bluuebunny/crossref_metadata_2025_split huggingface dataset:
Fuel buildup shapes post-fire fuel decomposition through soil heating effects on plants, fungi, and soil chemistry
Authors: Hopkins Jacob R. , Semenova-Nelsen Tatiana A. , Huffman Jean M. , Jones Neil J. , Robertson Kevin M. , Platt William J. , Sikes Benjamin A. 
Published: May 2024

AbstractForty percent of terrestrial ecosystems require recurrent fires engineered by feedbacks between fire and plant fuels. Fuel loads control fire intensity which alters soil nutrients and shapes soil microbial and plant community responses to fire. Changes to post-fire plant fuel production are well known to feed back to future fires, but post-fire decomposition of new fuels is poorly understood. Our study sought to quantify how pre-fire fuel loading impacted post-fire fuel decomposition through soil abiotic properties, plant and soil fungal communities. In a longleaf pine savanna, both near and away from overstory pines, we manipulated pre-fire plot fuel loads to modify soil heating. We then assessed how fuel load and soil heating influenced post-fire plant fuel decomposition through changes to soil chemistry, vegetation, and fungi. Larger fuel loads, particularly beneath pines, increased soil heating and reduced decomposition of newly deposited fuels during the eight months following fire. Fire intensity effects on soil nutrients had the most consistent effects on decomposition with plant and fungal communities playing secondary roles. This demonstrates how fuel load and soil heating influence post-fire decomposition through fire-driven changes to soil abiotic properties, plant communities, and soil fungi. Further, since fire effects on decomposition and fire-fuel feedbacks were temporally dynamic this illustrates the importance of considering fire-fuel feedbacks across time. Understanding the importance of these feedbacks among ecosystems can help increase our predictive ability to manage fuels and the effects of repeated fires.
Real-time monitoring of attenuated cytomegalovirus using Raman spectroscopy allows non-destructive characterization during flow
Authors: Athalye Shreya Milind , Maruthamuthu Murali K. , Esmaili Ehsan , Boodaghidizaji Miad , Raffaele Jessica , Selvamani Vidhya , Smith Joseph P. , Matos Tiago , Rustandi Richard R. , Ardekani Arezoo M. , Verma Mohit S. 
Published: May 2024

AbstractReal-time monitoring of viral particles can have a crucial impact on vaccine manufacturing and can alleviate public health by supporting continuous supply. Spectroscopic methods such as Raman spectroscopy can provide rapid and non-invasive measurements. Here, we have developed a Raman spectroscopy-based tool to monitor the quality and quantity of viral particles in a continuous flow set-up. The attenuated human cytomegalovirus (CMV) is characterized across a wide range of concentrations (4.50 x 109to 2.90 x 1011particles/mL) and flow rates (100 µm/s to 1000 µm/s) within a square quartz capillary. This process analytical technology (PAT) tool enables the detection of viral particles even at high flow rates such as 1000 µm/s. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) and dynamic light scattering (DLS) demonstrated that the samples maintain their integrity even after laser exposure, reiterating the non-invasive nature of Raman spectroscopy. To the best of our knowledge, this is thefirstreport on characterizing CMV particles using Raman spectroscopy. We have also demonstrated the limit of detection (LoD) (2.36 x 1010particles/mL) for CMV particles in continuous flow (via the Raman spectroscopy method) by addressing the effect of flow rate, concentration, and integrity of samples. This technology could enhance our understanding of the quality control in bio-manufacturing processes required in vaccine production.
CELLama: Foundation Model for Single Cell and Spatial Transcriptomics by Cell Embedding Leveraging Language Model Abilities
Authors: Choi Hongyoon , Park Jeongbin , Kim Sumin , Kim Jiwon , Lee Dongjoo , Bae Sungwoo , Shin Haenara , Lee Daeseung 
Published: May 2024

AbstractLarge-scale single-cell RNA sequencing (scRNA-seq) and spatial transcriptomics (ST) have transformed biomedical research into a data-driven field, enabling the creation of comprehensive data atlases. These methodologies facilitate detailed understanding of biology and pathophysiology, aiding in the discovery of new therapeutic targets. However, the complexity and sheer volume of data from these technologies present analytical challenges, particularly in robust cell typing, integration and understanding complex spatial relationships of cells. To address these challenges, we developed CELLama (Cell Embedding Leverage Language Model Abilities), a framework that leverage language model to transform cell data into ’sentences’ that encapsulate gene expressions and metadata, enabling universal cellular data embedding for various analysis. CELLama, serving as a foundation model, supports flexible applications ranging from cell typing to the analysis of spatial contexts, independently of manual reference data selection or intricate dataset-specific analytical workflows. Our results demonstrate that CELLama has significant potential to transform cellular analysis in various contexts, from determining cell types across multi-tissue atlases and their interactions to unraveling intricate tissue dynamics.
Direct single-molecule detection and super-resolution imaging with a low-cost portable smartphone-based microscope
Authors: Loretan Morgane , Barella Mariano , Fuchs Nathan , Kocabey Samet , Kołątaj Karol , Stefani Fernando D. , Acuna Guillermo P. 
Published: May 2024

ABSTRACTWe present a novel, low-cost, portable smartphone-based fluorescence microscope capable of directly detecting single molecules without signal amplification. The setup leverages the image sensors and data handling capacity of mass-produced smartphones, making it adaptable to any smartphone and capable of detecting single molecules across the visible spectral range. We showcase this capability through single-molecule measurements on DNA origami models and super-resolution microscopy of biological cells by single-molecule localization microscopy. This development paves the way for biotechnology innovations making use of massively distributed or personalized assays with single-molecule sensitivity with the potential to revolutionize digital bioassays, point-of-care diagnostics, field expeditions, STEM outreach, and life science education.
Concurrent Joint Contact in Anterior Cruciate Ligament Injury induces cartilage micro-injury and subchondral bone sclerosis, resulting in knee osteoarthritis
Authors: Takahata Kei , Lin Yu-Yang , Osipov Benjamin , Arakawa Kohei , Enomoto Saaya , Christiansen Blaine A. , Kokubun Takanori 
Published: May 2024

ABSTRACTObjectiveAnterior Cruciate Ligament (ACL) injury initiates post-traumatic osteoarthritis (PTOA) via two distinct processes: initial direct contact injury of the cartilage surface during ACL injury, and secondary joint instability due to the ACL deficiency. Using the well-established Compression-induced ACL rupture method (ACL-R) and a novel Non-Compression ACL-R model, we aimed to reveal the individual effects of cartilage compression and joint instability on PTOA progression after ACL injury in mice.DesignTwelve-week-old C57BL/6J male were randomly divided to three experimental groups: Compression ACL-R, Non-Compression ACL-R, and Intact. Following ACL injury, we performed joint laxity testing and microscopic analysis of the articular cartilage surface at 0 days, in vivo optical imaging of matrix-metalloproteinase (MMP) activity at 3 and 7 days, and histological and microCT analysis at 0, 7, 14, and 28 days.ResultsThe Compression ACL-R group exhibited a significant increase of cartilage roughness immediately after injury compared with the Non-Compression group. At 7 days, the Compression group exhibited increased MMP-induced fluorescence intensity and MMP-13 positive cell ratio of chondrocytes. Moreover, histological cartilage degeneration was observable in the Compression group at the same time point. Sclerosis of tibial subchondral bone in the Compression group was more significantly developed than in the Non-Compression group at 28 days.ConclusionsBoth Compression and Non-Compression ACL injury initiated PTOA progression due to joint instability. However, joint contact during ACL rupture also caused initial micro-damage on the cartilage surface and initiated early MMP activity, which could accelerate PTOA progression compared to ACL injury without concurrent joint contact.
Multifunctional molecular hybrid for targeted colorectal cancer cells: Integrating doxorubicin, AS1411 aptamer, and T9/U4 ASO
Authors: Jiramitmongkon Kanpitcha , Rotkrua Pichayanoot , Khanchaitit Paisan , Arunpanichlert Jiraporn , Soontornworajit Boonchoy 
Published: May 2024

AbstractColorectal cancer (CRC) is one of the public-health concerns worldwide and it requires an effective treatment. However, existing treatment approaches encounter challenges related to specificity and efficacy. To address this issue, a platform for multifunctional drug delivery has been developed, combining bioactive materials with anticancer elements and specific recognition ligands into a single molecule. This study aimed to create a molecular hybrid (MH) containing doxorubicin, AS1411 aptamer, and T9/U4 ASO to regulate SW480 cell proliferation. The AS1411 aptamer targets nucleolin, overexpressed on cancer cell membranes, while T9/U4 ASO inhibits human telomerase RNA activity, further hindering cancer cell proliferation. AS-T9/U4_MH was synthesized via oligonucleotide hybridization, followed by doxorubicin loading and evaluation of its impact on cell proliferation. Binding capability of this MH was verified using fluorescence microscopy and flow cytometry, demonstrating specific recognition of SW480 cells due to nucleolin availability on the cell surface. These findings were corroborated by both microscopy and flow cytometry. AS-T9/U4_MH exhibited anti-proliferative effects, with the doxorubicin-loaded system demonstrating encapsulation and reduced toxicity. Moreover, the presence of Dox within AS-T9/U4_MH led to a notable reduction in hTERT and vimentin expression in SW480 cells. Additionally, examination of apoptotic pathways unveiled a marked decrease in Bcl-2 expression and a simultaneous increase in Bax expression in SW480 cells treated with Dox-loaded AS-T9/U4_MH, indicating its impact on promoting apoptosis. These results suggest that the molecular hybrid holds promise as a system for integrating chemotherapeutic drugs with bioactive materials for cancer treatment delivery.
Predicting MHC-I ligands across alleles and species: How far can we go?
Authors: Tadros Daniel M. , Racle Julien , Gfeller David 
Published: May 2024

ABSTRACTCD8+T-cell activation is initiated by the recognition of epitopes presented on class I major histocompatibility complex (MHC-I) molecules. Identifying such epitopes is useful for molecular understanding of cellular immune responses and can guide the development of personalized vaccines for various diseases including cancer. Here, we capitalize on high-quality MHC-I peptidomics data available from different species and an expanded architecture of our MHC-I ligand predictor (MixMHCpred) to carefully explore how much predictions can be extrapolated to MHC-I alleles without known ligands. Our results reveal high prediction accuracy for most MHC-I alleles in human and in laboratory mouse strains, but significantly lower accuracy in other species. Our work further outlines some of the molecular determinants of MHC-I ligand predictions accuracy across alleles and species. Robust benchmarking on external data shows that the pan-allele version of MixMHCpred (v3.0) outperforms other state-of-the-art MHC-I ligand predictors and can be used for CD8+T-cell epitope predictions.
mRNA psi profiling using nanopore DRS reveals cell type-specific pseudouridylation
Authors: McCormick Caroline A. , Meseonznik Michele , Qiu Yuchen , Fanari Oleksandra , Thomas Mitchell , Liu Yifang , Bloch Dylan , Klink Isabel N. , Jain Miten , Wanunu Meni , Rouhanifard Sara H. 
Published: May 2024

AbstractPseudouridine (psi) is one of the most abundant human mRNA modifications generated via psi synthases, includingTRUB1andPUS7. Nanopore direct RNA sequencing combined with our recently developed tool, Mod-pID, enables psi mapping, transcriptome-wide, without chemical derivatization of the input RNA and/or conversion to cDNA. This method is sensitive for detecting differences in the positional occupancy of psi across cell types, which can inform our understanding of the impact of psi on gene expression. We sequenced, mapped, and compared the positional psi occupancy across six immortalized human cell lines derived from diverse tissue types. We found that lung-derived cells have the highest proportion of psi, while liver-derived cells have the lowest. Further, we find that conserved psi positions on mRNAs produce higher levels of protein than expected, suggesting a role in translation regulation. Interestingly, we identify cell type-specific sites of psi modification in ubiquitously expressed genes. Finally, we characterize transcripts with multiple psi modifications and found that these psi sites can be conserved or cell type-specific, including examples of multiple psi modifications within the same motif. Our data suggest that psi modifications contribute to regulating translation and that cell type-specific trans-acting factors play a major role in driving pseudouridylation.
A Catalog of the Public T-cell Response to Cytomegalovirus
Authors: May Damon H. , Woodhouse Steven , Howie Bryan , Robins Harlan S. 
Published: May 2024

ABSTRACTECOclusters (Exposure Co-Occurrence clusters) are previously described groups of public T-cell receptors (TCRs) that tend to co-occur across T-cell repertoires from tens of thousands of donors. Each ECOcluster putatively represents the public T-cell response to a different prevalent immune exposure. We previously associated a 26,106-member ECOcluster with exposure to cytomegalovirus (CMV) and used it to define a sensitive, specific classifier for CMV seropositivity.Here, we provide the CMV-associated ECOcluster TCRs, describe the ECOcluster and explore some types of analysis that it enables. We assess the CMV specificity of its component HLA-COclusters (subgroups of co-occurring TCRs associated with the same HLA). We use TCR sequence similarity within HLA-ECOclusters to identify groups of TCRs putatively responding to the same antigen, and we find suggestions of different subgroups of CMV-exposed donors responding to different antigens.The CMV ECOcluster is the most complete catalog of the public T-cell response to CMV to date. We provide the CMV ECOcluster TCRs as a resource for research community use and exploration.
Super-enhancer interactomes from single cells link clustering and transcription
Authors: Le Derek J. , Hafner Antonina , Gaddam Sadhana , Wang Kevin C. , Boettiger Alistair N. 
Published: May 2024

SummaryRegulation of gene expression hinges on the interplay between enhancers and promoters, traditionally explored through pairwise analyses. Recent advancements in mapping genome folding, like GAM, SPRITE, and multi-contact Hi-C, have uncovered multi-way interactions among super-enhancers (SEs), spanning megabases, yet have not measured their frequency in single cells or the relationship between clustering and transcription. To close this gap, here we used multiplexed imaging to map the 3D positions of 376 SEs across thousands of mammalian nuclei. Notably, our single-cell images reveal that while SE-SE contacts are rare, SEs often form looser associations we termed “communities”. These communities, averaging 4-5 SEs, assemble cooperatively under the combined effects of genomic tethers, Pol2 clustering, and nuclear compartmentalization. Larger communities are associated with more frequent and larger transcriptional bursts. Our work provides insights about the SE interactome in single cells that challenge existing hypotheses on SE clustering in the context of transcriptional regulation.
Individual differences in prefrontal coding of visual features
Authors: Lin Qi , Lau Hakwan 
Published: May 2024

AbstractEach of us perceives the world differently. What may underlie such individual differences in perception? Here, we characterize the lateral prefrontal cortex’s role in vision using computational models, with a specific focus on individual differences. Using a 7T fMRI dataset, we found that encoding models relating visual features extracted from a deep neural network to brain responses to natural images robustly predict responses in patches of LPFC. We then explored the representational structures and screened for images with high predicted responses in LPFC. We observed more substantial individual differences in the coding schemes of LPFC compared to visual regions. Computational modeling suggests that the amplified individual differences could result from the random projection between sensory and high-level regions underlying flexible working memory. Our study demonstrates the under-appreciated role of LPFC in visual processing and suggests that LPFC may underlie the idiosyncrasies in how different individuals experience the visual world.
DeepES: Deep learning-based enzyme screening to identify orphan enzyme genes
Authors: Hirota Keisuke , Salim Felix , Yamada Takuji 
Published: May 2024

AbstractMotivationProgress in sequencing technology has led to determination of large numbers of protein sequences, and large enzyme databases are now available. Although many computational tools for enzyme annotation were developed, sequence information is unavailable for many enzymes, known as orphan enzymes. These orphan enzymes hinder sequence similarity-based functional annotation, leading gaps in understanding the association between sequences and enzymatic reactions.ResultsTherefore, we developed DeepES, a deep learning-based tool for enzyme screening to identify orphan enzyme genes, focusing on biosynthetic gene clusters and reaction class. DeepES uses protein sequences as inputs and evaluates whether the input genes contain biosynthetic gene clusters of interest by integrating the outputs of the binary classifier for each reaction class. The validation results suggested that DeepES can capture functional similarity between protein sequences, and it can be implemented to explore orphan enzyme genes. By applying DeepES to 4744 metagenome-assembled genomes, we identified candidate genes for 236 orphan enzymes, including those involved in short-chain fatty acid production as a characteristic pathway in human gut bacteria.Availability and implementationDeepES is available athttps://github.com/yamada-lab/DeepES. Model weights and the candidate genes are available at Zenodo (https://doi.org/10.5281/zenodo.11123900).
One size does not fit all: a novel approach for determining the Realised Viewshed Size for remote camera traps
Authors: Carswell B.M. , Avgar T. , Street G.M. , Boyle S.P. , Vander Wal E. 
Published: May 2024

Abstract1. Camera traps (CTs) have become cemented as an important tool of wildlife research, yet, their utility is now extending beyond academics, as CTs can contribute to more inclusive place-based wildlife management. From advances in analytics and technology, CT-based density estimates of wildlife is an emerging field of research. Most CT-based density methods require an estimate of the size of the viewshed monitored by each CT, a parameter that may be highly variable and difficult to quantify.2. Here, we developed and tested a standardized field and analytical method allowing us to predict the probability of photographic capture as it varies within CT viewshed. We investigated how capture probability changes due to environmental influences, i.e., vegetation structure, ambient temperature, speed of subject, time of day, in addition to internal factors from CTs themselves, i.e., sensitivity settings, number of photos taken, and CT brand. We then summarize these spatial capture probability kernels into aRealised Viewshed Size(RVS)—the capture-probability corrected size of a CTs viewshed3. We found that RVS values are heavily influenced by location-specific environmental factors, i.e., vegetation structure, technological delays associated with CTs themselves, i.e., refractory period, and internal CT settings, i.e., sensitivity, number of photographs taken. We also found that the RVS values computed using our methodology are substantially smaller than reported values in the literature.4. Imprecision surrounding CT viewshed areas can create propagating bias when implementing CT-based density estimators. Our method can change how practitioners consider photographs for use in CT density estimators thus increasing the reliability of CT-based density estimation, and contribute to more accessible wildlife management practices.
Maximising the translational potential of neurophysiology in amyotrophic lateral sclerosis: a study on compound muscle action potentials
Authors: McKinnon Scott , Qiang Zekai , Keerie Amy , Wells Tyler , Shaw Pamela J. , Alix James J.P. , Mead Richard J. 
Published: May 2024

AbstractTransgenic mouse models of amyotrophic lateral sclerosis, such as the widely used SOD1G93Amouse, enable investigation of disease mechanisms and testing of novel therapeutic interventions. However, treatments that have been considered successful in mice have often failed to translate into human benefit in clinical trials, particularly when relying on the so-called ‘survival’ read-out. Compound muscle action potentials (CMAPs), are a simple neurophysiological test that measures the summation of muscle fibre depolarisation in response to maximal stimulation of the innervating nerve. CMAPs can be measured in both mice and humans and decline with motor axon loss in ALS, making them a potential translational read-out of disease progression which could help bridge the preclinical and clinical divide. Herein we assess the translational potential of CMAPs and ascertain at what time points human and mouse data aligned most closely. We extracted data from 18 human studies and compared with results generated from SOD1G93Aand control mice at different ages across different muscles. We found that the relative CMAP amplitude difference between SOD1G93Aand control mice in tibialis anterior and gastrocnemius muscles at 70 days of age was most similar to the relative difference between baseline ALS patient CMAP measurements and healthy controls in the abductor pollicis brevis (APB) muscle. We also found that the relative decline in SOD1G93Atibialis anterior CMAP amplitude between 70-140 days was similar to that observed in 12 month human longitudinal studies in APB. Our findings suggest CMAP amplitudes can provide a ‘translational window’, from which to make comparisons between the SOD1G93Amodel and human ALS patients. CMAPs are easy to perform and can help determine the most clinically relevant starting/end points for preclinical studies and provide a basis for predicting potential clinical effect sizes.