bluuebunny/crossref_metadata_2025_split huggingface dataset:
FDG PET/CT Scan Still Can Help in Evaluation of Prostate Cancer
Authors: Doroudinia Abtin , Wolfe Taylor 
Published: November 2024

Abstract
Although 18F-FDG PET/CT scan is not the preferred modality to evaluate prostate cancer patients due to generally low uptake of FDG in prostate cancer cells, it can still be helpful in some selected cases with diagnostic dilemma. Here we are presenting an unusual prostate cancer case, status post radical prostatectomy, with heterogenous uptake in osseous lesions on 68Ga-PSMA PET/CT scan and low PSA values. He was referred for further evaluation with 18F-FDG PET/CT scan, revealing widely metastatic lesions in bone and liver, in addition to mildly avid recurrence in prostatectomy surgical bed and also metastasis in the spleen.
“Hot Tongue and Mouth” on 18F-FDG PET/CT Due to Buccolingual Masticatory Syndrome, Caused by Metoclopramide Antiemetic Treatment
Authors: Jochumsen Mads Ryø , Kramer Stine Maria Jentoft 
Published: November 2024

Abstract
We present a case of a 66-year-old man, where 18F-FDG PET/CT revealed intense FDG uptake in the tongue, lips, cheeks, and chewing musculature and distinct activation of the somatosensory and motor cortex corresponding to the mouth and tongue. The patient suffered from buccolingual masticatory syndrome, characterized by tardive dyskinesia, meaning uncontrollable, repetitive movements of the tongue, lips, cheeks, and masticatory musculature. In this case, the buccolingual masticatory syndrome was caused by metoclopramide antiemetic treatment. “Hot tongue” was previously described on 18F-FDG PET/CT in patients with tardive dyskinesia due to antipsychotic treatment, but the distinct activation of the lower facial motor cortex makes the present case stand out.
Norepinephrine Transporter–Targeted Cancer Theranostics—New Horizons
Authors: Higuchi Takahiro , Klimek Konrad , Groener Daniel , Chen Xinyu , Werner Rudolf A. 
Published: November 2024

Abstract
In the evolving landscape of precision oncology, this review delineates the role of radiopharmaceuticals targeting the norepinephrine transporter (NET), with a particular focus on the current clinical application of 123I-MIBG diagnostic imaging and 131I-MIBG therapeutics, in particular for pheochromocytoma, neuroblastoma, or paraganglioma. We will also highlight recently introduced 18F-labeled NET targeting imaging radiotracers, which would offer unparalleled resolution, enhanced tumor localization, and staging properties. Complementing these novel second-generation PET agents in a theranostic approach, astatine-211 meta-astatobenzylguanidine (211At-MABG) would leverage the advantages of alpha-particles to selectively target and eradicate NET-expressing tumor cells with minimal off-target effects.
Tips and tricks in the operative management of esophageal, trachea, and bronchial injuries: What you need to know
Authors: Wall Matthew J. , Mattox Kenneth L. 
Published: November 2024

ABSTRACT
Tracheal injuries can be immediately life-threatening. Fiberoptic bronchoscopy in the operating room can make the diagnosis and satisfy the principle of achieving an airway distal to the injury. Repair is performed with a single layer of absorbable suture. Esophageal injuries are diagnosed with imaging, endoscopy, or intraoperatively. In the chest, esophageal injuries are best repaired through posterolateral incisions. Repairs are performed in one or two layers, and drains are routinely used. For a damage-control approach to esophageal injuries, wide drainage can be considered. For both tracheal and esophageal injuries, the operative approach is based on the anatomic location of the injury and muscle flap buttressing of the repairs is routinely employed.
Feature selection with vector-symbolic architectures: a case study on microbial profiles of shotgun metagenomic samples of colorectal cancer
Authors: Cumbo Fabio , Truglia Simone , Weitschek Emanuel , Blankenberg Daniel 
Published: November 2024

ABSTRACTThe continuingly decreasing cost of next-generation sequencing has recently led to a significant increase in the number of microbiome-related studies, providing invaluable information for understanding host-microbiome interactions and their relation to diseases. A common approach in metagenomics consists of determining the composition of samples in terms of the amount and types of microbial species that populate them, with the goal to identify microbes whose profiles are able to differentiate samples under different conditions with advanced feature selection techniques. Here we propose a novel backward variable selection method based on the hyperdimensional computing paradigm, which takes inspiration from how the human brain works in the classification of concepts by encoding features into vectors in a high-dimensional space. We validated our method on public metagenomic samples collected from patients affected by colorectal cancer in a case/control scenario, by performing a comparative analysis with other state-of-the-art feature selection methods, obtaining promising results.AUTHOR SUMMARYCharacterizing the microbial composition of metagenomic samples is crucial for identifying potential biomarkers that can distinguish between healthy and diseased states. However, the high dimensionality and complexity of metagenomic data present significant challenges in the context of accurately selecting features. Our backward variable selection method, based on the hyperdimensional computing paradigm, offers a promising approach to overcoming these challenges. By effectively reducing the feature space while preserving essential information, this method enhances the ability to detect critical microbial signatures associated with diseases like colorectal cancer, leading to more precise diagnostic tools.
On non-random mating, adaptive evolution and information theory
Authors: Carvajal-Rodríguez Antonio 
Published: November 2024

ABSTRACTPopulation genetics describes evolutionary processes, focusing on the variation within and between species and the forces shaping this diversity. Evolution reflects information accumulated in genomes, enhancing organisms’ adaptation to their environment.In this paper, we propose a model that begins with the distribution of matings based on mutual fitness and progresses to viable adult genotype distribution. At each stage the changes result in different measures of information. The evolutionary dynamics of each stage of the model correspond to aspects such as the type of mating, the distributions of genotypes within matings, and the distribution of genotypes and haplotypes in the next generation. Changes in these distributions are caused by variation in fitness and result in Jeffreys divergence values other than zero. As an example, a model of hybrid sterility is developed at a biallelic locus, comparing the information indices associated with each stage of the evolutionary process.In conclusion, the informational perspective seems to facilitate the connection of causes and effects and allows the development of statistics to contrast null models of zero information (random mating, no selection, etc.). The informational perspective could contribute to clarify, deepen and expand the mathematical foundations of evolutionary theory.SIMPLE SUMMARYThe evolutionary process can be seen as a process of acquisition, storage, and updating of information by a population about the environment in which it lives. In this paper I propose a model that starts with the distribution of matings that occur according to mutual mating fitness and ends with the distribution of viable adult genotypes obtained after these matings. The result of the evolutionary dynamics associated with each stage of the model can be described in terms of information. This informational description facilitates the connection between causes and effects, as well as the development of statistics to test the null model of zero information, i.e. random mating and/or no effect of natural selection. Incorporating the informational perspective into the mathematical formalism of population genetics/genomics contributes to clarifying, expanding and deepening the mathematical description of evolutionary theory.
Modulation of B cell receptor activation by antibody competition
Authors: He Yuanyuan , Guo Zijian , Vahey Michael D. 
Published: November 2024

AbstractDuring repeated virus exposure, pre-existing antibodies can mask viral epitopes by competing with B cell receptors for antigen. Although this phenomenon has the potential to steer B cell responses away from conserved epitopes, the factors that influence epitope masking by competing antibodies remain unclear. Using engineered, influenza-reactive B cells, we investigate how antibodies influence the accessibility of epitopes on the viral surface. We find that membrane-proximal epitopes on influenza hemagglutinin are fundamentally at a disadvantage for B cell recognition because they can be blocked by both directly and indirectly competing antibodies. While many influenza-specific antibodies can inhibit B cell activation, the potency of masking depends on proximity of the targeted epitopes as well as antibody affinity, kinetics, and valency. Although most antibodies are inhibitory, we identify one that can enhance accessibility of hidden viral epitopes. Together, these findings establish rules for epitope masking that could help advance immunogen design.
Remote-control meiotic drive of sex chromosomes
Authors: Greenberg Naomi L. , Patten Manus M. , Schenkel Martijn A. 
Published: November 2024

AbstractSome selfish genetic elements drive at meiosis to achieve transmission distortion, breaking the rules of Mendelian segregation to enhance their own evolutionary success. It has been previously shown that positive modifiers of drive must act incisin order to gain the selfish benefit of drive and that suppressors of drive will be selected at any unlinked loci. Here, we model the evolution of an autosomaltrans-acting gene (Distorter) that causes the Y-chromosome (or even 0-chromosome) to drive. We show that such a gene may spread in the population when linked to a second locus,Assister, whose alleles are transmitted at different frequencies through sperm as compared to eggs, for which we consider various scenarios, e.g. genes subject to sexually antagonistic selection or sex-limited drive. Depending on the mechanistic details of sex-chromosome drive,Distorter’s spread can additionally facilitate transitions between XY and X0 sex determination. We discuss these results in relation to sex allocation theory, and as proof of principle for a novel type of naturally occurring or synthetically useful sex-ratio-distorting selfish genetic element.
Transcriptome sample statistics of the responses the sugar beet root maggot,Tetanops myopaeformishas while experiencing susceptible and resistant reactions with sugar beet,Beta vulgarisssp. vulgaris
Authors: Acharya Sudha , Alkharouf Nadim W. , Tehseen Muhammad Massub , Chu Chenggen , Klink Vincent P. 
Published: November 2024

AbstractThe sugar beet root maggot (SBRM),Tetanops myopaeformis(von Röder), is a devastating insect pathogen of sugar beet (SB), Beta vulgaris ssp, vulgaris (B. vulgaris), one of only two plants in the world from which significant global raw sugar is produced, $1 billion, U.S., $4.6 B, globally. Experiments reveal the SBRM larval transcriptome experiencing two different susceptible or resistant responses by sugar beet SBRM larvae were sampled at time = 0 hours post infection [hpi]), prior to being introduced toB. vulgarisand after infection on F1016 and F1024 (resistant), and F1010 and L19 (susceptible) for 24, 48, and 72 hpi when the larvae were removed for transcriptomic analysis. The transcriptomic analyses included determining the number of reads per sample, mapping the transcripts to the recently sequenced SBRM TmSBRM_v1.0 draft genome, identifying genes that relate to the resistant and susceptible responses. Moreover, the RNA-seq experiments provide data for generating differential expression analyses between the various sample types, thus, yielding an understanding SBRM biology, the development of new control strategies for this pathogen, relationship to model genetic organisms likeDrosophila melanogaster, relationship to pathogenic non-model organisms, and aid in agronomic improvement of sugar beet for stakeholders.
Design and Synthesis of Triazine-Based Hydrogel for Combined Targeted Doxorubicin Delivery and PI3K Inhibition
Authors: Mandal Subhasis , Bhoumick Avinandan , Singh Arpana , Konar Sukanya , Banerjee Arkajyoti , Ghosh Arnab , Sen Prosenjit 
Published: November 2024

ABSTRACTMelanoma, an aggressive skin cancer originating from melanocytes, presents substantial challenges due to its high metastatic potential and resistance to conventional therapies. Hydrogels, three-dimensional networks of hydrophilic polymers with high water-retention capacities, offer significant promise for controlled drug delivery applications. In this study, we report the synthesis and characterization of hydrogelators based on the triazine molecular scaffold, which self-assemble into fibrous networks conducive to hydrogel formation. Rheological analysis confirmed their hydrogelation properties, while microscopic techniques including FE-SEM and FEG-TEM provided insights into their morphological networks. The drug delivery capability of these hydrogelators was evaluated using doxorubicin, a widely employed anticancer agent, demonstrating enhanced biocompatibility and reduced side effects compared to free doxorubicin. Additionally, the hydrogelators exhibited inhibitory activity against phosphoinositide 3-kinase (PI3K), a key enzyme frequently mutated in cancer, and also involved in melanoma progression. The dual functionality of this delivery system – controlled drug release and PI3K inhibition – highlights the potential of triazine-based hydrogelators as innovative therapeutic platforms for melanoma treatment.
The Protein Language Visualizer: Sequence Similarity Networks for the Era of Language Models
Authors: Espinoza-Herrera Javier , Manríquez-García María F. , Medina-Bermejo Sofía , López-Jasso Ailyn , Shi Karry , Mead Dyllan , Veskimägi Sarah M. , O’Connor Maeve , Siordia Adriana , Roethler Nathaniel , Jinich Adrian 
Published: November 2024

AbstractThe advent of high-throughput sequencing technologies and the availability of biological “big data” has accelerated the discovery of new protein sequences, making it challenging to keep pace with their functional annotation. To address this annotation challenge, techniques such as Sequence Similarity Networks (SSNs) have been employed to visually group proteins for faster identification. In this paper, we introduce an alternative visual analysis tool. Our simple and modular Protein Language Visualizer (PLVis) pipeline combines pre-trained PLM embeddings, dimensionality reduction algorithms and clustering methods to enable rapid assessment of proteins based on their neighbors. The resulting interactive visualizations can be enriched with multiple layers of biological and structural annotations. We present a head-to-head comparison of PLVis with SSNs and find concordant clustering patterns, with PLVis offering the additional advantage of revealing relationships between proteins that would appear as isolated nodes in an SSN. Next, we quantitatively validate the intuitive notion that well-separated clusters in a PLVis capture sequence similarity information with more fidelity than large, central “fuzzy” regions of the projection, where relative distances should be interpreted with caution. Also, we present case studies that demonstrate the value of the pipeline for exploring multi-organism full proteome comparisons. Finally, we make this pipeline accessible to a wider research community by sharing thePLVis Colab Notebook. PLVis offers a low-barrier platform for researchers to explore and compare proteomes through the lens of language models.
Spatial context allows the evolution the control of nitrification by plants
Authors: Ardichvili Alice Nadia , Barot Sébastien , Lata Jean-Christophe , Loeuille Nicolas 
Published: November 2024

AbstractSome plant species inhibit or stimulate soil nitrification, the transformation of ammonium into nitrate by microorganisms. The control of nitrification may in turn alter ecosystem productivity and functioning. Given the potential positive impacts of nitrification control on plant fitness, we aim to determine the conditions under which nitrification control is likely to have been selected, and the consequences of that selection on ecosystem functioning. We investigate both the role of the abiotic context (nutrient availability and diffusion) and the role of other plant traits (mortality and dispersal). A first mean-field model shows that when nitrogen pools are shared among individuals within the plant population, the control of nitrification is counter-selected. A tragedy of the commons occurs because the costs of controlling nitrification (ie. of producing root exudates) only affect the controlling individuals while benefits are shared among all individuals. We then assume that the effects of the control of nitrification are spatially restricted to the rhizosphere, and we build a spatially explicit, individual-based model in which mutation of control of nitrification is possible. Plant capacity to control nitrification evolves when the plant environment is sufficiently private and generation time sufficiently long, leading to higher fitness benefits of the construction process. In such cases, plants evolve to inhibit nitrification when losses of nitrate are greater than losses of ammonium and evolve to stimulate nitrification when losses of ammonium are greater than losses of nitrate. Finally, biomass production tends to be maximal at the selected strategy when the diffusion of ammonium and nitrate is low. Our results help predict which strategies should be selected and likely to be found in different plants in different parts of the world.
Electrical charge-mediated transformation for efficient plant genome editing
Authors: Augustine Sruthy Maria , Cherian Anoop Vadakan , Paridhi Paridhi , Rashid Md Mamunur , Ugwuanyi Samson , Knoblauch Babette , Tzigos Stavros , Pullamsetti Soni Savai , Snowdon Rod 
Published: November 2024

AbstractGenome editing technologies possess significant potential to enhance plant breeding; however, the delivery of editing constructs poses challenges in numerous crop species due to their resistance to transformation or tissue culture. This study introduces an innovative approach for the delivery of ribonucleoprotein (RNP) complexes and plasmid vectors into intact, regenerable faba bean plant tissues. This is accomplished by applying an electric current that makes plant cell walls and membranes permeable, thereby allowing the entry of macromolecular constructs into the cell and nucleus. This study assessed the efficacy of electric pulse-mediated transfection in faba bean by generating stable GFP-expressing faba bean plants. Furthermore, we incorporated it into faba bean leaf tissue and demonstrated its application in both embryos and leaf tissues. We demonstrate DNA-free genome editing by targeting the endogenous phytoene desaturase gene (PDS), achieving a mutation success rate of 50%. This method is efficient and economical, necessitating limited technical training. It is applicable to both leaf and embryo tissues, thereby enhancing its utility for crop improvement. This technique shows potential for the development of new crop varieties that can more effectively address global climate challenges.
Towards robust machine olfaction: debiasing GC-MS data enhances prostate cancer diagnosis from urine volatiles
Authors: Rotteveel Adan , Lee Wen-Yee , Kountouri Zoi , Stefanou Nikolas , Kivell Howard , Gluck Clifford , Zhang Shuguang , Mershin Andreas 
Published: November 2024

AbstractWe present here a generalizable approach to de-biasing and de-trending before clustering complex datasets, using the specific example of prostate cancer diagnosis from gas chromatography-mass spectrometry ion chromatograms. We endeavor to mimic the olfactory cancer diagnostic prowess of trained dogs to establish, in perceptual space (as opposed to analytical chemistry space), a robustly recognizable signal that can be associated with the presence or absence of prostate cancer in the person who provided the urine sample. Upon performing principal component analysis, we found that using unsupervised clustering, the data had a strong tendency to cluster with respect to the urine sample source medical center, so a bias detector and baseline-drift remover had to be created as part of our pre-processing. Our machine olfaction approach marks a departure from conventional analytical chemistry sample analysis that leads to identification of the constituent compounds by name and concentration and moves us towards a generalizable, adaptable biomarker which in this case we call the emergent scent character. These scent characters are informed by measurements performed on volatile organic compounds (VOCs) but are not in themselves lists of VOCs or any of their physicochemical parameters added linearly. Ultimately, we use techniques prevalent in machine vision repurposed for machine olfaction by allowing for recognition and categorization of our scent character patterns as if they were images.
Population genomics ofMarchantia polymorphasubspeciesruderalisreveals evidence of climate adaptation
Authors: Wu Shuangyang , Jandrasits Katharina , Swarts Kelly , Roetzer Johannes , Akimcheva Svetlana , Shimamura Masaki , Hisanaga Tetsuya , Berger Frédéric , Dolan Liam 
Published: November 2024

ABSTRACTSexual reproduction results in the development of haploid and diploid cell states during the life cycle. In bryophytes the dominant multicellular haploid phase produces motile sperm that swim through water to the egg to effect fertilization from which a relatively small diploid phase develops. In angiosperms, the reduced multicellular haploid phase produces non-motile sperm that is delivered to the egg through a pollen tube to effect fertilization from which the dominant diploid phase develops. These different life cycle characteristics are likely to impact the distribution of genetic variation among populations. However, little is known about the distribution of genetic variation among populations of bryophytes. To understand how genetic variation is distributed among populations of a bryophyte and to establish the foundation for population genetics research in bryophytes, we described the genetic diversity of collections ofMarchantia polymorphasubspeciesruderalis, a cosmopolitan ruderal liverwort. We explored genetic diversity of this species using 78 genetically unique (non-clonal) accessions from a total of 209 collected from 37 sites in Europe and Japan. There was no detectable population structure among European populations but significant genetic differentiation between Japanese and European populations. By associating genetic variation across the genome with global climate data, we identified summer temperature and precipitation as climate factors influencing the frequency of adaptative alleles. We speculate that the requirement for water through which motile sperm swim imposes a constraint on the life cycle to which the plant genetically adapts.