bluuebunny/crossref_metadata_2025_split huggingface dataset:
Magnetic resonance biomarkers for timely diagnostic of radiation dose-rate effects
Authors: Zagrean-Tuza C. , Suditu M. , Popescu R. C. , Bacalum M. , Negut D. , Vasilca S. , Hanganu A. , Fidel I. , Serafin D. , Tesileanu O. , Chiricuta I.C. , Sadet A. , Voda M.A. , Vasos P.R. 
Published: April 2023

AbstractDiagnostic of radiation effects can be obtained within hours from delivery relying on spectroscopic detection of cell metabolite concentrations. Clinical and pre-clinical studies show that radiation delivery with elevated dose-rates can achieve tumor suppression while minimizing toxicity to surrounding areas. Diagnostic biomarkers detected on short timescales are needed to orient high dose-rate radiation delivery. We have designed an1H magnetic resonance approach to observe metabolite concentrations, in particular Choline, Creatine, and Lactate, in order to detect radiation dose and dose-rate effects within hours from radiation delivery. The results of our metabolic profiling method in glioblastoma cells are consistent with observations from clinical studies guided by magnetic resonance spectroscopy for radiotherapy of head tumors. At 5 Gy/min we have observed increases in lactate concentrations and decreases in [Cho]/[Cr] ratios at increasing radiation doses. An increase of the radiation dose-rate to 35 Gy/min is correlated with an increase of [Cho]/[Cr] consistent with a reduction in radiation-induced oxidative effects at high dose-rates. The observed biomarkers can be translated for radiation pulse sequences optimization.One Sentence SummaryMagnetic resonance biomarkers to monitor biological effectiveness within hours after radiation delivery can be optimized for glioblastoma cells and are of potential use for the design of radiotherapy with high dose-rates.
Pesticidal Effects OfGmelina arborea(Roxb) Powders On Beans Weevil (Callosobruchus maculatus) At Vom
Authors: Olanrewaju Ojuolape Damilola , Edamaku Precious Josiah , Nwite Ofodile Peter , Usman Umoru , Murtala Aliyu Mohammed 
Published: April 2023

ABSTRACTCowpea (Vigna unguiculata (L.) Walp. is one of the most nutritious grain legumes where it is valuable as a source of dietary protein yet most of the yields are lost as a result of infestation by pest especially Callosobruchus maculatus. cowpea weevil which is one of the most prevalent and a major destructive insect pest of stored legumes. Controlling of the pest by use of synthetic pesticides is raising serious concern on the environmental safety and consumer health hazards. This study was aimed at determining the pesticidal efficacy of Gmelina arborea stem bark and leaf powder on C. maculatus. The experiment was laid in a Completely Randomized Design (CRD) with three application rates (10g/200g grains, 10g/200g grains and 5+5g/200g cowpea grain) of the botanicals (leaf and stem bark powders and combination of leaf stem bark powders respectively) replicated three times was used in the assessment. The parameters and data collected in the experiment are; percentage of weevil mortality, Grain damaged, Number of Exit holes, newly emerged weevil, percentage of weight damaged. All data generated were statistically analyzed. The results of this study demonstrated the active potentials of these G. arborea plant parts as plant-derived pesticides against cowpea weevil. The effect of treated plant parts on percentage mortality rate showed significant difference (P < 0.05) over the untreated (control) as mixed leaf and stem bark powders recorded the highest mortality rate (85.00%). The leaf (51.70%) and stem bark (43.30%) powders also showed higher effect (51.70%) respectively while the lowest mortality rate was observed in the control (21.67%). The untreated (control) gave the highest number of newly emerged weevils (2.33) whereas the lowest (5.33) was found in Gmelina leaf + stem bark powders Gmelina leaf + stem bark powders attained the highest beans damage (11.00) while the lowest (9.67) was recorded in Gmelina leaf powders. The exit holes made by the weevils at the end of the experiment amongst G. arborea plant parts were highest (9.33) in Gmelina stem bark powders whereas lowest was recorded on Gmelina leaf + stem bark powders (5.33). Leaf + Stem bark powders was the most effective throughout the experiment followed by the leaf and stem bark powders respectively. In view of these findings G. arborea leaf and stem bark powders have a strong bioactivity and is effective against C. maculatus. Therefore, since these plant parts have no any adverse effects on the grains and safe to the environment, they are recommended for future usage in storage grains to control of C. maculatus.
Single Cell Resolution Spatial Mapping of Human Hematopoiesis Reveals Aging-Associated Topographic Remodeling
Authors: Sarachakov Aleksandr , Varlamova Arina , Svekolkin Viktor , Galkin Ilia , Valencia Itzel , Unkenholz Caitlin , Pannellini Tania , Akaeva Aida , Smirnova Sofia , Ovcharov Pavel , Polyakova Margarita , Tabakov Dmitrii , Postovalova Ekaterina , Sethi Isha , Shin Nara , Bagaev Alexander , Itkin Tomer , Crane Genevieve , Kluk Michael , Geyer Julia , Inghirami Giorgio , Patel Sanjay 
Published: April 2023

ABSTRACTThe spatial anatomy of hematopoiesis in bone marrow has been extensively studied in mice and other preclinical models, but technical challenges have precluded a commensurate exploration in humans. Institutional pathology archives contain thousands of paraffinized bone marrow core biopsy tissue specimens, providing a rich resource for studying the intact human bone marrow topography in a variety of physiologic states. Thus, we developed an end-to-end pipeline involving multiparameter whole tissue staining, in situ imaging at single-cell resolution, and artificial intelligence (AI)-based digital image analysis, and then applied it to a cohort of disease-free samples to survey alterations in the hematopoietic topography associated with aging. Our data indicate heterogeneity in marrow adipose tissue (MAT) content within each age group, and an inverse correlation between MAT content and proportions of early myeloid and erythroid precursors, irrespective of age. We identify consistent endosteal and perivascular positioning of hematopoietic stem and progenitor cells (HSPCs) with medullary localization of more differentiated elements and, importantly, uncover new evidence of aging-associated changes in cellular and vascular morphologies, microarchitectural alterations suggestive of inflammaging, and diminution of a potentially active megakaryocytic niche. Overall, our findings suggest that there is topographic remodeling of human hematopoiesis associated with aging. More generally, we demonstrate the potential to deeply unravel the spatial biology of normal and pathologic human bone marrow states using intact archival tissue specimens.
Paracetamol/acetaminophen hepatotoxicity: new markers for monitoring the elimination of the reactive N-Acetyl-p-benzoquinone imine
Authors: Gorrochategui Eva , Vee Marc Le , Selmi Habiba , Gérard Anne , Chaker Jade , Krais Annette M , Lindh Christian , Fardel Olivier , Chevrier Cécile , Cann Pierre Le , Miller Gary W , Barouki Robert , Jégou Bernard , Gicquel Thomas , Kristensen David , David Arthur 
Published: April 2023

AbstractParacetamol/acetaminophen (N-acetyl-p-aminophenol, APAP) overdose is one of the most important causes of drug-induced liver injury worldwide. Hepatotoxicity induced by APAP is mainly caused by the production of N-acetyl-p-benzoquinone imine (NAPQI), a highly reactive intermediate formed predominantly via the cytochrome P450 2E1. Here, we used human studies andin vitromodels to demonstrate that NAPQI-derived thiomethyl metabolites identified using high-resolution mass spectrometry could serve to monitor NAPQI detoxification and elimination in patients (after intake at recommended dose or after intoxication), and to study inter-individual variability in NAPQI production. Usingin vitrohuman models, we showed that these thiomethyl metabolites are directly linked to NAPQI detoxification since they are mainly formed after exposure to glutathione-derived conjugates via an overlooked pathway called the thiomethyl shunt. These long-term thiomethyl metabolites have great potential in future clinical studies in order to provide a more reliable history of APAP ingestion in case of acute intoxication or to study underlying causes involved in APAP-induced hepatotoxicity.One Sentence SummaryThiomethyl metabolites are new markers to monitor the elimination of the toxic N-acetyl-p-benzoquinone imine after therapeutic use or intoxication.
The double life of trichomes: understanding their dual role in herbivory and herbicide resistance
Authors: Johnson Nia M , Baucom Regina S 
Published: April 2023

AbstractExternal features of organisms often serve as the first line of defense in their immediate environments. Trichomes are hair-like appendages on plant surfaces that can defend against damaging agents such as pathogens, herbivores, and UV radiation. It is currently unknown if the variation observed in trichome traits represents dual or conflicting roles against different types of stressors. Here, we assess whether trichomes serve as an herbicide resistance trait and how it coincides with the conventionally studied defensive strategy of herbivory resistance. In a series of experiments, we exposed the annual invasive velvetleaf (Abutilon theophrasti) to glyphosate (active ingredient in the herbicide ‘Roundup’) to investigate whether trichome traits (shape and density) are linked to herbicide resistance and to test whether herbicide alters selection on plant trichomes. We found that an increased proportion of branched trichomes positively impacted herbicide resistance as well as chewing herbivory resistance. We also found evidence that glyphosate imposes positive selection on branched trichomes in velvetleaf. Overall, our results indicate that branched trichomes can contribute to both herbicide and herbivory resistance, serving as a dual structural form of resistance reducing plant injury. If our results are to be applied more broadly, it would suggest that herbicide exposure can alter the composition of plant trichomes, potentially impacting trichome-mediated defenses against various external stressors.
The Influence of Brain MRI Defacing Algorithms on Brain-Age Predictions via 3D Convolutional Neural Networks
Authors: Cali Ryan J. , Bhatt Ravi R. , Thomopoulos Sophia I. , Gadewar Shruti , Gari Iyad Ba , Chattopadhyay Tamoghna , Jahanshad Neda , Thompson Paul M. ,   the Alzheimer’s Disease Neuroimaging Initiative
Published: April 2023

AbstractIn brain imaging research, it is becoming standard practice to remove the face from the individual’s 3D structural MRI scan to ensure data privacy standards are met. Face removal - or ‘defacing’ - is being advocated for large, multi-site studies where data is transferred across geographically diverse sites. Several methods have been developed to limit the loss of important brain data by accurately and precisely removing non-brain facial tissue. At the same time, deep learning methods such as convolutional neural networks (CNNs) are increasingly being used in medical imaging research for diagnostic classification and prognosis in neurological diseases. These neural networks train predictive models based on patterns in large numbers of images. Because of this, defacing scans could remove informative data. Here, we evaluated 4 popular defacing methods to identify the effects of defacing on ‘brain age’ prediction – a common benchmarking task of predicting a subject’s chronological age from their 3D T1-weighted brain MRI. We compared brain-age calculations using defaced MRIs to those that were directly brain extracted, and those with both brain and face. Significant differences were present when comparing average per-subject error rates between algorithms in both the defaced brain data and the extracted facial tissue. Results also indicated brain age accuracy depends on defacing and the choice of algorithm. In a secondary analysis, we also examined how well comparable CNNs could predict chronological age from the facial region only (the extracted portion of the defaced image), as well as visualize areas of importance in facial tissue for predictive tasks using CNNs. We obtained better performance in age prediction when using the extracted face portion alone than images of the brain, suggesting the need for caution when defacing methods are used in medical image analysis.
Collecting-Gathering Biophysics of the BlackwormL. variegatus
Authors: Tuazon Harry , Nguyen Chantal , Kaufman Emily , Tiwari Ishant , Bermudez Jessica , Chudasama Darshan , Peleg Orit , Bhamla M. Saad 
Published: April 2023

AbstractMany organisms exhibit collecting and gathering behaviors as a foraging and survival method. Certain benthic macroinvertebrates are classified as collector-gatherers due to their collection of particulate matter as a food source, such as the aquatic oligochaeteLumbriculus variegatus(California blackworms). Blackworms demonstrate the ability to ingest organic and inorganic materials, including microplastics, but previous work has only qualitatively described their possible collecting behaviors for such materials. The mechanism through which blackworms consolidate discrete particles into a larger clumps remains unexplored quantitatively. By analyzing a group of blackworms in a large arena with an aqueous algae solution, we discover that their relative collecting efficiency is proportional to population size. Examining individual blackworms under a microscope reveals that both algae and microplastics physically adhere to the worm’s body due to external mucus secretions, which cause the materials to clump around the worm. We observe that this clumping reduces the worm’s exploration of its environment, potentially due to thigmotaxis. To validate the observed biophysical mechanisms, we create an active polymer model of a worm moving in a field of particulate debris with a short-range attractive force on its body to simulate its adhesive nature. We find that the attractive force increases gathering efficiency. This study offers insights into the mechanisms of collecting-gathering behavior, informing the design of robotic systems, as well as advancing our understanding the ecological impacts of microplastics on benthic invertebrates.
Ribozyme synthesis of both L- and D- amino acid oligos
Authors: Wang Yuhong 
Published: April 2023

ABSTRACTThe ribosome is responsible for assembling proteins using 20 naturally occurring L-handed amino acids. However, incorporating non-natural amino acids into a protein is a challenging process needs improvement. In this study, we report a new possible approach to creating nonnatural peptides using ribozymes inspired by the peptidyl transfer center. These RNA scaffolds, which are approximately 100 nucleotides in length, bind to RNase T1 truncated tRNA-like chimeras and bring them into close proximity to facilitate peptide ligation. We used single-molecule fluorescence resonance energy transfer (smFRET) to show close distances between RNA-RNA, tRNALys-tRNALys, and RNA-tRNALyspairs, which strongly suggests that the mechanism of peptide ligation is due to the proximity of the substrate through dimerization of the enzymes. Mass spectrometry analysis confirmed the detection of oligopeptides from four amino acids, including L-Lysine, D-Lysine, L-Phenylalanine, and D-Phenylalanine. These results indicate that ribozymes have greater flexibility in accommodating nonnatural amino acids. Our findings pave the way for potentially new avenues in the synthesis of nonnatural peptides, beyond the limitations of ribosomal peptide synthesis and other existing methods.GRAPHICAL ABSTRACT
Combining LIANA and Tensor-cell2cell to decipher cell-cell communication across multiple samples
Authors: Baghdassarian Hratch , Dimitrov Daniel , Armingol Erick , Saez-Rodriguez Julio , Lewis Nathan E. 
Published: April 2023

AbstractIn recent years, data-driven inference of cell-cell communication has helped reveal coordinated biological processes across cell types. While multiple cell-cell communication tools exist, results are specific to the tool of choice, due to the diverse assumptions made across computational frameworks. Moreover, tools are often limited to analyzing single samples or to performing pairwise comparisons. As experimental design complexity and sample numbers continue to increase in single-cell datasets, so does the need for generalizable methods to decipher cell-cell communication in such scenarios. Here, we integrate two tools, LIANA and Tensor-cell2cell, which combined can deploy multiple existing methods and resources, to enable the robust and flexible identification of cell-cell communication programs across multiple samples. In this protocol, we show how the integration of our tools facilitates the choice of method to infer cell-cell communication and subsequently perform an unsupervised deconvolution to obtain and summarize biological insights. We explain how to perform the analysis step-by-step in both Python and R, and we provide online tutorials with detailed instructions available athttps://ccc-protocols.readthedocs.io/. This protocol typically takes ∼1.5h to complete from installation to downstream visualizations on a GPU-enabled computer, for a dataset of ∼63k cells, 10 cell types, and 12 samples.
A small epitope shared by p53 and an unrelated protein upregulated after adenovirus infection
Authors: Miciak Jessica J. , Bunz Fred 
Published: April 2023

AbstractCancers commonly harbor point mutations inTP53that cause overexpression of functionally inactive p53 proteins. These mutant forms of p53 are immunogenic, and therefore present tantalizing targets for new forms of immunotherapy. Understanding how the immune system recognizes p53 is an important prerequisite for the development of targeted therapeutic strategies designed to exploit this common neoantigen. Monoclonal antibodies have been extensively used to probe the structural conformation of the varied isoforms of p53 and their respective mutants, and are still indispensable tools for studying the complex biological functions of these proteins. In this report, we describe the mapping of a novel epitope on p53 that appears to be shared by heat shock proteins (HSPs), which are typically upregulated in response to a variety of viral infections.
Serial Lift-Out – Sampling the Molecular Anatomy of Whole Organisms
Authors: Schiøtz Oda Helene , Kaiser Christoph J.O. , Klumpe Sven , Morado Dustin R. , Poege Matthias , Schneider Jonathan , Beck Florian , Thompson Christopher , Plitzko M. Jürgen 
Published: April 2023

AbstractCryo-focused ion beam milling of frozen-hydrated cells and subsequent cryo-electron tomography (cryo-ET) has enabled the structural elucidation of macromolecular complexes directly inside cells. Application of the technique to multicellular organisms and tissues, however, is still limited by sample preparation. While high-pressure freezing enables the vitrification of thicker samples, it prolongs subsequent preparation due to increased thinning times and the need for extraction procedures. Additionally, thinning removes large portions of the specimen, restricting the imageable volume to the thickness of the final lamella, typically < 300 nm. Here, we introduce Serial Lift-Out, an enhanced lift-out technique that increases throughput and obtainable contextual information by preparing multiple sections from single transfers. We apply Serial Lift-Out toC. elegansL1 larvae yielding a cryo-ET dataset sampling the worm’s anterior-posterior axis and resolve its ribosome structure to 7 Å, illustrating how Serial Lift-Out enables the study of multicellular molecular anatomy.
Computational design of intrinsically disordered protein regions by matching bulk molecular properties
Authors: Strome Bob , Elemam Khaled , Pritisanac Iva , Forman-Kay Julie D. , Moses Alan M. 
Published: April 2023

AbstractAlgorithms for computational protein design usually begin with a 3D structure and design an amino acid sequence that will fold into that structure. Since intrinsically disordered protein regions lack stable 3D structures, strategies for their design have been limited. Here we describe and validate a general computational strategy for design of intrinsically disordered regions (IDRs). Our algorithm designs synthetic IDRs by minimizing the distance of an initially random amino acid sequence to a known IDR in a high-dimensional space of molecular properties, such as repeat content, charge and hydrophobicity. We tested a handful of IDRs designed to target proteins to mitochondria and heat-induced condensates, and several showed the expected patterns in cells.One sentence summaryWe design synthetic mitochondrial targeting signals and condensate forming intrinsically disordered regions
The bacterial community of the European spruce bark beetle in space and time
Authors: Moussa Abdelhameed , Nones Stefano , Vannucchi Patrizia Elena , Shahzad Gul-i-Rayna , Dittmer Jessica , Corretto Erika , Schebeck Martin , Faccoli Massimo , Battisti Andrea , Stauffer Christian , Schuler Hannes 
Published: April 2023

AbstractThe European spruce bark beetleIps typographusis a pest causing severe damages in forests dominated by the Norway spruce in Europe. Microorganisms play an essential role in the host species performance, including nutrition, fitness as well as in overcoming host defenses. Here, we performed high-throughput 16S rRNA metabarcoding ofI. typographusacross different populations in Europe, to assess its bacterial community. We investigated four postglacial refugial areas in Europe and focused specifically on a current bark beetle hot spot in the Dolomites where we compared populations with different epidemiological phases (outbreaking vs. non-outbreaking) and across different seasons (pre-overwintering vs. overwintering). Our results show that the bacterial community structure varied among populations from the refugial areas and between different regions within the Dolomites. We found a significant difference in the bacterial community between pre-overwintering and overwintering individuals, but we did not find differences between epidemic and endemic populations. The prevalence of the genusErwiniawhich was present in every individual andPseudoxanthomonasin almost every individual across all populations, suggests that these taxa form the core bacterial community ofI. typographus. Furthermore, several additional bacterial taxa occurred in all populations, but with variable frequencies. This study highlights a complex interaction ofI. typographusand various bacterial taxa across different regions and ecological phases ofI. typographuspopulations and provides new insights into the role of microorganisms in the biology of this important pest species.