbouring regions and synchronously in regions antipodal to the North Pole. We reveal a close connection with dominant modes of atmosphere circulation, controlling about 75% of the common pan-Arctic impact variability (2002–2022), also affecting the Greenland Ice Sheet. We emphasize that it is necessary to consider such atmospheric driving patterns when projecting impacts, particularly caused by extremes, in an increasingly warmer Arctic.
Effects of arbuscular mycorrhizal fungi in the rhizosphere of two olive (Olea europaea) varieties Arbequina and Barnea under water deficit conditions
Authors: Bonetto Mariana , Cofré Noelia , Calvo Franco , Silvente Sonia
Published: July 2024

One strategy to improve olive (Olea europaea) tree drought tolerance is through the symbiosis of arbuscular mycorrhizal fungi (AMF), which helps alleviate water deficit through a combination of morphophysiological effects. Cuttings of olive varieties Arbequina (A) and Barnea (B) were grown with (+AMF) or without (−AMF) inoculum in the olive grove rhizosphere soil. One year after establishment, pots were exposed to four different water regimes: (1) control (100% of crop evapotranspiration); (2) short-period drought (20 days); (3) long-period drought (25 days); and (4) rewatering (R). To evaluate the influence of AMF on tolerance to water stress, stem water potential, stomatal conductance and the biomarkers for water deficit malondialdehyde, proline, soluble sugars, phenols, and flavonoids were evaluated at the end of the irrigation regimes. Stem water potential showed higher values in A(+) and B(+) in all water conditions, and the opposite was true for stomatal conductance. For proline and soluble sugars, the stem water potential trend is repeated with some exceptions. AMF inoculum spore communities from A(+ and −) and B(+ and −) were characterised at the morphospecies level in terms of richness and abundance. Certain morphospecies were identified as potential drought indicators. These results highlight that the benefits of symbiotic relationships between olive and native AMF can help to mitigate the effects of abiotic stress in soils affected by drought.
Investigating influences on pet attachment in France: Insights from the adaptation of the French Lexington Attachment to Pets Scale
Authors: Blanchard Tiphaine , Zaboski-Pena Luana , Harroche Ilana , Théodon Ophélie , Meynadier Annabelle
Published: July 2024

This study aimed to assess the French version of the Lexington Attachment to Pets Scale (LAPS) and to explore the factors influencing the attachment between French pet owners and their cats and dogs. Given the absence of a French tool to evaluate pet attachment, LAPS was translated into French using a rigorous back-translation method. An online survey was developed to assess LAPS scores, socio-demographic data, and owner characteristics, resulting in 1872 eligible responses. The French LAPS demonstrated strong reliability as well as good internal consistency and repeatability. Median LAPS scores were higher for dog owners (58.5) compared with cat owners (52.0), while individuals who owned both species showed significantly higher scores for their dogs than for their cats. Factors associated with higher attachment scores for owners of both species included the female gender of the owner, living without children, and lower educational background. This study reinforces the existing body of evidence about gender and pet type differences in terms of attachment and highlights the potential influence of social desirability bias. It provides valuable insights into the complexities of human-animal bonds in the French context and shows the influence of social standards on pet attachment.
Public Territorial Governance and Community-Based Tourism for Sustainable Local Development: A Case-Study of Paraty, Brazil
Authors: de Almeida Thiago Chagas , Emmendoerfer Magnus Luiz , Knupp Marcos Eduardo Carvalho Gonçalves
Published: July 2024

Community-Based Tourism (CBT) is a mode of tourism management that has several foundations articulated for Sustainable Local Development (SLD). Nevertheless, achieving its principles often depends on the interaction with other territorial actors, that is, on Public Territorial Governance (PTG). Consequently, this case study identifies how PTG mechanisms can involve CBT in the process of co-promoting SLD by focusing on the Paraty/Brazil Municipal Tourism Council (COMTUR). This was studied because it is a PTG space open to local CBT initiatives that discuss SLD-related agendas. We collected data through the document analysis of COMTUR minutes and the on-site observation of COMTUR meetings. Data were interpreted by the thematic content analysis technique. The results show that PTG can involve CBT in the process of co-promotion of SLD, through four main elements: Co-need, co-potentiality, co-effectiveness, and co-legitimacy.

Information

© The Authors 2024
Expression of an engineered salt-inducible proline biosynthetic operon in a glutamic acid over-producing mutant, Halomonas elongata GOP, confers increased proline yield due to enhanced growth under high-salinity conditions
Authors: Khanh Huynh Cong , Kaothien-Nakayama Pulla , Zou Ziyan , Nakayama Hideki
Published: July 2024

L-Proline (Pro) is an essential amino acid additive in livestock and aquaculture feeds. Previously, we created a Pro overproducing Halomonas elongata HN6 by introducing an engineered salt-inducible Pro biosynthetic mCherry-proBm1AC operon and deleting a putA gene that encoded a Pro catabolic enzyme in the genome of H. elongata OUT30018. Here, we report a generation of a novel Pro overproducing H. elongata HN10 strain with improved salt tolerance and higher Pro yield by expressing the mCherry-proBm1AC operon and deleting the putA gene in the genome of a spontaneous mutant H. elongata Glutamic acid Over-Producing, which overproduces glutamic acid (Glu) that is a precursor for Pro biosynthesis. The optimal salt concentration for growth of H. elongata HN10 was found to be 7% to 8% w/v NaCl, and the average Pro yield of 166 mg/L was achieved when H. elongata HN10 was cultivated in M63 minimal medium containing 4% w/v glucose and 8% w/v NaCl.
A comprehensive review and comparison of existing computational methods for protein function prediction
Authors: Lin Baohui , Luo Xiaoling , Liu Yumeng , Jin Xiaopeng
Published: July 2024

Protein function prediction is critical for understanding the cellular physiological and biochemical processes, and it opens up new possibilities for advancements in fields such as disease research and drug discovery. During the past decades, with the exponential growth of protein sequence data, many computational methods for predicting protein function have been proposed. Therefore, a systematic review and comparison of these methods are necessary. In this study, we divide these methods into four different categories, including sequence-based methods, 3D structure-based methods, PPI network-based methods and hybrid information-based methods. Furthermore, their advantages and disadvantages are discussed, and then their performance is comprehensively evaluated and compared. Finally, we discuss the challenges and opportunities present in this field.
Utilizing profile hidden Markov model databases for discovering viruses from metagenomic data: a comprehensive review
Authors: Yu Runzhou , Huang Ziyi , Lam Theo Y C , Sun Yanni
Published: July 2024

Profile hidden Markov models (pHMMs) are able to achieve high sensitivity in remote homology search, making them popular choices for detecting novel or highly diverged viruses in metagenomic data. However, many existing pHMM databases have different design focuses, making it difficult for users to decide the proper one to use. In this review, we provide a thorough evaluation and comparison for multiple commonly used profile HMM databases for viral sequence discovery in metagenomic data. We characterized the databases by comparing their sizes, their taxonomic coverage, and the properties of their models using quantitative metrics. Subsequently, we assessed their performance in virus identification across multiple application scenarios, utilizing both simulated and real metagenomic data. We aim to offer researchers a thorough and critical assessment of the strengths and limitations of different databases. Furthermore, based on the experimental results obtained from the simulated and real metagenomic data, we provided practical suggestions for users to optimize their use of pHMM databases, thus enhancing the quality and reliability of their findings in the field of viral metagenomics.
Statistical modeling and significance estimation of multi-way chromatin contacts with HyperloopFinder
Authors: Wang Weibing , Ye Yusen , Gao Lin
Published: July 2024

Recent advances in chromatin conformation capture technologies, such as SPRITE and Pore-C, have enabled the detection of simultaneous contacts among multiple chromatin loci. This has made it possible to investigate the cooperative transcriptional regulation involving multiple genes and regulatory elements at the resolution of a single molecule. However, these technologies are unavoidably subject to the random polymer looping effect and technical biases, making it challenging to distinguish genuine regulatory relationships directly from random polymer interactions. Here, we present HyperloopFinder, a method for identifying regulatory multi-way chromatin contacts (hyperloops) by jointly modeling the random polymer looping effect and technical biases to estimate the statistical significance of multi-way contacts. The results show that our model can accurately estimate the expected interaction frequency of multi-way contacts based on the distance distribution of pairwise contacts, revealing that most multi-way contacts can be formed by randomly linking the pairwise contacts adjacent to each other. Moreover, we observed the spatial colocalization of the interaction sites of hyperloops from image-based data. Our results also revealed that hyperloops can function as scaffolds for the cooperation among multiple genes and regulatory elements. In summary, our work contributes novel insights into higher-order chromatin structures and functions and has the potential to enhance our understanding of transcriptional regulation and other cellular processes.
Enhancing vascular access planning in CKD: validating the 40% KFRE threshold for predicting ESKD in a French retrospective cohort study
Authors: Ingwiller Maxime , Keller Nicolas , Krummel Thierry , Prinz Eric , Steinmetz Lydie , Hannedouche Thierry , Florens Nans
Published: July 2024

Background

Establishing the optimal timing for creating vascular access in patients with chronic kidney disease (CKD) is a critical and challenging aspect of patient management. The Kidney Disease: Improving Global Outcomes guidelines propose using a 40% 2-year threshold based on the Kidney Failure Risk Equation (KFRE) for this purpose. However, the effectiveness of this threshold compared with traditional methods, such as estimated glomerular filtration rate (eGFR), is not well-established.

Methods

In this monocentric retrospective cohort study, we analyzed data from patients referred for vascular mapping before arteriovenous fistula (AVF) creation between April 2013 and June 2023. The study aimed to compare the ≥40% 2-year KFRE threshold with a <15 mL/min/1.73 m² eGFR threshold for predicting end-stage kidney disease (ESKD). We assessed the probability of ESKD, considering death before AVF creation as a competing risk. Discrimination between KFRE and eGFR was evaluated using C-statistics.

Results

The study included 238 patients with a mean age of 65.2 years and a mean eGFR of 13.3 mL/min/1.73 m². Over a median follow-up of 10.7 months, 178 patients developed ESKD, and 21 died before ESKD. Probability of ESKD at 1 year was 77.6% (95% CI 69.9%–85.3%) using a ≥40% 4-variable KFRE threshold versus 65.8% (95% CI 58.3%–73.3%) using a <15 mL/min/1.73 m² eGFR threshold. The C-statistics indicated better predictive ability for the 8-variable KFRE at 6 months [0.82 (95% CI 0.76–0.88)], while both 4- and 8-variable KFRE models were effective for 1-year predictions [0.835 (95% CI 0.78–0.89) and 0.82 (95% CI 0.76–0.875), respectively]. Sensitivity and specificity analyses favored the ≥40% KFRE threshold over the eGFR threshold.

Conclusions

This study suggests that using a ≥40% 2-year KFRE threshold for planning vascular access in CKD patients is promising and potentially superior to the traditional <15 mL/min/1.73 m² eGFR threshold. This approach may offer a balance between minimizing premature AVF creation and the risk of starting dialysis via a central venous catheter.
Physics-guided deep learning-based inversion for airborne electromagnetic data
Authors: Wu Sihong , Huang Qinghua , Zhao Li
Published: July 2024

The Earth's subsurface structure provides critical insights into sustainable resource management and geologic evolution. The airborne electromagnetic (AEM) method is an efficient data acquisition technique and can be used to image the underground resistivity structure with high spatial resolution. However, inversion of the increasingly huge volume of AEM data poses a heavy computational burden. In this study, we develop a hybrid deep learning-based approach by using the physics-guided neural network (PGNN) which incorporates the governing physical laws into the loss function to solve the AEM inverse problem. The PGNN integrates the strength of data-driven method for representation learning with electromagnetic laws and allows for the underlying physical constraints to be strictly satisfied. We validate the effectiveness of our approach using both synthetic and field datasets. Compared with the classic Gauss–Newton method, our PGNN inversion system shows strong robustness against multiple noise sources and reduces the risk of being trapped in local extrema. Moreover, the PGNN-inverted results are physically more consistent with the AEM observations compared to the purely data-driven approach. Application to the field AEM data from Northern Australia demonstrates that the PGNN-based inversion framework effectively estimates the subsurface electrical properties with considerable lateral continuity and significantly higher efficiency, completing the inversion of more than 2734000 AEM soundings taking only minutes on a common PC. Our proposed PGNN-based method shows great promise for large-scale underground resistivity imaging, and the well-identified subsurface resistivity structure can effectively improve our understanding of resource distributions and geological hazards.
Lateral and vertical variations of seismic anisotropy in the lithosphere–asthenosphere system underneath Central Europe from long-term splitting measurements
Authors: Fröhlich Yvonne , Grund Michael , Ritter Joachim R R
Published: July 2024

Backazimuthal variations in the shear wave splitting of core-refracted shear waves (SKS, SKKS and PKS phases, jointly referred to as XKS) at the Black Forest Observatory (BFO, Southwest Germany) indicate small-scale lateral and partly vertical variations of the seismic anisotropy. However, existing anisotropy studies and models for the nearby Upper Rhine Graben (URG) area in the northern Alpine foreland are mostly based on short-term recordings and by this suffer from a limited backazimuthal coverage and averaging over a wide or the whole backazimuth range. To identify and delimit laterally confined anisotropy regimes in this region, we carry out XKS splitting measurements at six neighbouring (semi-)permanent broad-band seismological recording stations (interstation distance 10–80 km). We manually analyse long-term (partly > 20 yr) recordings to achieve a sufficient backazimuthal coverage to resolve complex anisotropy. The splitting parameters (fast polarization direction $\phi $, delay time $\delta t$) are determined in a single- and multi-event analysis. We test structural anisotropy models with one layer with horizontal or tilted symmetry axis and with two layers with horizontal symmetry axes (transverse isotropy). To account for lateral variations around a single recording site, modelling is compared for the whole and for limited backazimuth ranges. Based on this, we provide a 3-D block model with spatial variation of anisotropic properties. Based on delay times > 0.3 s and missing discrepancies between SKS and SKKS phases, which do not support lower mantle anisotropy, the found anisotropy is placed in the lithosphere and asthenosphere. The spatial distribution as well as the lateral and backazimuthal variations of the splitting parameters confirm lateral and partly vertical variations in anisotropy. On the east side of the URG, we suggest two anisotropic layers in the Moldanubian Zone (south) and one anisotropic layer in the Saxothuringian Zone (north). In the Moldanubian Zone, a change of the fast polarization directions is observed between the east and the west side of the URG, indicating different textures. At the boundary between the two terranes, an inclined anisotropy is modelled which may be related with deformation during Variscan subduction. Regarding the observation of numerous null measurements and inconsistent splitting parameters, especially (southwest of BFO) in the southern URG, different hypothesis are tested: scattering of the seismic wavefield due to small-scale lateral heterogeneities, a vertical a-axis due to a vertical mantle flow related to the Kaiserstuhl Volcanic Complex, as well as a different preferred orientation of the olivine crystals (not A-type, but C-type) due to specific ambient conditions (high temperature, water content).