bluuebunny/crossref_metadata_2025_split huggingface dataset:
Groundwater-dependent ecosystem map exposes global dryland protection needs
Authors: Rohde Melissa M. , Albano Christine M. , Huggins Xander , Klausmeyer Kirk R. , Morton Charles , Sharman Ali , Zaveri Esha , Saito Laurel , Freed Zach , Howard Jeanette K. , Job Nancy , Richter Holly , Toderich Kristina , Rodella Aude-Sophie , Gleeson Tom , Huntington Justin , Chandanpurkar Hrishikesh A. , Purdy Adam J. , Famiglietti James S. , Singer Michael Bliss , Roberts Dar A. , Caylor Kelly , Stella John C. 
Published: July 2024

AbstractGroundwater is the most ubiquitous source of liquid freshwater globally, yet its role in supporting diverse ecosystems is rarely acknowledged1,2. However, the location and extent of groundwater-dependent ecosystems (GDEs) are unknown in many geographies, and protection measures are lacking1,3. Here, we map GDEs at high-resolution (roughly 30 m) and find them present on more than one-third of global drylands analysed, including important global biodiversity hotspots4. GDEs are more extensive and contiguous in landscapes dominated by pastoralism with lower rates of groundwater depletion, suggesting that many GDEs are likely to have already been lost due to water and land use practices. Nevertheless, 53% of GDEs exist within regions showing declining groundwater trends, which highlights the urgent need to protect GDEs from the threat of groundwater depletion. However, we found that only 21% of GDEs exist on protected lands or in jurisdictions with sustainable groundwater management policies, invoking a call to action to protect these vital ecosystems. Furthermore, we examine the linkage of GDEs with cultural and socio-economic factors in the Greater Sahel region, where GDEs play an essential role in supporting biodiversity and rural livelihoods, to explore other means for protection of GDEs in politically unstable regions. Our GDE map provides critical information for prioritizing and developing policies and protection mechanisms across various local, regional or international scales to safeguard these important ecosystems and the societies dependent on them.
Symbolic recording of signalling and cis-regulatory element activity to DNA
Authors: Chen Wei , Choi Junhong , Li Xiaoyi , Nathans Jenny F. , Martin Beth , Yang Wei , Hamazaki Nobuhiko , Qiu Chengxiang , Lalanne Jean-Benoît , Regalado Samuel , Kim Haedong , Agarwal Vikram , Nichols Eva , Leith Anh , Lee Choli , Shendure Jay 
Published: July 2024

AbstractMeasurements of gene expression or signal transduction activity are conventionally performed using methods that require either the destruction or live imaging of a biological sample within the timeframe of interest. Here we demonstrate an alternative paradigm in which such biological activities are stably recorded to the genome. Enhancer-driven genomic recording of transcriptional activity in multiplex (ENGRAM) is based on the signal-dependent production of prime editing guide RNAs that mediate the insertion of signal-specific barcodes (symbols) into a genomically encoded recording unit. We show how this strategy can be used for multiplex recording of the cell-type-specific activities of dozens to hundreds of cis-regulatory elements with high fidelity, sensitivity and reproducibility. Leveraging signal transduction pathway-responsive cis-regulatory elements, we also demonstrate time- and concentration-dependent genomic recording of WNT, NF-κB and Tet-On activities. By coupling ENGRAM to sequential genome editing via DNA Typewriter1, we stably record information about the temporal dynamics of two orthogonal signalling pathways to genomic DNA. Finally we apply ENGRAM to integratively record the transient activity of nearly 100 transcription factor consensus motifs across daily windows spanning the differentiation of mouse embryonic stem cells into gastruloids, an in vitro model of early mammalian development. Although these are proof-of-concept experiments and much work remains to fully realize the possibilities, the symbolic recording of biological signals or states within cells, to the genome and over time, has broad potential to complement contemporary paradigms for how we make measurements in biological systems.
Astrocytes require perineuronal nets to maintain synaptic homeostasis in mice
Authors: Tewari Bhanu P. , Woo AnnaLin M. , Prim Courtney E. , Chaunsali Lata , Patel Dipan C. , Kimbrough Ian F. , Engel Kaliroi , Browning Jack L. , Campbell Susan L. , Sontheimer Harald 
Published: July 2024

AbstractPerineuronal nets (PNNs) are densely packed extracellular matrices that cover the cell body of fast-spiking inhibitory neurons. PNNs stabilize synapses inhibiting synaptic plasticity. Here we show that synaptic terminals of fast-spiking interneurons localize to holes in the PNNs in the adult mouse somatosensory cortex. Approximately 95% of holes in the PNNs contain synapses and astrocytic processes expressing Kir4.1, glutamate and GABA transporters. Hence, holes in the PNNs contain tripartite synapses. In the adult mouse brain, PNN degradation causes an expanded astrocytic coverage of the neuronal somata without altering the axon terminals. The loss of PNNs impairs astrocytic transmitter and potassium uptake, resulting in the spillage of glutamate into the extrasynaptic space. Our data show that PNNs and astrocytes cooperate to contain synaptically released signals in physiological conditions. Their combined action is altered in mouse models of Alzheimer’s disease and epilepsy where PNNs are disrupted.
Terahertz tunable three-dimensional photonic jets
Authors: Rezaei Behrooz , Yahyapour Babak , Darafsheh Arash 
Published: July 2024

AbstractHighly localized electromagnetic field distributions near the “shadow-side” surface of certain transparent mesoscale bodies illuminated by light waves are called photonic jets. We demonstrated formation of three-dimensional (3D) tunable photonic jets in terahertz regime (terajets, TJs) by dielectric micro-objects -including spheres, cylinders, and cubes-coated with a bulk Dirac semimetal (BDS) layer, under uniform beam illumination. The optical characteristics of the produced TJs can be modulated dynamically through tuning the BDS layer’s index of refraction via changing its Fermi energy. It is demonstrated that the Fermi energy of BDS layer has a significant impact on tuning the optical characteristics of the produced photonic jets for both TE and TM polarizations. A notable polarization dependency of the characteristics of the TJs was also observed. The impact of obliquity of the incident beam was studied as well and it was demonstrated that electromagnetic field distributions corresponding to asymmetric photonic jets can be formed in which the intensity at the focal region is preserved in a wide angular range which could find potential application in scanning devices. It was found that the maximum intensity of the TJ occurs at a non-trivial morphology-dependent source-angle.
Characterization and application of LDH with chitosan composites investigated by positron annihilation lifetime spectroscopy and surface texture for the adsorption of methyl orange
Authors: Abdel-Hady E. E. , Hafez Sarah H. M. , Mohamed Hamdy F. M. , Elsharkawy Mohamed R. M. 
Published: July 2024

AbstractWith a rapid increase in industrial growth around the world, the demand for an entirely novel category of nanoparticles and technologies for wastewater treatment has become a key concern for environmental protection. Recently, hybrids of layered double hydroxides (LDH), particularly those containing LDH, have gained attention as potential nanoscale adsorbents for water treatment. Recent research has shown that LDH-containing composites are interesting versatile materials with the ability to be used in energy storage, photocatalysis, nanocomposites, and water treatment. In the current work, LDH-containing composites were utilized as adsorbents for the purpose of purifying water. The adsorbents investigated are Zn–Co–Fe/LDH/Chitosan-in situ sample preparation (LDH/CS1) and Zn–Co–Fe/LDH/Chitosan-ex situ sample preparation (LDH/CS2). Furthermore, LDH/CS1 and LDH/CS2 were investigated for wastewater treatment from methyl orange dye (MO) with various adsorption conditions. When the initial MO concentration was 20 mg/L and the amount of adsorbent was 0.1 g, the removal efficiency reached 72.8 and 91.7% for LDH/CS1 and LDH/CS2, respectively. The MO’s maximum adsorption capabilities are 160.78 and 165.89 mg/g for LDH/CS1 and LDH/CS2, respectively, which is much greater than that of comparable commercial adsorbents. MO adsorption onto LDH/CS1 and LDH/CS2 was best characterized by the pseudo-second-order kinetic model. The equilibrium adsorption data was followed by the Freundlich and Langmuir models. The adsorption is favorable as evidenced by the equilibrium parameter RL values for MO adsorption onto LDH/CS1 and LDH/CS2, which were 0.227 and 0.144, respectively. Using the free volume distribution method and the positron annihilation lifetime technique, the nanostructure of the materials was examined.
Novel insight into nicotinamide adenine dinucleotide and related metabolites in cancer patients undergoing surgery
Authors: Fujita Hiroaki , Wakiya Taiichi , Tatara Yota , Ishido Keinosuke , Sakamoto Yoshiyuki , Kimura Norihisa , Morohashi Hajime , Miura Takuya , Muroya Takahiro , Akasaka Harue , Yokoyama Hiroshi , Kanda Taishu , Kubota Shunsuke , Ichisawa Aika , Ogasawara Kenta , Kuwata Daisuke , Takahashi Yoshiya , Nakamura Akie , Yamazaki Keisuke , Yamada Takahiro , Matsuyama Ryo , Kanou Masanobu , Yamana Kei , Itoh Ken , Hakamada Kenichi 
Published: July 2024

AbstractNicotinamide adenine dinucleotide (NAD +) plays a pivotal role in numerous cellular functions. Reduced NAD + levels are postulated to be associated with cancer. As interest in understanding NAD + dynamics in cancer patients with therapeutic applications in mind grows, there remains a shortage of comprehensive data. This study delves into NAD + dynamics in patients undergoing surgery for different digestive system cancers. This prospective study enrolled 99 patients with eight different cancers. Fasting blood samples were obtained during the perioperative period. The concentrations of NAD + , nicotinamide mononucleotide (NMN), and nicotinamide riboside were analyzed using tandem mass spectrometry. After erythrocyte volume adjustment, NAD + remained relatively stable after surgery. Meanwhile, NMN decreased the day after surgery and displayed a recovery trend. Interestingly, liver and pancreatic cancer patients exhibited poor postoperative NMN recovery, suggesting a potential cancer type-specific influence on NAD + metabolism. This study illuminated the behavior of NAD + in surgically treated cancer patients. We identified which cancer types have particularly low levels and at what point depletion occurs during the perioperative period. These insights suggest the need for personalized NAD + supplementation strategies, calibrated to individual patient needs and treatment timelines. Clinical trial registration jRCT1020210066.
COVID-19 and Parkinson’s disease: a single-center study and Mendelian randomization study
Authors: Yin Jianhong , Zhang Song , Zheng Qian , Feng Zhanhui 
Published: July 2024

AbstractTo investigate the association between COVID-19 and Parkinson’s disease (PD) via a single-center study and a Mendelian randomization (MR) study. A questionnaire-based survey was conducted among PD patients at a single center from December 7, 2022, to March 10, 2023. Logistic regression analysis was performed to identify the infection-related risk factors. Subsequently, bidirectional two-sample Mendelian randomization was employed to explore the association between COVID-19 and PD. In the cross-sectional analysis, it was found that the prevalence of COVID-19 infection in PD patients was 65.7%. Forty-eight (35.3%) PD patients experienced exacerbation of motor symptoms following COVID-19 infection. Long PD disease duration (≥ 10 years) (OR: 3.327, P = 0.045) and long time since last vaccination (> 12 m) (OR: 4.916, P = 0.035) were identified as significant risk factors related to infection. The MR analysis results supported that PD increases the COVID-19 susceptibility (β = 0.081, OR = 1.084, P = 0.006). However, the MR analysis showed that PD did not increases the COVID-19 severity and hospitalization, and no significant association of COVID-19 on PD was observed. The findings from this cross-sectional study suggest that individuals with PD may experience worsened motor symptoms following COVID-19 infection. Long disease duration (≥10 years) and long time since last vaccination (> 12 m) are identified as important risk factors for infection in these patients. Furthermore, our MR study provides evidence supporting an association between PD and COVID-19 susceptibility.
Reliability of impedance spectroscopy versus digital radiograph and ICDAS-II in occlusal caries detection: a prospective clinical trial
Authors: R. AbdELkader Amr , Hafez Ibrahim Shereen , Elsayed Hassanein Olfat 
Published: July 2024

AbstractThe traditional methods in early caries detection had many limitations. So, this study aimed to evaluate the clinical performance of alternating current impedance spectroscopy ACIST in comparison with digital radiograph and ICDAS-II in detection of occlusal carious lesions. Occlusal surfaces of molar and premolar teeth from 40 adult participants were examined by two observers using three diagnostic methods: (1) international caries detection and assessment system (ICDAS-II) (2) digital radiograph (DR) and (3) Cariescan Pro device (ACIST). Agreement analysis and the difference in sensitivities and specificities were evaluated. The results showed an excellent agreement in the different groups. The difference from the visual tactile against ACIST scoring for enamel caries detection, was statistically significant (p = 0.012) and the agreement was moderate (k = 0.509). For dentinal caries the difference was not statistically significant (p > 0.05) and the agreement was similarly moderate (k < 0.6). The difference from the digital radiograph against ACIST scoring, for enamel caries, digital radiography had significantly higher sensitivity and specificity than ACIST (p < 0.001) while for dentinal caries detection and overall, ACIST had higher sensitivity and digital radiography had higher specificity and the difference was statistically significant (p < 0.001). Visual-tactile examination is a considered as feasible and valid technique for occlusal caries detection, digital radiography is superior to ACIST in diagnosing enamel caries, but it could underestimate the caries depth, ACIST is a reliable tool for detecting occlusal caries in dentin.
Resin-based dental pulp capping restoration enclosing silica and portlandite nanoparticles from natural resources
Authors: Elbatanony Mai M. , Safwat Engie M. , El-Sherif Sammar , Hassan Mohammad L. 
Published: July 2024

AbstractNatural-based materials represent green choices for biomedical applications. In this study, resin pulp capping restoration enclosing strengthening silica and bioactive portlandite nanofillers were prepared from industrial wastes. Silica nanoparticles were isolated from rice husk by heat treatment, followed by dissolution/precipitation treatment. Portlandite nanoparticles were prepared by calcination of carbonated lime waste followed by ultrasonic treatment. Both were characterized using x-ray diffraction, energy dispersive x-ray, and transmission electron microscopy. For preparing pulp capping restoration, silica (after silanization) and/or portlandite nanoparticles were mixed with 40/60 weight ratio of bisphenol A-glycidyl methacrylate and triethylene glycol dimethacrylate. Groups A, B, and C enclosing 50 wt.% silica, 25 wt.% silica + 25 wt.% portlandite, and 50 wt.% portlandite, respectively, were prepared. All groups underwent microhardness, compressive strength, calcium release, pH, and apatite forming ability inspection in comparison to mineral trioxide aggregate (MTA) positive control. In comparison to MTA, all experimental groups showed significantly higher compressive strength, group B showed comparable microhardness, and group C showed significantly higher calcium release. Groups B and C showed prominent hydroxyapatite formation. Thus, the preparation of economic, silica-fortified, bioactive pulp capping material from under-utilized agricultural residues (rice husk) and zero-value industrial waste (carbonated lime from sugar industry) could be achieved.
Longitudinal experiences of Canadians receiving compassionate access to psilocybin-assisted psychotherapy
Authors: de la Salle Sara , Kettner Hannes , Thibault Lévesque Julien , Garel Nicolas , Dames Shannon , Patchett-Marble Ryan , Rej Soham , Gloeckler Sara , Erritzoe David , Carhart-Harris Robin , Greenway Kyle T. 
Published: July 2024

AbstractRecent clinical trials have found that the serotonergic psychedelic psilocybin effectively alleviates anxiodepressive symptoms in patients with life-threatening illnesses when given in a supportive environment. These outcomes prompted Canada to establish legal pathways for therapeutic access to psilocybin, coupled with psychological support. Despite over one-hundred Canadians receiving compassionate access since 2020, there has been little examination of these ‘real-world’ patients. We conducted a prospective longitudinal survey which focused on Canadians who were granted Section 56 exemptions for legal psilocybin-assisted psychotherapy. Surveys assessing various symptom dimensions were conducted at baseline, two weeks following the session (endpoint), and optionally one day post-session. Participant characteristics were examined using descriptive statistics, and paired sample t-tests were used to quantify changes from baseline to the two-week post-treatment endpoint. Eight participants with Section 56 exemptions (four females, Mage = 52.3 years), all with cancer diagnoses, fully completed baseline and endpoint surveys. Significant improvements in anxiety and depression symptoms, pain, fear of COVID-19, quality of life, and spiritual well-being were observed. Attitudes towards death, medical assistance in dying, and desire for hastened death remained unchanged. While most participants found the psilocybin sessions highly meaningful, if challenging, one reported a substantial decrease in well-being due to the experience. These preliminary data are amongst the first to suggest that psilocybin-assisted psychotherapy can produce psychiatric benefits in real-world patients akin to those observed in clinical trials. Limited enrollment and individual reports of negative experiences indicate the need for formal real-world evaluation programs to surveil the ongoing expansion of legal access to psychedelics.
Tool skill impacts the archaeological evidence across technological primates
Authors: Luncz Lydia V. , Slania Nora E. , Almeida-Warren Katarina , Carvalho Susana , Falótico Tiago , Malaivijitnond Suchinda , Arroyo Adrián , de la Torre Ignacio , Proffitt Tomos 
Published: July 2024

AbstractThe archaeological record offers insights into our evolutionary past by revealing ancient behaviour through stone and fossil remains. Percussive foraging is suggested to be particularly relevant for the emergence of tool-use in our lineage, yet early hominin percussive behaviours remain largely understudied compared to flaked technology. Stone tool-use of extant primates allows the simultaneous investigation of their artefacts and the associated behaviours. This is important for understanding the development of tool surface modification, and crucial for interpreting damage patterns in the archaeological record. Here, we compare the behaviour and the resulting material record across stone tool-using primates. We investigate the relationship of nut-cracking technique and stone tool modification across chimpanzees, capuchins, and long-tailed macaques by conducting standardized field experiments with comparable raw materials. We show that different techniques likely emerged in response to diverse nut hardness, leading to variation in foraging success across species. Our experiments further demonstrate a correlation between techniques and the intensity of visible percussive damage on the tools. Tools used with more precision and efficiency as demonstrated by macaques, show fewer use wear traces. This suggests that some percussive techniques may be less readily identified in the archaeological record.
Metaheuristic integrated machine learning classification of colon cancer using STFT LASSO and EHO feature extraction from microarray gene expressions
Authors: Nair Ajin R. , Rajaguru Harikumar , Karthika M. S. , Keerthivasan C. 
Published: July 2024

AbstractThe microarray gene expression data poses a tremendous challenge due to their curse of dimensionality problem. The sheer volume of features far surpasses available samples, leading to overfitting and reduced classification accuracy. Thus the dimensionality of microarray gene expression data must be reduced with efficient feature extraction methods to reduce the volume of data and extract meaningful information to enhance the classification accuracy and interpretability. In this research, we discover the uniqueness of applying STFT (Short Term Fourier Transform), LASSO (Least Absolute Shrinkage and Selection Operator), and EHO (Elephant Herding Optimisation) for extracting significant features from lung cancer and reducing the dimensionality of the microarray gene expression database. The classification of lung cancer is performed using the following classifiers: Gaussian Mixture Model (GMM), Particle Swarm Optimization (PSO) with GMM, Detrended Fluctuation Analysis (DFA), Naive Bayes classifier (NBC), Firefly with GMM, Support Vector Machine with Radial Basis Kernel (SVM-RBF) and Flower Pollination Optimization (FPO) with GMM. The EHO feature extraction with the FPO-GMM classifier attained the highest accuracy in the range of 96.77, with an F1 score of 97.5, MCC of 0.92 and Kappa of 0.92. The reported results underline the significance of utilizing STFT, LASSO, and EHO for feature extraction in reducing the dimensionality of microarray gene expression data. These methodologies also help in improved and early diagnosis of lung cancer with enhanced classification accuracy and interpretability.
Innovative graph neural network approach for predicting soil heavy metal pollution in the Pearl River Basin, China
Authors: Zha Yannan , Yang Yao 
Published: July 2024

AbstractPredicting soil heavy metal (HM) content is crucial for monitoring soil quality and ensuring ecological health. However, existing methods often neglect the spatial dependency of data. To address this gap, our study introduces a novel graph neural network (GNN) model, Multi-Scale Attention-based Graph Neural Network for Heavy Metal Prediction (MSA-GNN-HMP). The model integrates multi-scale graph convolutional network (MS-GCN) and attention-based GNN (AGNN) to capture spatial relationships. Using surface soil samples from the Pearl River Basin, we evaluate the MSA-GNN-HMP model against four other models. The experimental results show that the MSA-GNN-HMP model has the best predictive performance for Cd and Pb, with a coefficient of determination (R2) of 0.841 for Cd and 0.886 for Pb, and the lowest mean absolute error (MAE) of 0.403 mg kg−1 for Cd and 0.670 mg kg−1 for Pb, as well as the lowest root mean square error (RMSE) of 0.563 mg kg−1for Cd and 0.898 mg kg−1 for Pb. In feature importance analysis, latitude and longitude emerged as key factors influencing the heavy metal content. The spatial distribution prediction trend of heavy metal elements by different prediction methods is basically consistent, with the high-value areas of Cd and Pb respectively distributed in the northwest and northeast of the basin center. However, the MSA-GNN-HMP model demonstrates superior detail representation in spatial prediction. MSA-GNN-HMP model has excellent spatial information representation capabilities and can more accurately predict heavy metal content and spatial distribution, providing a new theoretical basis for monitoring, assessing, and managing soil pollution.