bluuebunny/crossref_metadata_2025_split huggingface dataset:
Using the Disruptive Score to Identify Publications That Changed Plastic Surgery Practice
Authors: Neubauer Daniel C. , Blum Jessica D. , Labou Stephanie G. , Heskett Karen M. , Calvo Richard Y. , Reid Christopher M. , Martin Matthew J. , Gosman Amanda A. 
Published: September 2023

Purpose
The impact of academic publications is often characterized by the total number of future citations. However, this metric does not adequately characterize the true impact in terms of changing practices or paradigms. A new metric called the “disruption score” (DS) has been developed and validated in nonsurgical publications. This study aims to use the DS to identify the most disruptive publications in plastic surgery.
The DS, a ratio of 2 numbers, varies between −1 and +1. Scores closer to −1 are developing papers that summarize the known literature while papers closer to +1 are disruptive—they result in a paradigm shift in the field of study.

Methods
A search was performed for all articles from 1954 to 2014 in the following journals: Plastic and Reconstructive Surgery; Aesthetic Surgery Journal; Journal of Plastic, Reconstructive, and Aesthetic Surgery; Annals of Plastic Surgery; Aesthetic Plastic Surgery; Clinics in Plastic Surgery; and Plastic Surgery. The disruptive score was calculated for each article.
The top 100 papers ranked by DS were examined and any editorials/viewpoints, publications with less than 26 citations, or less than 3 references were excluded because of their subjective nature and smaller academic contribution. The remaining 64 publications were analyzed for topic, study type, and citation count.

Results
A total of 32,622 articles were found with a DS range from 0.385 to 0.923. The mean score of the top 64 articles was 0.539 with an average citation count of 195 and 9 references. Plastic and Reconstructive Surgery had the most disruptive papers with 50. There were no randomized controlled trials with a majority of the studies being technical descriptions or case series.

Conclusions
There are many ways to measure academic success, but there are fewer ways to measure the impact of academic contributions. The DS is a novel measurement that can demonstrate when an article results in a paradigm shift as opposed to just total citation count. When applied to the plastic surgery literature, the DS demonstrates that technical innovation and creativity are the most academically impactful. Future evaluations of academic success should include the DS to measure the quality of academic contributions.
Land use configuration shapes climate change risk to gallery forests in a savannah ecosystem
Authors: Schulte to Bühne Henrike , Tobias Joseph A. , Durant Sarah M. , Pettorelli Nathalie 
Published: September 2023

AbstractInteractions between anthropogenic pressures make it difficult to predict biodiversity change and plan conservation interventions. Climate change is expected to drive widespread ecological change in the tropics over the coming decades, but it is unclear where and when these changes are going to intensify, or reduce, the impacts of additional pressures from human land use. To address this uncertainty, we apply a novel risk assessment framework to show how land use configuration modifies risks arising from climate change to gallery forests, an important vegetation type in tropical savannahs. Our analysis shows that the spatial distribution of climate change (specifically, change in annual rainfall) interacts with the spatial distribution of land use (specifically, cropland), as well as the biophysical context of the study site (the W-Arly-Pendjari transboundary protected area in West Africa), to shape the risk that changes in rainfall pose to gallery forests in the region. Due to the pathways by which rainfall change and land use interact, risks are especially elevated in core protected areas, warranting particular attention from conservation managers. Overall, our work illustrates how unexpected patterns in risks can arise through interactions between pressures on biodiversity, highlighting the importance of considering mechanistic pathways for predicting biodiversity outcomes under multifacetted global environmental change.
TSWIFT, a novel method for iterative staining of embedded and mounted human brain sections
Authors: Porter Corey M , Truttmann Matthias C. 
Published: September 2023

AbstractComprehensive characterization of protein networks in mounted brain tissue represents a major challenge in brain and neurodegenerative disease research. In this study, we develop a simple staining method, called TSWIFT, to iteratively stain pre-mounted formalin fixed, paraffin embedded (FFPE) brain sections, thus enabling high-dimensional sample phenotyping. We show that TSWIFT conserves tissue architecture and allows for relabeling a single mounted FFPE sample more than 10 times, even after prolonged storage at 4 °C. Using TSWIFT, we profile the abundance and localization of the HSP70 family chaperones HSC70 (HSPA8) and BiP (HSPA5) in mounted human brain tissue. Our results establish TSWIFT as an efficient method to obtain integrated high-dimensional knowledge of cellular proteomes by analyzing mounted FFPE human brain tissue.
NSD1 supports cell growth and regulates autophagy in HPV-negative head and neck squamous cell carcinoma
Authors: Topchu Iuliia , Bychkov Igor , Gursel Demirkan , Makhov Petr , Boumber Yanis 
Published: September 2023

AbstractHead and neck squamous cell carcinoma (HNSCC) is the sixth most common cancer worldwide. Despite advances in therapeutic management and immunotherapy, the five-year survival rate for head and neck cancer remains at ∼66% of all diagnosed cases. A better definition of drivers of HPV-negative HNSCC that are targetable points of tumor vulnerability could lead to significant clinical advances. NSD1 is a histone methyltransferase which catalyzes histone H3 lysine 36 di-methylation (H3K36me2); mutations inactivating NSD1 have been linked to improved outcomes in HNSCC. In this study, we show that NSD1 induces H3K36me2levels in HNSCC, and that the depletion of NSD1 reduces HNSCC of cell growthin vitroandin vivo. We also find that NSD1 strongly promotes activation of the Akt/mTORC1 signaling pathway. NSD1 depletion in HNSCC induces an autophagic gene program activation, causes accumulation of the p62 and LC3B-II proteins, and decreases the autophagic signaling protein ULK1 at both protein and mRNA levels. Reflecting these signaling defects, knockdown of NSD1 disrupts autophagic flux in HNSCC cells. Taken together, these data identify positive regulation of Akt/mTORC1 signaling and autophagy as novel NSD1 functions in HNSCC, suggesting that NSD1 may be of value as a therapeutic target in this cancer.
Cardiomyocyte-specific Loss of Glutamyl-prolyl-tRNA Synthetase Leads to Disturbed Protein Homeostasis and Dilated Cardiomyopathy
Authors: Wu Jiangbin , Hollinger Jared , Bonanno Emily , Jiang Feng , Yao Peng 
Published: September 2023

AbstractGlutamyl-prolyl-tRNA synthetase (EPRS1), an aminoacyl-tRNA synthetase (ARS) ligating glutamic acid and proline to their corresponding tRNAs, plays an essential role in decoding proline codons during translation elongation. The physiological function of EPRS1 in cardiomyocytes (CMs) and the potential effects of CM-specific loss of EPRS1 remain unknown. Here, we found that heterozygousEprs1knockout in CMs does not cause any significant changes in CM hypertrophy induced by pressure overload, while homozygous knockout leads to dilated cardiomyopathy, heart failure, and lethality at around 1 month afterEprs1deletion. Transcriptomic profiling of early-stageEprs1knockout hearts suggests a significantly decreased expression of multiple ion channel genes and an increased gene expression in proapoptotic pathways and integrated stress response. Proteomic analysis shows decreased protein expression of multi-aminoacyl-tRNA synthetase complex components, fatty acid, and branched-chain amino acid metabolic enzymes, as well as a compensatory increase in cytosolic translation machine-related proteins. Immunoblot analysis indicated that multiple proline-rich proteins were reduced at the early stage, which might contribute to cardiac dysfunction ofEprs1knockout mice. Taken together, this study demonstrates the physiological and molecular outcome of loss-of-function of EPRS1in vivoand provides valuable insights into the potential side effects on CMs resulting from the EPRS1-targeting therapeutic approach.
Bering:joint cell segmentation and annotation for spatial transcriptomics with transferred graph embeddings
Authors: Jin Kang , Zhang Zuobai , Zhang Ke , Viggiani Francesca , Callahan Claire , Tang Jian , Aronow Bruce J. , Shu Jian 
Published: September 2023

AbstractSingle-cell spatial transcriptomics such asin-situhybridization or sequencing technologies can provide subcellular resolution that enables the identification of individual cell identities, locations, and a deep understanding of subcellular mechanisms. However, accurate segmentation and annotation that allows individual cell boundaries to be determined remains a major challenge that limits all the above and downstream insights. Current machine learning methods heavily rely on nuclei or cell body staining, resulting in the significant loss of both transcriptome depth and the limited ability to learn latent representations of spatial colocalization relationships. Here, we proposeBering, a graph deep learning model that leverages transcript colocalization relationships for joint noise-aware cell segmentation and molecular annotation in 2D and 3D spatial transcriptomics data. Graph embeddings for the cell annotation are transferred as a component of multi-modal input for cell segmentation, which is employed to enrich gene relationships throughout the process. To evaluate performance, we benchmarkedBeringwith state-of-the-art methods and observed significant improvement in cell segmentation accuracies and numbers of detected transcripts across various spatial technologies and tissues. To streamline segmentation processes, we constructed expansive pre-trained models, which yield high segmentation accuracy in new data through transfer learning and self-distillation, demonstrating the generalizability ofBering.
A multivariate outcome test of covariance
Authors: Boetto Christophe , Frouin Arthur , Henches Léo , Auvergne Antoine , Suzuki Yuka , Patin Etienne , Bredon Marius , Chiu Alec ,   Milieu Interieur Consortium, Sankararaman Sriram , Zaitlen Noah , Kennedy Sean P. , Quintana-Murci Lluis , Duffy Darragh , Sokol Harry , Aschard Hugues 
Published: September 2023

AbstractMultivariate analysis is becoming central in studies investigating high-throughput molecular data, yet, some important features of these data are seldom explored. Here, we present MANOCCA (Multivariate Analysis of Conditional CovAriance), a powerful method to test for the effect of a predictor on the covariance matrix of a multivariate outcome. The proposed test is by construction orthogonal to tests based on the mean and variance, and is able to capture effects that are missed by both approaches. We first compare the performances of MANOCCA with existing correlation-based methods and show that MANOCCA is the only test correctly calibrated in simulation mimicking omics data. We then investigate the impact of reducing the dimensionality of the data using principal component analysis when the sample size is smaller than the number of pairwise covariance terms analysed. We show that, in many realistic scenarios, the maximum power can be achieved with a limited number of components. Finally, we apply MANOCCA to 1,000 healthy individuals from the Milieu Interieur cohort, to assess the effect of health, lifestyle and genetic factors on the covariance of two sets of phenotypes, blood biomarkers and flow cytometry-based immune phenotypes. Our analyses identify significant associations between multiple factors and the covariance of both omics data.
Integrated genomics provides insights for the evolution of the polyphosphate accumulation trait ofCa.Accumulibacter
Authors: Xie Xiaojing , Deng Xuhan , Chen Liping , Yuan Jing , Chen Hang , Wei Chaohai , Liu Xianghui , Wuertz Stefan , Qiu Guanglei 
Published: September 2023

AbstractCandidatusAccumulibacter plays a major role in enhanced biological phosphorus removal (EBPR), but the key genomic elements in metagenome assembled genomes enabling their phosphorus cycling ability remain unclear. Pangenome analyses were performed to systematically compare the genomic makeup ofCa.Accumulibacter and non-Ca. Accumulibacter members within the Rhodocyclaceae family. Metatranscriptomic analyses of an enrichment culture ofCa.Accumulibacter clade IIC strain SCUT-2 were performed to investigate gene transcription characteristics in a typical anaerobic-aerobic cycle. Two hundred ninety-eight core genes were shown to be obtained byCa.Accumulibacter at their least common ancestor. One hundred twenty-four of them were acquired via horizontal gene transfer (HGT) based on best-match analysis against the NCBI database. Fourty-four laterally derived genes were actively transcribed in a typical EBPR cycle, including the polyphosphate kinase 2 (PPK2) gene. Genes in the phosphate regulon (Pho) were poorly transcribed. Via a systematical analysis of the occurrences of these genes in closely relatedDechloromonas-polyphosphate accumulating organisms (PAOs) andPropionivibrio-non-PAOs, a Pho dysregulation hypothesis is proposed to explain the mechanism of EBPR. It states that the PhoU acquired by HGT fails in regulating the high-affinity phosphate transport (Pst) system. To avoid phosphate poisoning, the laterally acquired PPK2 is employed to condense excess phosphate into polyphosphate. Alternatively, genes encoding PhoU and PPK2 are obtained from different donor bacteria, leading to unmatched phosphate concentration thresholds for their activation/inactivation. PPK2 tends to reduce the intracellular phosphate to concentration levels perceived by PhoU as low-phosphate states. PhoU is not activated to turn off the Pst system, resulting in continuous phosphate uptake. In conclusion, based on integrated genomic analyses, the HGT ofphoU andppk2 and the resultant Pho dysregulation may have triggered the development and evolution of the P cycling trait inCa.Accumulibacter.
Distinct T Cell Receptor (TCR) gene segment usage and MHC-restriction between foetal and adult thymus
Authors: Rowell Jasmine , Lau Ching-In , Ross Susan , Yanez Diana C. , Peña Oscar A. , Chain Benny , Crompton Tessa 
Published: September 2023

AbstractHere we sequenced rearranged TCRβ and TCRα chain sequences in CD4+CD8+ double positive (DP), CD4+CD8-single positive (SP4) and CD4-CD8+ (SP8) thymocyte populations from the foetus and young adult mouse. We found that life-stage had a greater impact on TCRβ and TCRα gene segment usage than cell-type. Foetal repertoires showed bias towards 3’TRAV and 5’TRAJ rearrangements in all populations, whereas adult repertoires used more 5’TRAV gene segments, suggesting that progressive TCRα rearrangements occur less frequently in foetal DP cells. When we synchronised young adult DP thymocyte differentiation by hydrocortisone treatment the new recovering DP thymocyte population showed more foetal-like 3’TRAV and 5’TRAJ gene segment usage. In foetus we identified less influence of MHC-restriction on α-chain and β-chain combinatorial VxJ usage and CDR1xCDR2 (V region) usage in SP compared to adult, indicating weaker impact of MHC-restriction on the foetal TCR repertoire.The foetal TCRβ repertoire was less diverse, less evenly distributed, with fewer non-template insertions, and all foetal populations contained more clonotypic expansions than adult. The differences between the foetal and adult thymus TCR repertoires are consistent with the foetal thymus producing αβT-cells with properties and functions that are distinct from adult T-cells: their repertoire is less governed by MHC-restriction, with preference for particular gene segment usage, less diverse with more clonotypic expansions, and more closely encoded by genomic sequence.
Breeding alters females’ social positions by changing dominance dynamics
Authors: Dehnen Tobit , Nyaguthii Brendah , Cherono Wismer , Boogert Neeltje J. , Farine Damien R. 
Published: September 2023

AbstractAgonistic and affiliative interactions with group members dictate individuals’ access to resources, and investment in competing for resources is often traded off with other needs. For example, reproductive investment can reduce body condition and, thereby, an individual’s ability to win future agonistic interactions. However, group members may also alter their behaviour towards reproductive individuals, such as becoming more or less aggressive. Here, we investigated the social consequences of reproduction in female vulturine guineafowlAcryllium vulturinum, a plural breeder in which females disperse and are subordinate to males. We found opposing patterns for breeders’ within- and between-sex dominance interactions from before to after breeding. Specifically, while breeding females became far less likely to win dominance interactions with non-breeding females after breeding than before breeding, they received considerably fewer male aggressions than non-breeding females after breeding. Using agent-based models, we then show that hierarchies inferred using the Percolation and Conductance method are robust to such variation in interaction rates, while other common methods may be prone to systematically overestimating or underestimating particular individuals’ hierarchy positions. Our study highlights reproduction as a driver of dominance dynamics, and illustrates how the study of dominance may benefit from considering variation in interaction rates.
Phosphatidylinositol (PI) Lipids Modulate the Binding of Tau Fibrils on Lipid Bilayers
Authors: Chowdhury Unmesh D. , Paul Arnav , Bhargava B. L. 
Published: September 2023

AbstractPhosphatidylinositol (PI) lipids play a crucial role as a vital lipid component in cell membrane domain formation, contributing to cell signaling. In this study, we investigate the impact of PI lipids on the conformational dynamics of tubulin-associated unit (tau) fibrils through multiscale modelling. While prior experimental work by the Lecomte group has demonstrated the influence of PI lipids on the morphology and secondary structure of tau fragments, a detailed molecular understanding of the binding mechanism between tau and PI-incorporated lipids remains absent. Our molecular dynamics (MD) simulations reveal the intricate molecular mechanisms governing tau binding to PI-incorporated bilayers. Specifically, we conduct MD simulations on lipid patches containing 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (PC) and 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoglycerol (PG), enabling us to explore conformational changes in the R3–R4 section of tau fibrils. Control simulations are conducted on pure lipid patches without tau fibrils, as well as on tau fibrils within bulk water. Our findings demonstrate that PI-incorporated lipids exhibit a stronger affinity for binding to tau fibrils compared to pure PC/PG lipids. All-atom simulations highlight the potential docking sites for PI headgroups at positively charged residues (Lysine, Arginine) on the tau surface. Moreover, the aggregation of PI lipids facilitates tau binding to the membrane. These results not only enhance our comprehension of the disruption of PI-incorporated bilayers, but also shed light on the stability of the tau over the PI containing bilayers.
PMTPred: Machine Learning Based Prediction of Protein Methyltransferases using the Composition of k-spaced Amino Acid Pairs
Authors: Yadav Arvind Kumar , Gupta Pradeep Kumar , Singh Tiratha Raj 
Published: September 2023

AbstractProtein methyltransferases (PMTs) are a group of enzymes that help to catalyze the transfer of a methyl group to its substrates. These enzymes play an important role in epigenetic regulation and are able to methylate various substrates with DNA, RNA, protein, and smallmolecule secondary metabolites. Dysregulation of methyltransferases is involved in different types of human cancers. However, in light of the well-recognized significance of PMTs, it becomes crucial to have reliable and fast methods for identifying these proteins. In the present work, we propose a machine-learning-based method for the identification of PMTs. Various sequence-based features were calculated and prediction models were develped using different machine-learning methods. A ten-fold cross-validation technique was used for model training. The SVM-based CKSAAP model gave the best prediction and achieved the highest accuracy of 87.94% with balance sensitivity (88.8%) and specificity (87.11%) with MCC of 0.759 and AUROC of 0.945. Also, SVM performed better than the compared deep learning algorithms for the prediction of PMTs. Finally, the best model was implemented in standalone software of PMTPred to facilitate the prediction of PMTs. The PMTPred achieved 86.50% prediction accuracy with 82.33% sensitivity, 90.67% specificity and ROC value 0.939 on the blind dataset. The standalone software of PMTPred is freely available for download athttps://github.com/ArvindYadav7/PMTPredfor research and academic use.
In vivomulti-site electrophysiology enabled by flexible optrodes towards bi-directional spinal cord interrogation
Authors: Metuh Pietro , Meneghetti Marcello , Berg Rune W. , Markos Christos 
Published: September 2023

AbstractOptical neural interfaces combining optogenetics and electrophysiology have been demonstrated as powerful tools for distinguishing the causal roles of neural circuits in the nervous system. Functional optrodes for multipoint stimulation and recording have already been demonstrated in the brain. However, soft and flexible multimodal optrodes for the purpose of probing the spinal cord have remained undeveloped. Here, we present the design and fabrication of a novel optrode for multi-site optical stimulation and electrical recording in the spinal cord by combining optical fiber drawing of polymer material, laser micromachining, and integration of tungsten microelectrodes in a monolithic fiber-based structure. The results from space-resolved scattering measurements, electrochemical impedance spectroscopy, and an acutein vivoelectrophysiology experiment in an anesthetized rodent suggest this probe as a potential novel interface, which can serve as a part of therapeutic strategies against neurological conditions and injury in the spinal cord.