bluuebunny/crossref_metadata_2025_split huggingface dataset:
Repurposing non-pharmacological interventions for Alzheimer's disease through link prediction on biomedical literature
Authors: Xiao Yongkang , Hou Yu , Zhou Huixue , Diallo Gayo , Fiszman Marcelo , Wolfson Julian , Zhou Li , Kilicoglu Halil , Chen You , Su Chang , Xu Hua , Mantyh William G. , Zhang Rui 
Published: April 2024

AbstractNon-pharmaceutical interventions (NPI) have great potential to improve cognitive function but limited investigation to discover NPI repurposing for Alzheimer's Disease (AD). This is the first study to develop an innovative framework to extract and represent NPI information from biomedical literature in a knowledge graph (KG), and train link prediction models to repurpose novel NPIs for AD prevention. We constructed a comprehensive KG, called ADInt, by extracting NPI information from biomedical literature. We used the previously-created SuppKG and NPI lexicon to identify NPI entities. Four KG embedding models (i.e., TransE, RotatE, DistMult and ComplEX) and two novel graph convolutional network models (i.e., R-GCN and CompGCN) were trained and compared to learn the representation of ADInt. Models were evaluated and compared on two test sets (time slice and clinical trial ground truth) and the best performing model was used to predict novel NPIs for AD. Discovery patterns were applied to generate mechanistic pathways for high scoring candidates. The ADInt has 162,212 nodes and 1,017,284 edges. R-GCN performed best in time slice (MR = 5.2054, Hits@10 = 0.8496) and clinical trial ground truth (MR = 3.4996, Hits@10 = 0.9192) test sets. After evaluation by domain experts, 10 novel dietary supplements and 10 complementary and integrative health were proposed from the score table calculated by R-GCN. Among proposed novel NPIs, we found plausible mechanistic pathways for photodynamic therapy and Choerospondias axillaris to prevent AD, and validated psychotherapy and manual therapy techniques using real-world data analysis. The proposed framework shows potential for discovering new NPIs for AD prevention and understanding their mechanistic pathways.
Neighbour-induced changes in root exudation patterns of buckwheat results in altered root architecture of redroot pigweed
Authors: Eroğlu Çağla Görkem , Bennett Alexandra A. , Steininger-Mairinger Teresa , Hann Stephan , Puschenreiter Markus , Wirth Judith , Gfeller Aurélie 
Published: April 2024

AbstractRoots are crucial in plant adaptation through the exudation of various compounds which are influenced and modified by environmental factors. Buckwheat root exudate and root system response to neighbouring plants (buckwheat or redroot pigweed) and how these exudates affect redroot pigweed was investigated. Characterising root exudates in plant–plant interactions presents challenges, therefore a split-root system which enabled the application of differential treatments to parts of a single root system and non-destructive sampling was developed. Non-targeted metabolome profiling revealed that neighbour presence and identity induces systemic changes. Buckwheat and redroot pigweed neighbour presence upregulated 64 and 46 metabolites, respectively, with an overlap of only 7 metabolites. Root morphology analysis showed that, while the presence of redroot pigweed decreased the number of root tips in buckwheat, buckwheat decreased total root length and volume, surface area, number of root tips, and forks of redroot pigweed. Treatment with exudates (from the roots of buckwheat and redroot pigweed closely interacting) on redroot pigweed decreased the total root length and number of forks of redroot pigweed seedlings when compared to controls. These findings provide understanding of how plants modify their root exudate composition in the presence of neighbours and how this impacts each other’s root systems.
A multi-technique and multiscale comparative study on the efficiency of conservation methods for the stabilisation of waterlogged archaeological pine
Authors: Stelzner Ingrid , Stelzner Jörg , Fischer Björn , Hamann Elias , Zuber Marcus , Schuetz Philipp 
Published: April 2024

AbstractArchaeological wood can be preserved in waterlogged conditions. Due to their degradation in the ground, these archaeological remains are endangered after their discovery, since they decay irretrievably during drying. Conservation measures are used to preserve waterlogged archaeological objects, maintaining their shape and character as much as possible. However, different methods have been developed leading to varying results. This study compares their effectiveness in order to clarify their mode of action. The methods including alcohol-ether resin, lactitol/trehalose, melamine formaldehyde, polyethylene glycol impregnation prior to freeze–drying, saccharose and silicone oil were assessed by analysing mass changes and volume stability using structured-light 3D scanning. The state of the conserved wood samples including the spatial distribution of the conservation agent was examined using synchrotron micro-computed tomography. Raman spectroscopy was used to observe the agent´s spatial distribution within the cells. The findings demonstrated that melamine formaldehyde stabilises the degraded cell walls. The lumens are void, as in the case with alcohol-ether resin, while polyethylene glycol, silicone oil, saccharose and lactitol/trehalose also occupy the lumens. It is assumed that the drying method has an effect on the distribution of the solidifying agent. The knowledge gained affords insights into the mechanism of conservation methods, which in turn accounts for the varied outcomes. It also allows conclusions to be drawn about the condition and stability of conserved museum objects and serves as a starting point for the further development of conservation methods.
Morphological diversity in true and false crabs reveals the plesiomorphy of the megalopa phase
Authors: Braig Florian , Haug Carolin , Haug Joachim T. 
Published: April 2024

AbstractBrachyura and Anomala (or Anomura), also referred to as true and false crabs, form the species-rich and globally abundant group of Meiura, an ingroup of Decapoda. The evolutionary success of both groups is sometimes attributed to the process of carcinization (evolving a crab-like body), but might also be connected to the megalopa, a specific transitional larval phase. We investigate these questions, using outline analysis of the shields (carapaces) of more than 1500 meiuran crabs. We compare the morphological diversity of different developmental phases of major ingroups of true and false crabs. We find that morphological diversity of adults is larger in false crabs than in true crabs, indicating that taxonomic diversity and morphological diversity are not necessarily linked. The increasing morphological disparity of adults of true and false crabs with increasing phylogenetic distance furthermore indicates diverging evolution of the shield morphology of adult representatives of Meiura. Larvae of true crabs also show larger diversity than their adult counterparts, highlighting the importance of larvae for biodiversity studies. The megalopa phase of Meiura appears to be plesiomorphic, as it overlaps between true and false crabs and shows little diversity. Causes may be common evolutionary constraints on a developmental phase specialized for transitioning.
Unveiling the lead exposure attributed burden in Iran from 1990 to 2019 through the lens of the Global Burden of Disease study 2019
Authors: Karimi Hanie , Mahdavi Sara , Moghaddam Sahar Saeedi , Abbasi-Kangevari Mohsen , Soleimani Zahra , Esfahani Zahra , Masinaei Masoud , Fateh Sahar Mohammadi , Golestani Ali , Dilmaghani-Marand Arezou , Kompani Farzad , Rezaei Negar , Ghasemi Erfan , Larijani Bagher , Farzadfar Farshad 
Published: April 2024

AbstractThis study aimed to investigate the estimated burden attributed to lead exposure (LE), at the national and subnational levels from 1990 to 2019 in Iran. The burden attributed to LE was determined through the estimation of deaths, disability-adjusted life years (DALYs), years of life lost (YLLs) and years lived with disability (YLDs) using the comparative risk assessment method of Global Burden of Disease (GBD) study presenting as age-standardized per 100,000 person year (PY) with 95% uncertainty intervals (95% UI). Furthermore, the burden of each disease were recorded independently. Eventually, the age-standardized YLLs, DALYs, deaths and YLDs rates attributed to LE demonstrated a decrease of 50.7%, 48.9%, 38.0%, and 36.4%, respectively, from 1990 to 2019. The most important causes of LE burden are divided into two acute and chronic categories: acute, mainly causes mental disorders (DALYs rate of 36.0 in 2019), and chronic, results in cardiovascular diseases (CVDs) (DALYs rate of 391.8) and chronic kidney diseases (CKDs) (DALYs rate of 26.6), with CVDs bearing the most significant burden. At the sub-national level, a decrease in burden was evident in most provinces; moreover, low and low-middle SDI provinces born the highest burden. The burden increased mainly by ageing and was higher in males than females. It was concluded that although the overall decrease in the burden; still it is high, especially in low and low-middle SDI provinces, in advanced ages and in males. Among IDID, CKDs and CVDs that are the most important causes of LE-attributed burden in Iran; CVDs bear the highest burden.
Signatures of adaptation at key insecticide resistance loci in Anopheles gambiae in Southern Ghana revealed by reduced-coverage WGS
Authors: Dennis Tristan P. W. , Essandoh John , Mable Barbara K. , Viana Mafalda S. , Yawson Alexander E. , Weetman David. 
Published: April 2024

AbstractResistance to insecticides and adaptation to a diverse range of environments present challenges to Anopheles gambiae s.l. mosquito control efforts in sub-Saharan Africa. Whole-genome-sequencing is often employed for identifying the genomic basis underlying adaptation in Anopheles, but remains expensive for large-scale surveys. Reduced coverage whole-genome-sequencing can identify regions of the genome involved in adaptation at a lower cost, but is currently untested in Anopheles mosquitoes. Here, we use reduced coverage WGS to investigate population genetic structure and identify signatures of local adaptation in Anopheles mosquitoes across southern Ghana. In contrast to previous analyses, we find no structuring by ecoregion, with Anopheles coluzzii and Anopheles gambiae populations largely displaying the hallmarks of large, unstructured populations. However, we find signatures of selection at insecticide resistance loci that appear ubiquitous across ecoregions in An. coluzzii, and strongest in forest ecoregions in An. gambiae. Our study highlights resistance candidate genes in this region, and validates reduced coverage WGS, potentially to very low coverage levels, for population genomics and exploratory surveys for adaptation in Anopheles taxa.
Terahertz binary computing in a coupled toroidal metasurface
Authors: Bhattacharya Angana , Chouhan Bhagwat Singh , Sharma Kajal , Halawani Sami M. , Ahmad Amir , Kumar Gagan 
Published: April 2024

AbstractThe applications of terahertz metamaterials are being actively explored in recent times for applications in high-speed communication devices, miniature photonic circuits, and bio-chemical devices because of their wide advantages. The toroidal resonance, a new type of metasurface resonance, has been examined with great interest to utilize its properties in terahertz metasurface applications. This study reports a proof of concept design of a toroidal metasurface that experimentally demonstrates binary computing operations in the terahertz frequency regime. The analog computing of binary operations is achieved by the passive tuning of distance between the split ring resonators comprising the meta-molecule. The amplitude modulation is utilized as a method of determining the Boolean logic outputs of the system. The proposed metasurface could be further optimized for high amplitude modulations and active logic gate operations using tunable materials including graphene and ITO. The proposed metasurface consists of three split-ring resonators, and the near-field coupling between the adjacent resonators dictates the Boolean operations. A multipole analysis of the scattered powers of terahertz radiation determines the toroidal excitation in the metasurface. The proposed metasurfaces experimentally define AND Boolean logic operation at 0.89 terahertz, and OR Boolean logic operation at 0.97 terahertz. Numerical simulations support the experimentally obtained results. Additionally, we numerically report the excitation of NAND operation at 0.87 THz. Such toroidal analog computing metasurfaces could find applications in digitized terahertz circuits and integrated photonic devices.
Comparison of DNA extraction methods on different sample matrices within the same terrestrial ecosystem
Authors: Galla Giulio , Praeg Nadine , Rzehak Theresa , Sprecher Else , Colla Filippo , Seeber Julia , Illmer Paul , Hauffe Heidi C. 
Published: April 2024

AbstractMetataxonomic studies of ecosystem microbiotas require the simultaneous processing of samples with contrasting physical and biochemical traits. However, there are no published studies of comparisons of different DNA extraction kits to characterize the microbiotas of the main components of terrestrial ecosystems. Here, and to our knowledge for the first time, five DNA extraction kits were used to investigate the composition and diversity of the microbiota of a subset of samples typically studied in terrestrial ecosystems such as bulk soil, rhizosphere soil, invertebrate taxa and mammalian feces. DNA extraction kit was associated with changes in the relative abundance of hundreds of ASVs, in the same samples, resulting in significant differences in alpha and beta diversity estimates of their microbiotas. Importantly, the impact of DNA extraction kit on sample diversity varies according to sample type, with mammalian feces and soil samples showing the most and least consistent diversity estimates across DNA extraction kits, respectively. We show that the MACHEREY–NAGEL NucleoSpin® Soil kit was associated with the highest alpha diversity estimates, providing the highest contribution to the overall sample diversity, as indicated by comparisons with computationally assembled reference communities, and is recommended to be used for any large-scale microbiota study of terrestrial ecosystems.
Visual function loss in fungal sphenoid sinusitis: clinical characteristics and outcomes
Authors: Chen Fei , Shao Yonghui , Huang Qian , Chen Yue , Yang Bentao , Jiang Libin 
Published: April 2024

AbstractPotentially fatal fungal sphenoid sinusitis (FSS) causes visual damage. However, few studies have reported on its visual impairment and prognosis. Five hundred and eleven FSS patients with ocular complications treated at Beijing Tongren Hospital were recruited and clinical features and visual outcomes were determined. Thirty-two of the 511 patients (6%) had visual impairment, with 13 and 19 patients having invasive and noninvasive FSS, respectively. Eighteen patients (56.25%) had diabetes and 2 patient (6.25%) had long-term systemic use of antibiotics (n = 1) and corticosteroids (n = 1). All patients had visual impairment, which was more severe in invasive FSS than in noninvasive FSS. Bony wall defects and sclerosis were observed in 19 patients (59.38%), and 11 patients (34.38%) had microcalcification in their sphenoid sinusitis on computed tomography (CT). After a 5-year follow-up, three patients (9.38%) died. Patients with noninvasive FSS had a higher improvement rate in visual acuity than their counterparts. In the multivariate analysis, sphenoid sinus wall sclerosis on CT was associated with better visual prognosis. FSS can cause vision loss with persistent headaches, particularly in those with diabetes. CT showed the sphenoid sinus wall sclerosis, indicating a better visual prognosis in FSS with visual impairment.
Chromatography affinity resin with photosynthetically-sourced protein A ligand
Authors: Owens Nisha A. , Anborgh Pieter H. , Kolotilin Igor 
Published: April 2024

AbstractGreen, photosynthesizing plants can be proficiently used as cost-effective, single-use, fully biodegradable bioreactors for environmentally-friendly production of a variety of valuable recombinant proteins. Being near-infinitely scalable and most energy-efficient in generating biomass, plants represent profoundly valid alternatives to conventionally used stationary fermenters. To validate this, we produced a plastome-engineered tobacco bioreactor line expressing a recombinant variant of the protein A from Staphylococcus aureus, an affinity ligand widely useful in antibody purification processes, reaching accumulation levels up to ~ 250 mg per 1 kg of fresh leaf biomass. Chromatography resin manufactured from photosynthetically-sourced recombinant protein A ligand conjugated to agarose beads demonstrated the innate pH-driven ability to bind and elute IgG-type antibodies and allowed one-step efficient purification of functional monoclonal antibodies from the supernatants of the producing hybridomas. The results of this study emphasize the versatility of plant-based recombinant protein production and illustrate its vast potential in reducing the cost of diverse biotechnological applications, particularly the downstream processing and purification of monoclonal antibodies.
SMORES: a simple microfluidic operating room for the examination and surgery of Stentor coeruleus
Authors: Zhang Kevin S. , Rodriguez Ramon , Tang Sindy K. Y. 
Published: April 2024

AbstractCiliates are powerful unicellular model organisms that have been used to elucidate fundamental biological processes. However, the high motility of ciliates presents a major challenge in studies using live-cell microscopy and microsurgery. While various immobilization methods have been developed, they are physiologically disruptive to the cell and incompatible with microscopy and/or microsurgery. Here, we describe a Simple Microfluidic Operating Room for the Examination and Surgery of Stentor coeruleus (SMORES). SMORES uses Quake valve-based microfluidics to trap, compress, and perform surgery on Stentor as our model ciliate. Compared with previous methods, immobilization by physical compression in SMORES is more effective and uniform. The mean velocity of compressed cells is 24 times less than that of uncompressed cells. The compression is minimally disruptive to the cell and is easily applied or removed using a 3D-printed pressure rig. We demonstrate cell immobilization for up to 2 h without sacrificing cell viability. SMORES is compatible with confocal microscopy and is capable of media exchange for pharmacokinetic studies. Finally, the modular design of SMORES allows laser ablation or mechanical dissection of a cell into many cell fragments at once. These capabilities are expected to enable biological studies previously impossible in ciliates and other motile species.
Impact of using glucose as a sole carbon source to analyze the effect of biochar on the kinetics of biomethane production
Authors: Valentin Marvin T. , Białowiec Andrzej 
Published: April 2024

AbstractThe adaptation of biochar in anaerobic digestion (AD) positively influences the conversion of substrate to biomethane and promotes system stability. This study investigated the influence of biochar (BC) doses (0 to 8 g/L) on the Biochemical Methane Potential (BMP) of glucose during a 60-day AD in a mesophilic batch-type reactor. The first 6.5 weeks of the experimentation were dedicated to the microorganism’s adaptation to the biochar and degradation of organics from the used inoculum (3 phases of the glucose feeding). The last 2 weeks (4th phase of glucose feeding) represented the assumption, that glucose is the sole carbon source in the system. A machine learning model based on the autoregressive integrated moving average (ARIMA) method was used to model the cumulative BMP. The results showed that the BMP increased with the amount of BC added. The highest BMP was obtained at a dose of 8 g/L, with a maximum cumulative BMP of 390.33 mL CH4/g-VS added. Likewise, the system showed stability in the pH (7.17 to 8.17). In contrast, non-amended reactors produced only 135.06 mL CH4/g-VS and became acidic at the end of the operation. Reducing the influence of carbon from inoculum, sharpened the positive effect of BC on the kinetics of biomethane production from glucose.
Study on monitoring broken rails of heavy haul railway based on ultrasonic guided wave
Authors: Xu Xining , Wen Ziyu , Ni Yi , Shao Bohuai , Ma Xinyu , Pan Zecheng 
Published: April 2024

AbstractReal-time monitoring of broken rails in heavy haul railways is crucial for ensuring the safe operation of railway lines. U78CrV steel is a common material used for heavy haul line rails in China. In this study, the semi-analytical finite element (SAFE) method is employed to calculate the dispersion curves and modal shapes of ultrasonic guided waves in U78CrV heavy steel rails. Guided wave modes that are suitable for detecting rail cracks across the entire cross-section are selected based on the total energy of each mode and the vibration energy in the rail head, web, and foot. The excitation method for the chosen mode is determined by analyzing the energy distribution of the mode shape on the rail surface. The ultrasonic guided wave (UGW) signal in the rail is analyzed using ANSYS three-dimensional finite element simulation. The group velocity of the primary mode in the guided wave signal is obtained through continuous wavelet transform to confirm the existence of the selected mode. It is validated that the selected mode can be excited by examining the similarity between the vibration shapes of a specific rail section and all modal vibration shapes obtained through SAFE. Through simulation and field verification, the guided wave mode selected and excited in this study demonstrates good sensitivity to cracks at the rail head, web, and foot, and it can propagate over distances exceeding 1 km in the rail. By detecting the reflected signal of the selected mode or the degree of attenuation of the transmitted wave, long-distance monitoring of broken rails in heavy-haul railway tracks can be achieved.
Thermodynamic and molecular dynamic insights into how fusion influences peptide-tag recognition of an antibody
Authors: Miyanabe Kazuhiro , Yamashita Takefumi , Tsumoto Kouhei 
Published: April 2024

AbstractTo understand the effect of protein fusion on the recognition of a peptide-tag by an antibody, we fused a CCR5-derived peptide-tag (pep1) to GFP and investigated its recognition by an anti-pep1 antibody, 4B08. First, to characterize the thermodynamic properties associated with the pep1-4B08 binding, isothermal titration calorimetry experiments were conducted. It was found that pep1 fused to the C-terminus of GFP (GFP-CT) enhanced the enthalpic gain by 2.1 kcal mol−1 and the entropic loss only by 0.9 kcal mol−1, resulting in an 8-fold increase in the binding affinity compared to the unfused pep1. On the other hand, pep1 fused to the N-terminus of GFP (GFP-NT) enhanced the enthalpic gain by 3.0 kcal mol−1 and the entropic loss by 3.2 kcal mol−1, leading to no significant enhancement of the binding affinity. To gain deeper insights, molecular dynamics simulations of GFP-NT, GFP-CT, and pep1 were performed. The results showed that the location of the fusion point sensitively affects the interaction energy, the solvent accessible surface area, and the fluctuation of pep1 in the unbound state, which explains the difference in the experimental thermodynamic properties.