bluuebunny/crossref_metadata_2025_split huggingface dataset:
CryoET of β-amyloid and tau within postmortem Alzheimer’s disease brain
Authors: Gilbert Madeleine A. G. , Fatima Nayab , Jenkins Joshua , O’Sullivan Thomas J. , Schertel Andreas , Halfon Yehuda , Wilkinson Martin , Morrema Tjado H. J. , Geibel Mirjam , Read Randy J. , Ranson Neil A. , Radford Sheena E. , Hoozemans Jeroen J. M. , Frank René A. W. 
Published: July 2024

AbstractA defining pathological feature of most neurodegenerative diseases is the assembly of proteins into amyloid that form disease-specific structures1. In Alzheimer’s disease, this is characterized by the deposition of β-amyloid and tau with disease-specific conformations. The in situ structure of amyloid in the human brain is unknown. Here, using cryo-fluorescence microscopy-targeted cryo-sectioning, cryo-focused ion beam-scanning electron microscopy lift-out and cryo-electron tomography, we determined in-tissue architectures of β-amyloid and tau pathology in a postmortem Alzheimer’s disease donor brain. β-amyloid plaques contained a mixture of fibrils, some of which were branched, and protofilaments, arranged in parallel arrays and lattice-like structures. Extracellular vesicles and cuboidal particles defined the non-amyloid constituents of β-amyloid plaques. By contrast, tau inclusions formed parallel clusters of unbranched filaments. Subtomogram averaging a cluster of 136 tau filaments in a single tomogram revealed the polypeptide backbone conformation and filament polarity orientation of paired helical filaments within tissue. Filaments within most clusters were similar to each other, but were different between clusters, showing amyloid heterogeneity that is spatially organized by subcellular location. The in situ structural approaches outlined here for human donor tissues have applications to a broad range of neurodegenerative diseases.
Resolving chaperone-assisted protein folding on the ribosome at the peptide level
Authors: Wales Thomas E. , Pajak Aleksandra , Roeselová Alžběta , Shivakumaraswamy Santosh , Howell Steven , Kjær Svend , Hartl F. Ulrich , Engen John R. , Balchin David 
Published: July 2024

AbstractProtein folding in vivo begins during synthesis on the ribosome and is modulated by molecular chaperones that engage the nascent polypeptide. How these features of protein biogenesis influence the maturation pathway of nascent proteins is incompletely understood. Here, we use hydrogen–deuterium exchange mass spectrometry to define, at peptide resolution, the cotranslational chaperone-assisted folding pathway of Escherichia coli dihydrofolate reductase. The nascent polypeptide folds along an unanticipated pathway through structured intermediates not populated during refolding from denaturant. Association with the ribosome allows these intermediates to form, as otherwise destabilizing carboxy-terminal sequences remain confined in the ribosome exit tunnel. Trigger factor binds partially folded states without disrupting their structure, and the nascent chain is poised to complete folding immediately upon emergence of the C terminus from the exit tunnel. By mapping interactions between the nascent chain and ribosomal proteins, we trace the path of the emerging polypeptide during synthesis. Our work reveals new mechanisms by which cellular factors shape the conformational search for the native state.
Explaining Conformational Diversity in Protein Families through Molecular Motions
Authors: Lombard Valentin , Grudinin Sergei , Laine Elodie 
Published: July 2024

AbstractProteins play a central role in biological processes, and understanding their conformational variability is crucial for unraveling their functional mechanisms. Recent advancements in high-throughput technologies have enhanced our knowledge of protein structures, yet predicting their multiple conformational states and motions remains challenging. This study introduces Dimensionality Analysis for protein Conformational Exploration (DANCE) for a systematic and comprehensive description of protein families conformational variability. DANCE accommodates both experimental and predicted structures. It is suitable for analysing anything from single proteins to superfamilies. Employing it, we clustered all experimentally resolved protein structures available in the Protein Data Bank into conformational collections and characterized them as sets of linear motions. The resource facilitates access and exploitation of the multiple states adopted by a protein and its homologs. Beyond descriptive analysis, we assessed classical dimensionality reduction techniques for sampling unseen states on a representative benchmark. This work improves our understanding of how proteins deform to perform their functions and opens ways to a standardised evaluation of methods designed to sample and generate protein conformations.
Improving data archiving practices in ancient genomics
Authors: Bergström Anders 
Published: July 2024

AbstractAncient DNA is producing a rich record of past genetic diversity in humans and other species. However, unless the primary data is appropriately archived, its long-term value will not be fully realised. I surveyed publicly archived data from 42 recent ancient genomics studies. Half of the studies archived incomplete datasets, preventing accurate replication and representing a loss of data of potential future use. No studies met all criteria that could be considered best practice. Based on these results, I make six recommendations for data producers: (1) archive all sequencing reads, not just those that aligned to a reference genome, (2) archive read alignments too, but as secondary analysis files, (3) provide correct experiment metadata on samples, libraries and sequencing runs, (4) provide informative sample metadata, (5) archive data from low-coverage and negative experiments, and (6) document archiving choices in papers, and peer review these. Given the reliance on destructive sampling of finite material, ancient genomics studies have a particularly strong responsibility to ensure the longevity and reusability of generated data.
Dataset of the rumen microbiota and epithelial transcriptomics and proteomics in goat affected by solid diets
Authors: Chai Jianmin , Lv Xiaokang , Zhuang Yimin , Diao Qiyu , Cui Kai , Deng Feilong , Li Ying , Zhang Naifeng 
Published: July 2024

AbstractAlthough early solid diet supplementation is a common practice to improve the growth and development in goat kids, its biological mechanism how solid diet induces rumen microbiota and epithelial development is still unknow. In this study, rumen fermentation parameters, 16S rRNA sequencing for rumen content and epithelial microbiota, transcriptomics and proteomics of epithelium were determined to classify the effects of solid diet supplementation. Here, we classified the changes of goat phenotypes (i.e., growth performance, rumen fermentation and development) and linked them to the changes of rumen microbiota, transcriptome and expressed proteins. The mechanism of solid diet improving rumen development was elucidated preliminarily. Moreover, different roles between the rumen content and epithelial microbiota were identified. Thess datasets expands our understanding of the association between the early diet intervention and rumen development, providing the useful information how nutrient strategy affects rumen function and subsequently improves the host growth. The generated data provides insights in the importance of rumen niche microbiota and microbe-host interactions, which benefits future studies.
Spatial variations and health risk assessment of heavy metal levels in groundwater of Qatar
Authors: Manawi Yehia , Subeh Mosab , Al-Marri Jaber , Al-Sulaiti Huda 
Published: July 2024

AbstractThe present work’s objective is to give a comprehensive overview of the quality of groundwater in Qatar in terms of heavy metals content as well as investigating the cause and effect of the elevation in their levels above the WHO/US-EPA standards. The scope of the study included (1) physical and chemical analysis of 82 groundwater samples collected from various locations around Qatar, (2) development of ArcGIS maps depicting the variations in the levels, (3) assessment of the human health risks associated with the existing levels using three of the most used models which are: Hazard index (HI), Nemerow comprehensive pollution index (NCPI) and Incremental Lifetime Cancer Risk (ILCR). There is no extensive study ever reported to assess the health risks linked with the consumption of groundwater characterized with such heavy metals levels in Qatar. The chronic daily intake (CDI) of the investigated heavy metals (Ag, Mn, Cr, V, Mo and Sr) through ingestion and dermal pathways had a range of 1.4 × 10–5–6.7 × 10–1 mg/kg/day while the NCPI’s range was reported at 0–4.39. Moreover, the HI and ILCR were found to have a range of 0–3.2 and 5.6 × 10–4–5.5 × 10–2, respectively. The assessment of health risks, conducted in the present work, could be beneficial in building the baseline of heavy metals levels in groundwater in Qatar. This will also help in the determination of any future contamination of groundwater.
Estimation of apparent thermal inertia of roofing materials from aerial thermal imagery
Authors: Mandanici Emanuele , Lo Grasso Gabriele , Tini Maria A. , Zanutta Antonio 
Published: July 2024

Abstract
The rapid expansion of urban areas and soil sealing is enhancing the Urban Heat Island (UHI) phenomenon, especially during heat waves. The different thermal inertia of the building materials compared to natural surfaces is one of the major driving factors of UHI. The present contribution aims to test a methodology for mapping the Apparent Thermal Inertia (ATI)—a proxy that can be derived from remote sensing data—of roofing surfaces at the scale of an entire city and with a high spatial resolution. Day and night aerial thermal images with the resolution of 0.5 m were acquired over two test areas in Bologna (Italy), together with satellite multispectral data. Statistics on the buildings in the test areas are computed considering different classes of roofing materials (e.g. bituminous sheath, clay tiles, metal sheet, gravel tiles). Observed median ATI values for each class range from 0.03 to 0.09 K

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1

with interquartile ranges between 0.02 and 0.14 K

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, so the intra-class variability in some cases appears higher than the variability among different material classes, proving the importance of ATI mapping for UHI investigations.
The factors of quality of life among patients after myocardial infarction in Poland: a cross-sectional study. The quality of life among patients after myocardial infarction
Authors: Kolarczyk Ewelina , Kohanová Dominika , Witkowska Agnieszka , Szymiczek Marek , Młynarska Agnieszka 
Published: July 2024

AbstractThe quality of life (QoL) is now recognised as a central indicator of the effectiveness of interventions especially in patients after myocardial infarction (MI). The QoL may be important predict poor outcomes in cardiac patients.The present work aims to increase knowledge of the level of QoL in patients after MI. Moreover, the paper analyses the QoL in relation to sociodemographic factors and the degree of functioning in chronic disease. The study was conducted among 231 patients who were hospitalized due to MI within the period of June 2021 to June 2022 in the Hospital in Racibórz in Poland. The WHO Quality of Life Questionnaire and the Chronic Disease Functioning Scale were used. The analysis showed a statistically significant correlation (coefficient value 0.5 <|r/rho|≤ 0.7) between general functioning in chronic disease and the average QoL (rho = 0.56; p < 0.001)and somatic QoL levels(rho = 0.52; p < 0.001), as well as a moderately strong positive correlation with the QoL level on the psychological domain (rho = 0.50; p < 0.001), social domain(rho = 0.48; p < 0.001) and environmental domain (rho = 0.43; p < 0.001). The results of this study suggested that healthcare workers adopts appropriate policies for the implementation of quality of life, which can reduce the number of repetitive referrals to the hospital and costs imposed on the health system.
Utilizing combusted PET plastic waste and biogenic oils as efficient pour point depressants for crude oil
Authors: Ghobashy Mohamed Mohamady , Rashad A. M. , Attia S. K. , Elsayed A. E. , Osman D. I. 
Published: July 2024

AbstractThe deposition of paraffin on pipelines during crude oil transit and low-temperature restart processes poses a significant challenge for the oil industry. Addressing this issue necessitates the exploration of innovative materials and methods. Pour point depressants (PPDs) emerge as crucial processing aids to modify paraffin crystallization and enhance crude oil flow. This study focuses on the combustion of polyethylene terephthalate (PET) waste, a prevalent plastic, in two distinct oils (castor and jatropha). The resulting black waxy substances (PET/Castor and PET/Jatropha) were introduced in varying weights (1000, 2000, and 3000 ppm) to crude oil. The PET/castor oil combination demonstrated a remarkable reduction in pour point from 18 to −21 °C at 3000 ppm concentration, significantly more effective than PET/jatropha blends. Substantial decreases in viscosity (up to 75%) and shear stress (up to 72%) were also observed for both blends, most prominently at lower temperatures near the pour point. The synergistic effect of PET and oils as nucleating agents that alter crystallization patterns and restrict crystal growth contributes to this enhanced low-temperature flow. This highlights the potential of PET plastic waste as an economical, abundant, and eco-friendly additive to develop high-performance PPDs for crude oil.
Multi-scale analysis of the community structure of the Twitter discourse around the Italian general elections of September 2022
Authors: Federico Lorenzo , Mounim Ayoub , Caldarelli Guido , Riotta Gianni 
Published: July 2024

AbstractWe perform a multi-scale analysis of the geometric structure of the network of X (Twitter at the time of data collection) interactions surrounding the Italian snap general elections of September 25th 2022. We identify within it the communities related to the major Italian political parties and after it we analyse both the large-scale structure of interactions between different parties, showing that it resembles the coalitions formed in the run-up to the elections and the internal structure of each community. We observe that some parties have a very centralised communication with the major leaders clearly occupying the central role, while others have a more horizontal communication strategy, with many accounts playing an important role. We observe that this can be characterized by checking whether the network in the community has a strongly connected giant component or not.
Combined detection of serum EFNA1 and MMP13 as diagnostic biomarker for gastric cancer
Authors: Chu Ling-Yu , Wu Fang-Cai , Guo Hai-Peng , Xie Jian-Jun , Qu Qi-Qi , Li Xin-Hao , Xu Yi-Wei , Peng Yu-Hui , Qiu Bo 
Published: July 2024

AbstractWe previously identified that serum EFNA1 and MMP13 were potential biomarker for early detection of esophageal squamous cell carcinoma. In this study, our aim is to explore the diagnostic value of serum EFNA1 and MMP13 for gastric cancer. We used enzyme-linked immunosorbent assay (ELISA) to detect the expression levels of serum EFNA1 and MMP13 in 210 GCs and 223 normal controls. The diagnostic value of EFNA1 and MMP13 was evaluated in an independent cohorts of GC patients and normal controls (n = 238 and 195, respectively). Receiver operating characteristics were used to calculate diagnostic accuracy. In training and validation cohorts, serum EFNA1 and MMP13 levels in the GC groups were significantly higher than those in the normal controls (P < 0.001). The area under the curve (AUC) of the combined detection of serum EFNA1 and MMP13 for GC was improved (0.794), compared with single biomarker used. Similar results were observed in the validation cohort. Importantly, the combined measurement of serum EFNA1 and MMP13 to detect early-stage GC also had acceptable diagnostic accuracy in training and validation cohort. Combined detection of serum EFNA1 and MMP13 could help identify early-stage GC, suggesting that it may be a promising tool for the early detection of GC.
Synthesis and preliminary evaluation of novel PET probes for GSK-3 imaging
Authors: Gundam Surendra Reddy , Bansal Aditya , Kethamreddy Manasa , Ghatamaneni Sujala , Lowe Val J. , Murray Melissa E. , Pandey Mukesh K. 
Published: July 2024

AbstractNon-invasive imaging of GSK-3 expression in the brain will help to understand the role of GSK-3 in disease pathology and progression. Herein, we report the radiosynthesis and evaluation of two novel isonicotinamide based 18F labeled PET probes, [18F]2 and [18F]6 for noninvasive imaging of GSK3. Among the developed PET probes, the in vitro blood–brain permeability coefficient of 2 (38 ± 20 × 10–6 cm/s, n = 3) was found to be better than 6 (8.75 ± 3.90 × 10–6 cm/s, n = 5). The reference compounds 2 and 6 showed nanomolar affinity towards GSK-3α and GSK-3β. PET probe [18F]2 showed higher stability (100%) in mouse and human serums compared to [18F]6 (67.01 ± 4.93%, n = 3) in mouse serum and 66.20 ± 6.38%, n = 3) in human serum at 120 min post incubation. The in vivo imaging and blocking studies were performed in wild-type mice only with [18F]2 due to its observed stability. [18F]2 showed a SUV of 0.92 ± 0.28 (n = 6) in mice brain as early as 5 min post-injection followed by gradual clearance over time.
Understanding the flexion-relaxation phenomenon in non-specific chronic low back pain patients throught immersive virtual reality feedback approach
Authors: Rose-Dulcina Kevin , Dubessy Margaux , Armand Stéphane , Genevay Stéphane 
Published: July 2024

AbstractThe flexion-relaxation phenomenon (FRP) is frequently absent among non-specific chronic low back pain (NSCLBP) patients. However, it is unknown whether this absence is intrinsic to their pathology or merely a consequence of reduced trunk flexion. Immersive virtual reality (IVR) can create a patient avatar whose range of motion can be modulated to differ from the real movement. The present study enrolled 15 NSCLBP patients and 15 asymptomatic participants with similar characteristics to disentangle the relationship between range of motion and the FRP in NSCLBP using IVR. Trunk kinematics and lumbar muscle electromyography were assessed. The IVR environment was combined with a motion capture system to create avatars that moved like each participant. The IVR display showed a closed room and a mirror reflecting the subject’s avatar with a target line to be reached by trunk flexion. The avatar’s trunk movements were modulated from reality, leading the participants to flex their trunk more than their voluntary maximum trunk flexion. Under IVR conditions, NSCLBP patients significantly increased their trunk flexion angle, which was coupled with a significant improvement in the FRP. The absence of the FRP among the NSCLBP population appeared to be primarily related to reduced trunk flexion.
Evaluation of the teratogenic potency of bulk zinc oxide and its nanoparticles on embryos of the freshwater snail, Helisoma duryi
Authors: Kandeil Manar A. , Eissa Samia H. , Salem Hoda K. , Hassan Sama S. 
Published: July 2024

AbstractBulk zinc oxide (ZnO-BPs) and its nanoparticles (ZnO-NPs) are frequently used in various products for humans. Helisoma duryi embryos can serve as effective model organisms for studying the toxicity of NPs. This study aimed to compare the teratogenic potency of ZnO-BPs and ZnO NPs in the embryonic stages of H. duryi to evaluate the utility of this snail as a bioindicator for ZnO-NPs in the aquatic environment. The mechanisms of teratogenesis were evaluated by determination of the LC50, studying the effect of sub-lethal concentrations of both ZnO forms on the embryos, and studying their enzyme activity, oxidative stress, and biochemical analysis. The SDS-PAGE electrophoresis was undertaken to assess the effect of ZnO-BPs and ZnO NPs on protein synthesis. The results revealed that the veliger stage of H. duryi is the specific stage for bulk and nano ZnO. ZnO-NPs proved to be more toxic to snails’ embryos than ZnO-BPs. Exposure to ZnO influences specific types of defects in development, which in the case of BPs are far less drastic than those caused by NPs. Thus, the toxicity of ZnO-NPs in embryonic development is due to their unique physicochemical properties. The observed malformations include mainly hydropic malformation, exogastrulation, monophthalmia, shell misshapen, and cell lyses. Almost all tested oxidative biomarkers significantly changed, revealing that ZnONPs display more oxidative stress than ZnO-BPs. Also, the low concentration of ZnO induces many disturbances in the organic substances of veliger larvae, such as a decrease in the total protein and total lipid levels and an increase in the glycogen level. The results indicated that ZnO-BPs increase the number of protein bands. Conversely, ZnO-NPs concealed one band from treated egg masses, which was found in the control group. Embryos of snail are an appropriate model to control freshwater snails. This study demonstrates that H. duryi embryos can serve as effective model organisms to study the toxicity of ZnO-NPs.
Portable and affordable cold air plasma source with optimized bactericidal effect
Authors: Klenivskyi Myron , Khun Josef , Thonová Laura , Vaňková Eva , Scholtz Vladimír 
Published: July 2024

AbstractThe paper reports a low-cost handheld source of a cold air plasma intended for biomedical applications that can be made by anyone (detailed technical information and a step-by-step guide for creating the NTP source are provided). The plasma source employs a 1.4 W corona discharge in the needle-to-cone electrode configuration and is an extremely simple device, consisting basically of two electrodes and a cheap power supply. To achieve the best bactericidal effect, the plasma source has been optimized on Escherichia coli. The bactericidal ability of the plasma source was further tested on a wide range of microorganisms: Staphylococcus aureus as a representative of gram-positive bacteria, Pseudomonas aeruginosa as gram-negative bacteria, Candida albicans as yeasts, Trichophyton interdigitale as microfungi, and Deinococcus radiodurans as a representative of extremophilic bacteria resistant to many DNA-damaging agents, including ultraviolet and ionizing radiation. The testing showed that the plasma source inactivates all the microorganisms tested in several minutes (up to 105–107 CFU depending on a microorganism), proving its effectiveness against a wide spectrum of pathogens, in particular microfungi, yeasts, gram-positive and gram-negative bacteria. Studies of long-lived reactive species such as ozone, nitrogen oxides, hydrogen peroxide, nitrite, and nitrate revealed a strong correlation between ozone and the bactericidal effect, indicating that the bactericidal effect should generally be attributed to reactive oxygen species. This is the first comprehensive study of the bactericidal effect of a corona discharge in air and the formation of long-lived reactive species by the discharge, depending on both the interelectrode distance and the discharge current.