bluuebunny/crossref_metadata_2025_split huggingface dataset:
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

AbstractSaline-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

AbstractWe 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

AbstractEvidence 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

AbstractThe 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

AbstractThe 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

Abstract
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

Summary
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

ABSTRACT
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

Abstract
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

Abstract
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

Abstract
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

ABSTRACT

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 &lt;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 &lt;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 &lt;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

SUMMARY
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.