bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Present and Future Role of Rice‐Animal Co‐Culture Systems in Meeting Sustainable Development Goals
Authors: Chen Jie , Gao Guoping , Zhang Wenbo , Zhao Zhen , Penuelas Josep 
Published: August 2023

AbstractRice‐animal co‐culture (RAC) systems are an integrated farming approach to mitigate the diverse challenges facing the food system. Studies of the production potential and ecological mechanisms of RAC systems have demonstrated natural advantages over traditional production systems. The quantification of the advantages and the potential promotion of RAC systems at regional and global scales, however, remains unclear. Writing in Earth's Future, Cui et al. (2023, https://doi.org/10.1029/2022EF002984) comprehensively assessed an ecological RAC system and identified the potential benefits of global promotion using a meta‐analysis. In this commentary, we contextualized Cui et al.'s (2023, https://doi.org/10.1029/2022EF002984) study and further theoretically clarified the connections of RAC systems to the various sustainable development goals (SDGs) and targets, with references to the officially released list of SDG indicators. Moreover, we discussed the limitation of the current studies and pointed out some potential directions for future research to understand the present and future roles of RAC systems in meeting the multiple SDGs.
The 2022 Massive Open Online Course (MOOC) to train physiotherapists in the management of people with spinal cord injuries: a qualitative and quantitative analysis of learners’ experiences and its impact
Authors: Glinsky Joanne V. , Ilha Jocemar , Xiong Yuan , Gomez Guillermo , Rostagnor Stephan , Martín-Manjarrés Soraya , Tranter Keira , Muldoon Stephen , Weerts Eric , Harvey Lisa A. 
Published: August 2023

Abstract
Study design
Observational.

Objectives
To determine the learners’ experience and the impact of a Massive Open Online Course (MOOC) conducted to teach physiotherapists about the management of people with spinal cord injuries (SCI).

Methods
A SCI MOOC for physiotherapists was run in 5 different languages at the end of 2022. Qualitative and quantitative data were collected from different sources including registration details, pre- and post-MOOC Knowledge Assessments, a post-MOOC Evaluation, social media posts and online tracking of websites and emails. The data were used to answer four key questions: (i) what was the reach of the MOOC, (ii) what did participants think about the MOOC (iii) did the MOOC change participants’ knowledge and/or confidence, and (iv) did the MOOC change participants’ clinical practice or the way they teach others?

Results
25,737 people from 169 countries registered for the MOOC. 98% of participants who completed the Evaluation (n = 2281) rated the MOOC as either “good” or “very good”. Participants’ knowledge improved by a median (IQR) of 25% (10 to 45%) (n = 4016 participants) on the MOOC Knowledge Assessment. Participants reported changes in confidence, and intentions to change clinical practice and incorporate what they had learnt into the way they teach others in response to the MOOC.

Conclusion
The MOOC provided an efficient way to increase physiotherapists’ knowledge about the physiotherapy management of people with SCI. Participants enjoyed the MOOC, and indicated an intention to change clinical practice and the way they taught others.
Association between cumulative psychosocial adversity in the family and ADHD and autism: a family-based cohort study
Authors: Kanina Aleksandra , Larsson Henrik , Sjölander Arvid , Butwicka Agnieszka , Taylor Mark J. , Martini Miriam I. , Lichtenstein Paul , Lundberg Frida E. , Onofrio Brian M. D’ , Rosenqvist Mina A. 
Published: August 2023

AbstractCumulative exposure to psychosocial adversity at an early age has been shown to be a risk factor for attention-deficit hyperactivity disorder (ADHD) and autism that often co-occur. However, it is not clear if this association reflects a causal effect or familial confounding. We aimed to assess whether cumulative psychosocial adversity in the family increases the risk for ADHD and autism in offspring while accounting for unmeasured familial confounding. We used a population-based cohort of 1,877,901 individuals born in Sweden between 1990 and 2009. Participants were followed from the age of 3 until 2013, with a median follow up time of 13.8 years. We created a cumulative index based on 7 psychosocial adversity factors. We used Cox regression to estimate the hazard ratios (HRs) relating neurodevelopmental conditions to cumulative psychosocial adversity. To address familial confounding, the analyses were repeated in groups of relatives of different kinship: siblings and half-siblings and cousins. A dose-response relationship was observed between cumulative exposure to psychosocial adversity and ADHD at a general population level (covariate adjusted HRs (aHRs) with 95% confidence intervals ranged from 1.55 [one adversity; 1.53–1.58] to 2.65 [ ≥ 4 adversities; 1.98–3.54]). No clear dose-response relation was seen for autism (aHRs ranged from 1.04 [.59–1.84] to 1.37 [1.30–1.45]). HRs of ADHD and autism decreased with increasing level of kinship in the analysis of relatives. Cumulative exposure to psychosocial adversity was associated with both ADHD and autism in the general population, these associations were partly explained by unmeasured familial confounding between relatives. This highlights the need for using family-based designs in studies of psychosocial adversity and ADHD and autism.
Greatly enhanced tunneling electroresistance in ferroelectric tunnel junctions with a double barrier design
Authors: Xiao Wei , Zheng Xiaohong , Hao Hua , Kang Lili , Zhang Lei , Zeng Zhi 
Published: August 2023

AbstractWe propose that the double barrier effect is expected to enhance the tunneling electroresistance (TER) in the ferroelectric tunnel junctions (FTJs). To demonstrate the feasibility of this mechanism, we design a model structure of Pt/BaTiO3/LaAlO3/Pt/BaTiO3/LaAlO3/Pt double barrier ferroelectric tunnel junction (DB-FTJ), which can be considered as two identical Pt/BaTiO3/LaAlO3/Pt single barrier ferroelectric tunnel junctions (SB-FTJs) connected in series. Based on density functional calculation, we obtain the giant TER ratio of 2.210 × 108% in the DB-FTJ, which is at least three orders of magnitude larger than that of the SB-FTJs of Pt/BaTiO3/LaAlO3/Pt, together with an ultra-low resistance area product (0.093 KΩμm2) in the high conductance state of the DB-FTJ. Moreover, it is possible to control the direction of polarization of the two single ferroelectric barriers separately and thus four resistance states can be achieved, making DB-FTJs promising as multi-state memory devices.
Single-cell multiomic analysis of thymocyte development reveals drivers of CD4+ T cell and CD8+ T cell lineage commitment
Authors: Steier Zoë , Aylard Dominik A. , McIntyre Laura L. , Baldwin Isabel , Kim Esther Jeong Yoon , Lutes Lydia K. , Ergen Can , Huang Tse-Shun , Robey Ellen A. , Yosef Nir , Streets Aaron 
Published: August 2023

AbstractThe development of CD4+ T cells and CD8+ T cells in the thymus is critical to adaptive immunity and is widely studied as a model of lineage commitment. Recognition of self-peptide major histocompatibility complex (MHC) class I or II by the T cell antigen receptor (TCR) determines the CD8+ or CD4+ T cell lineage choice, respectively, but how distinct TCR signals drive transcriptional programs of lineage commitment remains largely unknown. Here we applied CITE-seq to measure RNA and surface proteins in thymocytes from wild-type and T cell lineage-restricted mice to generate a comprehensive timeline of cell states for each T cell lineage. These analyses identified a sequential process whereby all thymocytes initiate CD4+ T cell lineage differentiation during a first wave of TCR signaling, followed by a second TCR signaling wave that coincides with CD8+ T cell lineage specification. CITE-seq and pharmaceutical inhibition experiments implicated a TCR–calcineurin–NFAT–GATA3 axis in driving the CD4+ T cell fate. Our data provide a resource for understanding cell fate decisions and implicate a sequential selection process in guiding lineage choice.
Evaluating the role of the nuclear microenvironment in gene function by population-based modeling
Authors: Yildirim Asli , Hua Nan , Boninsegna Lorenzo , Zhan Yuxiang , Polles Guido , Gong Ke , Hao Shengli , Li Wenyuan , Zhou Xianghong Jasmine , Alber Frank 
Published: August 2023

AbstractThe nuclear folding of chromosomes relative to nuclear bodies is an integral part of gene function. Here, we demonstrate that population-based modeling—from ensemble Hi-C data—provides a detailed description of the nuclear microenvironment of genes and its role in gene function. We define the microenvironment by the subnuclear positions of genomic regions with respect to nuclear bodies, local chromatin compaction, and preferences in chromatin compartmentalization. These structural descriptors are determined in single-cell models, thereby revealing the structural variability between cells. We demonstrate that the microenvironment of a genomic region is linked to its functional potential in gene transcription, replication, and chromatin compartmentalization. Some chromatin regions feature a strong preference for a single microenvironment, due to association with specific nuclear bodies in most cells. Other chromatin shows high structural variability, which is a strong indicator of functional heterogeneity. Moreover, we identify specialized nuclear microenvironments, which distinguish chromatin in different functional states and reveal a key role of nuclear speckles in chromosome organization. We demonstrate that our method produces highly predictive three-dimensional genome structures, which accurately reproduce data from a variety of orthogonal experiments, thus considerably expanding the range of Hi-C data analysis.
Machine learning-based prediction of longitudinal cognitive decline in early Parkinson’s disease using multimodal features
Authors: Almgren Hannes , Camacho Milton , Hanganu Alexandru , Kibreab Mekale , Camicioli Richard , Ismail Zahinoor , Forkert Nils D. , Monchi Oury 
Published: August 2023

AbstractPatients with Parkinson’s Disease (PD) often suffer from cognitive decline. Accurate prediction of cognitive decline is essential for early treatment of at-risk patients. The aim of this study was to develop and evaluate a multimodal machine learning model for the prediction of continuous cognitive decline in patients with early PD. We included 213 PD patients from the Parkinson’s Progression Markers Initiative (PPMI) database. Machine learning was used to predict change in Montreal Cognitive Assessment (MoCA) score using the difference between baseline and 4-years follow-up data as outcome. Input features were categorized into four sets: clinical test scores, cerebrospinal fluid (CSF) biomarkers, brain volumes, and genetic variants. All combinations of input feature sets were added to a basic model, which consisted of demographics and baseline cognition. An iterative scheme using RReliefF-based feature ranking and support vector regression in combination with tenfold cross validation was used to determine the optimal number of predictive features and to evaluate model performance for each combination of input feature sets. Our best performing model consisted of a combination of the basic model, clinical test scores and CSF-based biomarkers. This model had 12 features, which included baseline cognition, CSF phosphorylated tau, CSF total tau, CSF amyloid-beta1-42, geriatric depression scale (GDS) scores, and anxiety scores. Interestingly, many of the predictive features in our model have previously been associated with Alzheimer’s disease, showing the importance of assessing Alzheimer’s disease pathology in patients with Parkinson’s disease.
Certification of qubits in the prepare-and-measure scenario with large input alphabet and connections with the Grothendieck constant
Authors: Diviánszky Péter , Márton István , Bene Erika , Vértesi Tamás 
Published: August 2023

AbstractWe address the problem of testing the quantumness of two-dimensional systems in the prepare-and-measure (PM) scenario, using a large number of preparations and a large number of measurement settings, with binary outcome measurements. In this scenario, we introduce constants, which we relate to the Grothendieck constant of order 3. We associate them with the white noise resistance of the prepared qubits and to the critical detection efficiency of the measurements performed. Large-scale numerical tools are used to bound the constants. This allows us to obtain new bounds on the minimum detection efficiency that a setup with 70 preparations and 70 measurement settings can tolerate.
Development of chitin nanofiber coatings for prolonging shelf life and inhibiting bacterial growth on fresh cucumbers
Authors: Tanpichai Supachok , Pumpuang Laphaslada , Srimarut Yanee , Woraprayote Weerapong , Malila Yuwares 
Published: August 2023

AbstractThe widespread usage of petroleum-based polymers as single-use packaging has had harmful effects on the environment. Herein, we developed sustainable chitin nanofiber (ChNF) coatings that prolong the shelf life of fresh cucumbers and delay the growth of pathogenic bacteria on their surfaces. ChNFs with varying degrees of acetylation were successfully prepared via deacetylation using NaOH with treatment times of 0–480 min and defibrillated using mechanical blending. With longer deacetylation reaction times, more acetamido groups (–NHCOCH3) in chitin molecules were converted to amino groups (–NH2), which imparted antibacterial properties to the ChNFs. The ChNF morphologies were affected by deacetylation reaction time. ChNFs deacetylated for 240 min had an average width of 9.0 nm and lengths of up to several μm, whereas rod-like structured ChNFs with a mean width of 7.3 nm and an average length of 222.3 nm were obtained with the reaction time of 480 min. Furthermore, we demonstrated a standalone ChNF coating to extend the shelf life of cucumbers. In comparison to the rod-like structured ChNFs, the 120 and 240-min deacetylated ChNFs exhibited a fibril-like structure, which considerably retarded the moisture loss of cucumbers and the growth rate of bacteria on their outer surfaces during storage. Cucumbers coated with these 120 and 240-min deacetylated ChNFs demonstrated a lower weight loss rate of ⁓ 3.9% day−1 compared to the uncoated cucumbers, which exhibited a weight loss rate of 4.6% day−1. This protective effect provided by these renewable ChNFs holds promising potential to reduce food waste and the use of petroleum-based packaging materials.
Colour information biases facial age estimation and reduces inter-observer variability
Authors: Hsieh Jean Y. J. , Boyce W. Paul , Goddard Erin , Clifford Colin W. G. 
Published: August 2023

AbstractAge estimation is a perceptual task that people perform automatically and effortlessly on a daily basis. Colour has been identified as one of the facial cues that contributes to age perception. To investigate further the role of colour in age perception, we manipulated the chromatic content of facial images holistically. In Experiment 1, images were shown in colour or grey scale; in Experiment 2, images were shown with red–green contrast increased or decreased; in Experiment 3, images were shown with modified yellow–blue contrast. We examined whether the presence of chromatic information biases the perception of age and/or affects inter-observer variability in age judgements, and whether specific chromatic information affects the perception of age. We found that the same face tended to be judged as younger with increased red–green contrast compared to decreased red–green contrast, suggesting that red–green contrast directly affects age perception. Inter-observer variability in age ratings was significantly lower when participants were asked to rate colour compared with grey scale versions of images. This finding indicates that colour carries information useful cues for age estimation.
Diffusible signal factors (DSFs) bind and repress VirF, the leading virulence activator of Shigella flexneri
Authors: Trirocco Rita , Pasqua Martina , Tramonti Angela , Colonna Bianca , Paiardini Alessandro , Prosseda Gianni 
Published: August 2023

AbstractShigella, the aetiological agent of human bacillary dysentery, controls the expression of its virulence determinants through an environmentally stimulated cascade of transcriptional activators. VirF is the leading activator and is essential for proper virulence expression. In this work, we report on in vitro and in vivo experiments showing that two autoinducers of the DSF family, XcDSF and BDSF interact with the jelly roll module of VirF causing its inhibition and affecting the expression of the entire virulence system of Shigella, including its ability to invade epithelial cells. We propose a molecular model explaining how the binding of XcDSF and BDSF causes inhibition of VirF by preventing its dimerization. Overall, our experimental results suggest that XcDSF and BDSF may contribute to ”colonisation resistance” in the human gut or, alternatively, may be exploited for the fine-tuning of Shigella virulence expression as the bacterium migrates from the lumen to approach the intestinal mucosa. Our findings also stress how a detailed understanding of the interaction of DSF ligands with VirF may contribute to the rational development of innovative antivirulence drugs to treat shigellosis.
Quantitative analysis of choroidal morphology in preeclampsia during pregnancy according to retinal change
Authors: Kim In Kee , Shin Jae Eun , Kim Min Jeong , Ra Ho , Baek Jiwon 
Published: August 2023

AbstractWe sought to investigate changes in choroidal hemodynamics in preeclampsia according to presence of retinal change by quantitatively assessing choroidal vessels using optical coherence tomography (OCT). This retrospective study included 106 eyes (of 53 patients) with preeclampsia, including 70 eyes without retinal change in patients with preeclampsia (Group A), 22 eyes with retinal change in patients with preeclampsia (Group B), and 14 eyes of normal pregnant women (controls). Subfoveal choroidal thickness (SFCT) was measured on OCT B-scan images, and choroidal vessel densities (CVDs) were calculated using binarized OCT B-scan and en face images. Their values were then correlated with clinical parameters associated with preeclampsia. SFCT was greater in Group B compared to Group A or controls (354.32 ± 65.13 vs. 288 ± 55.68 or 277.21 ± 50.08, both P < 0.001). CVD on B-scan images was greater in Group B compared to Group A or controls (76.4 ± 4.9 vs. 73.7 ± 5.3 or 71.5 ± 5.1; both P ≤ 0.046). CVD on en face images was also greater in Group B compared to Group A or controls (64.7 ± 0.8 vs. 63.6 ± 1.5 or 63.3 ± 1.3; both P ≤ 0.001). SFCT and CVD positively correlated with each other (P ≤ 0.009) and were greater in patients with blurred vision and vaginal bleeding (P ≤ 0.020 for blurred vision and P ≤ 0.024 for vaginal bleeding). SFCT and CVDs were higher in preeclampsia patients with retinal change compared to those without retinal change or controls. Both SFCT and CVD showed association with blurred vision and vaginal bleeding.
Water-efficient genotypes along with conservation measures significantly reduce the green and blue water footprints in sugarcane (Saccharum spp.)
Authors: Tayade A. S. , Vasantha S. , Anusha S. , Kumar R. Arun , Hemaprabha G. , Geetha P. , Krishnapriya V. , Reddy K. Sammi , Bhatt Rajan , Siddiqui Manzer H. , Kesawat Mahipal Singh 
Published: August 2023

AbstractSugarcane crop is irrigated using surface, overhead, and drip irrigation methods. Increased water use in sugarcane is a major concern around the world, implying the need for water accounting, developing water-efficient hybrids and water-saving agro-techniques for long-term conservation and use of water. “Water Footprint (WF)” is a measure of both direct and indirect water usage accountable for any product and/or process. In praxis, ‘Green Water Footprint’ (GWF) and ‘Blue Water Footprint’ (BWF) are extremely crucial for the restoration of essential ecosystem services (ES), such as sugarcane production. The WF metric was used as a priority tool in our study to evaluate water-efficient sugarcane hybrids, germplasm clones, deficit irrigation scheduling, crop geometry, and water conservation measures. Precise and accurate WF quantification would supplement the decision-making processes for managing available water resources in sugarcane agriculture. In split plot experimental design two research investigations on water management in sugarcane were undertaken at the ICAR-Sugarcane Breeding Institute, Coimbatore, Tamil Nadu, India. The major objective of the research trails was to find out suitable sugarcane hybrids and agronomic management practices to minimise water usage in sugarcane cultivation in water stressed and drought prone areas of tropical India. Our investigation comprised two phases; the first one being assessment of the impact of deficit irrigation scheduling, planting techniques and water conservation measures in sugarcane production, while the second phase dealt with genotypic evaluation under variable irrigation scheduling. Results showed that BWF reduced significantly in the first ratoon crop due to deficit irrigation scheduling coupled with planting of two budded setts and application of sugarcane trash at the rate of 5 t ha−1. Sugarcane hybrids viz., Co 85019, Co 10026, Co 12009, Co 13014, Co 14002, Co 14025, Co 15015, and Co 15018 were more water efficient, with a lower total WF. Among the germplasm clones, Fiji 55, ISH 111, ISH 107, Pathri, and Gungera exhibited lower GWF, BWF and total WF.
Image denoising in acoustic microscopy using block-matching and 4D filter
Authors: Gupta Shubham Kumar , Pal Rishant , Ahmad Azeem , Melandsø Frank , Habib Anowarul 
Published: August 2023

AbstractScanning acoustic microscopy (SAM) is a label-free imaging technique used in biomedical imaging, non-destructive testing, and material research to visualize surface and sub-surface structures. In ultrasonic imaging, noises in images can reduce contrast, edge and texture details, and resolution, negatively impacting post-processing algorithms. To reduce the noises in the scanned image, we have employed a 4D block-matching (BM4D) filter that can be used to denoise acoustic volumetric signals. BM4D filter utilizes the transform domain filtering technique with hard thresholding and Wiener filtering stages. The proposed algorithm produces the most suitable denoised output compared to other conventional filtering methods (Gaussian filter, median filter, and Wiener filter) when applied to noisy images. The output from the BM4D-filtered images was compared to the noise level with different conventional filters. Filtered images were qualitatively analyzed using metrics such as structural similarity index matrix (SSIM) and peak signal-to-noise ratio (PSNR). The combined qualitative and quantitative analysis demonstrates that the BM4D technique is the most suitable method for denoising acoustic imaging from the SAM. The proposed block matching filter opens a new avenue in the field of acoustic or photoacoustic image denoising, particularly in scenarios with poor signal-to-noise ratios.