bluuebunny/crossref_metadata_2025_split huggingface dataset:
Glacier thickness and ice volume of the Northern Andes
Authors: Van Wyk de Vries Maximillian , Carchipulla-Morales David , Wickert Andrew D. , Minaya Verónica G. 
Published: June 2022

AbstractTropical glacier melt provides valuable water to surrounding communities, but climate change is projected to cause the demise of many of these glaciers within the coming century. Understanding the future of tropical glaciers requires a detailed record of their thicknesses and volumes, which is currently lacking in the Northern Andes. We calculate present-day (2015–2021) ice-thicknesses for all glaciers in Colombia and Ecuador using six different methods, and combine these into multi-model ensemble mean ice thickness and volume maps. We compare our results against available field-based measurements, and show that current ice volumes in Ecuador and Colombia are 2.49 ± 0.25 km3and 1.68 ± 0.24 km3respectively. We detected no motion on any remaining ice in Venezuela. The overall ice volume in the region, 4.17 ± 0.35 km3, is half of the previous best estimate of 8.11 km3. These data can be used to better evaluate the status and distribution of water resources, as input for models of future glacier change, and to assess regional geohazards associated with ice-clad volcanoes.
Datasets for benchmarking antimicrobial resistance genes in bacterial metagenomic and whole genome sequencing
Authors: Raphenya Amogelang R. , Robertson James , Jamin Casper , de Oliveira Martins Leonardo , Maguire Finlay , McArthur Andrew G. , Hays John P. 
Published: June 2022

AbstractWhole genome sequencing (WGS) is a key tool in identifying and characterising disease-associated bacteria across clinical, agricultural, and environmental contexts. One increasingly common use of genomic and metagenomic sequencing is in identifying the type and range of antimicrobial resistance (AMR) genes present in bacterial isolates in order to make predictions regarding their AMR phenotype. However, there are a large number of alternative bioinformatics software and pipelines available, which can lead to dissimilar results. It is, therefore, vital that researchers carefully evaluate their genomic and metagenomic AMR analysis methods using a common dataset. To this end, as part of the Microbial Bioinformatics Hackathon and Workshop 2021, a ‘gold standard’ reference genomic and simulated metagenomic dataset was generated containing raw sequence reads mapped against their corresponding reference genome from a range of 174 potentially pathogenic bacteria. These datasets and their accompanying metadata are freely available for use in benchmarking studies of bacteria and their antimicrobial resistance genes and will help improve tool development for the identification of AMR genes in complex samples.
Hairy surfaces by cold drawing leading to dense lawns of high aspect ratio hairs
Authors: Müllers Stefan , Florea-Hüring Mara , von Vacano Bernhard , Bruchmann Bernd , Rühe Jürgen 
Published: June 2022

AbstractThe surfaces of many organisms are covered with hairs, which are essential for their survival in a complex environment. The generation of artificial hairy surfaces from polymer materials has proven to be challenging as it requires the generation of structures with very high aspect ratios (AR). We report on a technique for the fabrication of surfaces covered with dense layers of very high AR nanoscale polymer hairs. To this, templates having pores with diameters of several hundred nanometers are filled with a polymer melt by capillary action. The polymer is then allowed to cool and the template is mechanically removed. Depending on the conditions employed, the formed structures can be a simple replica of the pore, or the polymer is deformed very strongly by cold drawing to yield in long hairs, with hair densities significantly up to 6,6 × 108 hairs/cm2 at AR of much higher than 200. The mechanism of hair formation is attributed to a delicate balance between the adhesion forces of the polymer in the pore and the yield force acting on it during mechanically demolding. We demonstrate how with very little effort and within a timescale of seconds unique topographies can be obtained, which can dramatically tailor the wetting properties of common polymers.
Towards interpretable, medically grounded, EMR-based risk prediction models
Authors: Twick Isabell , Zahavi Guy , Benvenisti Haggai , Rubinstein Ronya , Woods Michael S. , Berkenstadt Haim , Nissan Aviram , Hosgor Enes , Assaf Dan 
Published: June 2022

AbstractMachine-learning based risk prediction models have the potential to improve patient outcomes by assessing risk more accurately than clinicians. Significant additional value lies in these models providing feedback about the factors that amplify an individual patient’s risk. Identification of risk factors enables more informed decisions on interventions to mitigate or ameliorate modifiable factors. For these reasons, risk prediction models must be explainable and grounded on medical knowledge. Current machine learning-based risk prediction models are frequently ‘black-box’ models whose inner workings cannot be understood easily, making it difficult to define risk drivers. Since machine learning models follow patterns in the data rather than looking for medically relevant relationships, possible risk factors identified by these models do not necessarily translate into actionable insights for clinicians. Here, we use the example of risk assessment for postoperative complications to demonstrate how explainable and medically grounded risk prediction models can be developed. Pre- and postoperative risk prediction models are trained based on clinically relevant inputs extracted from electronic medical record data. We show that these models have similar predictive performance as models that incorporate a wider range of inputs and explain the models’ decision-making process by visualizing how different model inputs and their values affect the models’ predictions.
TSP, a virulent Podovirus, can control the growth of Staphylococcus aureus for 12 h
Authors: Tabassum Rabia , Basit Abdul , Alvi Iqbal Ahmed , Asif Muhammad , ur Rehman Shafiq 
Published: June 2022

AbstractMethicillin-resistant Staphylococcus aureus (MRSA) is a prevailing nosocomial pathogen that is increasingly isolated in community settings. It shows resistance against all beta-lactam drugs and has acquired mechanisms to resist other groups of antibiotics. To tackle this emerging issue of MRSA, there is an urgent need for antibiotic alternatives, and utilizing lytic bacteriophages is one of the most promising therapeutic approaches. In the present study, a lytic bacteriophage TSP was isolated from hospital wastewater against MRSA. The phage efficiently inhibited bacterial growth for up to 12 h at MOI of 1 and 10. TSP phage showed activity against various isolates of MRSA and MSSA, isolated from different clinical samples, with variable antibiotic susceptibility patterns. The bacteriophage TSP showed stability at varying temperatures (25 °C, 37 °C) and pH values (5–9), while its maximum storage stability was observed at 4 °C. It had a short latent period (20 min) and burst size of 103 ± 5pfu/infected cells. TSP genome sequence and restriction analysis revealed that its genome has a linear confirmation and length of 17,987 bp with an average GC content of 29.7%. According to comparative genomic analysis and phylogenetic tree,TSP phage can be considered a member of genus “P68viruses”. The strong lytic activity and short latent period in addition to its lytic nature makes it a good candidate for phage therapy against MRSA infections, if it proves to be effective in in-vivo studies.
Temporal mapping of derived high-frequency gene variants supports the mosaic nature of the evolution of Homo sapiens
Authors: Andirkó Alejandro , Moriano Juan , Vitriolo Alessandro , Kuhlwilm Martin , Testa Giuseppe , Boeckx Cedric 
Published: June 2022

AbstractLarge-scale estimations of the time of emergence of variants are essential to examine hypotheses concerning human evolution with precision. Using an open repository of genetic variant age estimations, we offer here a temporal evaluation of various evolutionarily relevant datasets, such as Homo sapiens-specific variants, high-frequency variants found in genetic windows under positive selection, introgressed variants from extinct human species, as well as putative regulatory variants specific to various brain regions. We find a recurrent bimodal distribution of high-frequency variants, but also evidence for specific enrichments of gene categories in distinct time windows, pointing to different periods of phenotypic changes, resulting in a mosaic. With a temporal classification of genetic mutations in hand, we then applied a machine learning tool to predict what genes have changed more in certain time windows, and which tissues these genes may have impacted more. Overall, we provide a fine-grained temporal mapping of derived variants in Homo sapiens that helps to illuminate the intricate evolutionary history of our species.
Remineralization of early enamel lesions with a novel prepared tricalcium silicate paste
Authors: Hamdi Kareem , Hamama Hamdi H. , Motawea Amira , Fawzy Amr , Mahmoud Salah Hasab 
Published: June 2022

AbstractTo evaluate the remineralization potential of prepared tricalcium silicate (TCS) paste compared to silver diamine fluoride-potassium iodide (SDF-KI) and casein phosphopeptide-amorphous calcium phosphate (CPP-ACP) on artificial enamel lesions. Thirty permanent sound molars were collected for the study. After cleaning, root cutting, and applying acid-resistant nail varnish, leaving a 4 × 4 mm buccal window, the teeth were subjected to demineralization process. The teeth were divided into three treatment groups (n = 10). In each group, the teeth were sectioned buccolingually to obtain two halves (30 self-control and 30 experimental halves). The self-control halves were subjected to cross-sectional microhardness (CSMH), energy-dispersive X-ray spectroscopy at 50, 100, and 150 µm from the external enamel surface, and micromorphological analysis at the superficial enamel surface. The experimental halves were subjected to the same tests after 30 days of remineralization. Three-way analysis of variance (ANOVA) outcomes showed no significant difference in CSMH after treatment among the three different groups at the different levels (p > 0.05). Meanwhile, three-way ANOVA outcomes showed a significant difference in calcium/ phosphate ratio after treatment among the three different groups at the different levels. (p < 0.05). The tricalcium silicate paste used in this study showed potential remineralization in subsurface enamel lesions.
Reengineering the specificity of the highly selective Clostridium botulinum protease via directed evolution
Authors: Dyer Rebekah P. , Isoda Hariny M. , Salcedo Gabriela S. , Speciale Gaetano , Fletcher Madison H. , Le Linh Q. , Liu Yi , Brami-Cherrier Karen , Malik Shiazah Z. , Vazquez-Cintron Edwin J. , Chu Andrew C. , Rupp David C. , Jacky Birgitte P. S. , Nguyen Thu T. M. , Katz Benjamin B. , Steward Lance E. , Majumdar Sudipta , Brideau-Andersen Amy D. , Weiss Gregory A. 
Published: June 2022

AbstractThe botulinum neurotoxin serotype A (BoNT/A) cuts a single peptide bond in SNAP25, an activity used to treat a wide range of diseases. Reengineering the substrate specificity of BoNT/A’s protease domain (LC/A) could expand its therapeutic applications; however, LC/A’s extended substrate recognition (≈ 60 residues) challenges conventional approaches. We report a directed evolution method for retargeting LC/A and retaining its exquisite specificity. The resultant eight-mutation LC/A (omLC/A) has improved cleavage specificity and catalytic efficiency (1300- and 120-fold, respectively) for SNAP23 versus SNAP25 compared to a previously reported LC/A variant. Importantly, the BoNT/A holotoxin equipped with omLC/A retains its ability to form full-length holotoxin, infiltrate neurons, and cleave SNAP23. The identification of substrate control loops outside BoNT/A’s active site could guide the design of improved BoNT proteases and inhibitors.
Effects of active, inactive, and derivatives of Akkermansia muciniphila on the expression of the endocannabinoid system and PPARs genes
Authors: Ghaderi Farinaz , Sotoodehnejadnematalahi Fattah , Hajebrahimi Zahra , Fateh Abolfazl , Siadat Seyed Davar 
Published: June 2022

AbstractThis study aimed to investigate the effects of active and heat-inactivated forms of Akkermansia muciniphila, bacterium-derived outer membrane vesicles (OMVs), and cell-free supernatant on the transcription of endocannabinoid system (ECS) members, including cannabinoid receptors 1 and 2 (CB1 and CB2), fatty acid amide hydrolase (FAAH), and peroxisome proliferator-activated receptors (PPARs) genes (i.e., α, β/δ, and δ) in Caco-2 and HepG-2 cell lines. After the inoculation of A. muciniphila in brain heart infusion enriched medium, OMVs and cell-free supernatant were extracted. For the investigation of the effects of bacteria and its derivatives on the expression of ECS and PPARs genes, the aforementioned cells were treated by active and heat-inactivated bacteria, OMVs, and cell-free supernatant. Quantitative real-time polymerase chain reaction analysis revealed that both forms of the bacterium, bacterial-derived OMVs, and cell-free supernatant could affect the expression of CB1, CB2, FAAH, and PPARs genes (i.e., α, β/δ, and δ) significantly (P < 0.05). Considering the engagement of the aforementioned genes in metabolic pathways, it might be suggested that both forms of the bacterium, OMVs, and cell-free supernatant might have the potential to serve as a probiotic, paraprobiotic, and postbiotic candidate to prevent obesity, metabolic disorders, and liver diseases.
Filamentous crystal growth in organic liquids and selection of crystal morphology
Authors: Yashima Takumi , Tani Marie , Kurita Rei 
Published: June 2022

AbstractFilamentous crystals such as whisker crystals are often seen not only in metallic liquids, but also in organic liquids and solutions. They are interesting as reinforce materials. However, it remains challenging to induce filamentous crystals due to an incomplete understanding of the mechanisms behind their formation. In this paper, we investigate filamentous crystal growth in viscous organic liquids. It is found that filamentous crystals grow via an extraordinary dynamical path, where the molecules locally evaporate to bubbles and then redeposite to the tip of growing crystalline filaments. We also succeeded in controlling whether filamentous or faceted crystal growth is selected by inducing or suppressing the bubbles.
Genetic structure of American bullfrog populations in Brazil
Authors: Jorgewich-Cohen Gabriel , Toledo Luís Felipe , Grant Taran 
Published: June 2022

AbstractNon-native species are a major problem affecting numerous biomes around the globe. Information on their population genetics is crucial for understanding their invasion history and dynamics. We evaluated the population structure of the non-native American bullfrog, Aquarana catesbeiana, in Brazil on the basis of 324 samples collected from feral and captive groups at 38 sites in seven of the nine states where feral populations occur. We genotyped all samples using previously developed, highly polymorphic microsatellite loci and performed a discriminant analysis of principal components together with Jost’s D index to quantify pairwise differentiation between populations. We then amplified 1,047 base pairs of the mitochondrial cytochrome b (cytb) gene from the most divergent samples from each genetic population and calculated their pairwise differences. Both the microsatellite and cytb data indicated that bullfrogs comprise two populations. Population grouping 1 is widespread and possesses two cytb haplotypes. Population grouping 2 is restricted to only one state and possesses only one of the haplotypes from Population grouping 1. We show that there were two imports of bullfrogs to Brazil and that there is low genetic exchange between population groupings. Also, we find that there is no genetic divergence among feral and captive populations suggesting continuous releases. The limited genetic variability present in the country is associated to the small number of introductions and founders. Feral bullfrogs are highly associated to leaks from farms, and control measures should focus on preventing escapes using other resources than genetics, as feral and captive populations do not differ.
Implementation of sodium alginate-Fe3O4 to localize undiagnosed small pulmonary nodules for surgical management in a preclinical rabbit model
Authors: Zhang Zhi-xuan , Lv Lu , Shi Ai-hua , Li Yun-hao , Wang Tian-ren , Guo Yuan-hang , Hu Bao-juan , Yan Xiao-peng , Fu Jun-ke , Ma Feng , Wang Hao-hua , Lv Yi , Zhang Yong 
Published: June 2022

AbstractMany methods are used to locate preoperative small pulmonary nodules. However, deficiencies of complications and success rates exist. We introduce a novel magnetic gel for small pulmonary nodules localization in rabbit model, and furtherly evaluate its safety and feasibility. Rabbits were used as the experimental objects. A magnetic gel was used as a tracer magnet, mixed as sodium alginate-Fe3O4 magnetic fluid and calcium gluconate solution. In short-term localization, a coaxial double-cavity puncture needle was applied to inject the gel into the lung after thoracotomy, and a pursuit magnet made of Nd-Fe-B permanent magnetic materials was used to attract the gel representing location of the nodule. In long-term localization, the gel was injected under X-ray guidance. Imaging changes to the lung were observed under X-ray daily. Thoracotomy was performed to excise tissue containing the gel, and hematoxylin–eosin staining was used to observe the tissue on postoperative days 1, 3, 5, and 7. Observe tissues morphology of heart, liver, spleen, and kidney in the same way. The gel was formed after injection and drew lung tissue to form a protrusion from the lung surface under the applied magnetic field. No complication was observed. The shape and position of the gel had not changed when viewed under X-ray. Pathological analysis showed the gel had a clear boundary without diffusion of magnetic fluid. All tissues retained good histologic morphology and no magnetic fluid was observed. Our study preliminarily suggested that the technique using sodium alginate-Fe3O4 magnetic gel to locate small pulmonary nodules with guidance of X-ray, and to search for them under an applied magnetic field during the operation is safe and feasible.
Risk factors associated with the infection of sheep with Dichelobacter nodosus
Authors: Storms Julia , Wirth Anna , Vasiliadis Danae , Jores Jörg , Kuhnert Peter , Distl Ottmar 
Published: June 2022

AbstractOvine footrot is a highly contagious foot disease caused by the gram-negative bacterium Dichelobacter nodosus (D. nodosus). In a recent report, we showed a prevalence of 42.9% D. nodosus positive swabs across Germany. In this follow-up study, we used real-time PCR results for D. nodosus and footrot scores of 9297 sheep from 208 flocks and collated these data with survey data on herd and animal characteristics and herd management. The aims of the present study were to investigate herd and animal factors associated with D. nodosus infection and footrot scores in individual sheep. Multivariable analyses with generalized mixed models showed that month of recording, breed, herdbook membership, use of antibiotics, and footbaths in the past 3–10 years, signs of footrot in the past 12 months and flock environment of the sheep, modelled as a random farm effect within region, were significant risk factors. Among the 21 different breeds, Romney had the lowest risk of D. nodosus infection, while Swifter had the highest risk and German Merino and German White Heath were the next breeds at highest risk of D. nodosus infection. The variance between farms in the prevalence of D. nodosus was large and accounted for 84% of the total variance in the mixed model analysis. We conclude that specific and as yet unknown effects influencing D. nodosus infections in flocks, as well as breed and weather, are the most important effects on D. nodosus infection in sheep, pointing towards the need to establish adequate infection control at farm level.
Extracting time series matching a small-angle X-ray scattering profile from trajectories of molecular dynamics simulations
Authors: Shimizu Masahiro , Okuda Aya , Morishima Ken , Inoue Rintaro , Sato Nobuhiro , Yunoki Yasuhiro , Urade Reiko , Sugiyama Masaaki 
Published: June 2022

AbstractSolving structural ensembles of flexible biomolecules is a challenging research area. Here, we propose a method to obtain possible structural ensembles of a biomolecule based on small-angle X-ray scattering (SAXS) and molecular dynamics simulations. Our idea is to clip a time series that matches a SAXS profile from a simulation trajectory. To examine its practicability, we applied our idea to a multi-domain protein ER-60 and successfully extracted time series longer than 1 micro second from trajectories of coarse-grained molecular dynamics simulations. In the extracted time series, the domain conformation was distributed continuously and smoothly in a conformational space. Preferred domain conformations were also observed. Diversity among scattering curves calculated from each ER-60 structure was interpreted to reflect an open-close motion of the protein. Although our approach did not provide a unique solution for the structural ensemble of the biomolecule, each extracted time series can be an element of the real behavior of ER-60. Considering its low computational cost, our approach will play a key role to identify biomolecular dynamics by integrating SAXS, simulations, and other experiments.
Coplanar embedding of multiple 3D cell models in hydrogel towards high-throughput micro-histology
Authors: Heub Sarah , Navaee Fatemeh , Migliozzi Daniel , Ledroit Diane , Boder-Pasche Stéphanie , Goldowsky Jonas , Vuille-Dit-Bille Emilie , Hofer Joëlle , Gaiser Carine , Revol Vincent , Suter-Dick Laura , Weder Gilles 
Published: June 2022

AbstractStandardised and high-throughput methods have been developed for the production and experimental handling of some 3D in vitro models. However, adapted analytical tools are still missing for scientists and researchers to fully exploit the potential of complex cellular models in pre-clinical drug testing and precision medicine. Histology is the established, cost-effective and gold standard method for structural and functional tissue analysis. However, standard histological processes are challenging and costly to apply to 3D cell models, as their small size often leads to poor alignment of samples, which lowers analysis throughput. This body of work proposes a new approach: HistoBrick facilitates histological processing of spheroids and organoids by enabling gel embedding of 3D cell models with precise coplanar alignment, parallel to the sectioning plane, thus minimising the loss of sample material. HistoBrick’s features are compatible with automation standards, potentially allowing automated sample transfer from a multi-well plate to the gel device. Moreover, HistoBrick’s technology was validated by demonstrating the alignment of HepG2 cultured spheroids measuring 150–200 µm in diameter with a height precision of ± 80 µm. HistoBrick allows up to 96 samples to be studied across minimal sections, paving the way towards high-throughput micro-histology.