bluuebunny/crossref_metadata_2025_split huggingface dataset:
Specimen, biological structure, and spatial ontologies in support of a Human Reference Atlas
Authors: Herr Bruce W. , Hardi Josef , Quardokus Ellen M. , Bueckle Andreas , Chen Lu , Wang Fusheng , Caron Anita R. , Osumi-Sutherland David , Musen Mark A. , Börner Katy 
Published: March 2023

AbstractThe Human Reference Atlas (HRA) is defined as a comprehensive, three-dimensional (3D) atlas of all the cells in the healthy human body. It is compiled by an international team of experts who develop standard terminologies that they link to 3D reference objects, describing anatomical structures. The third HRA release (v1.2) covers spatial reference data and ontology annotations for 26 organs. Experts access the HRA annotations via spreadsheets and view reference object models in 3D editing tools. This paper introduces the Common Coordinate Framework (CCF) Ontology v2.0.1 that interlinks specimen, biological structure, and spatial data, together with the CCF API that makes the HRA programmatically accessible and interoperable with Linked Open Data (LOD). We detail how real-world user needs and experimental data guide CCF Ontology design and implementation, present CCF Ontology classes and properties together with exemplary usage, and report on validation methods. The CCF Ontology graph database and API are used in the HuBMAP portal, HRA Organ Gallery, and other applications that support data queries across multiple, heterogeneous sources.
The HAInich: A multidisciplinary vision data-set for a better understanding of the forest ecosystem
Authors: Milz Stefan , Wäldchen Jana , Abouee Amin , Ravichandran Ashwanth A. , Schall Peter , Hagen Chris , Borer John , Lewandowski Benjamin , Wittich Hans-Christian , Mäder Patrick 
Published: March 2023

AbstractWe present a multidisciplinary forest ecosystem 3D perception dataset. The dataset was collected in the Hainich-Dün region in central Germany, which includes two dedicated areas, which are part of the Biodiversity Exploratories - a long term research platform for comparative and experimental biodiversity and ecosystem research. The dataset combines several disciplines, including computer science and robotics, biology, bio-geochemistry, and forestry science. We present results for common 3D perception tasks, including classification, depth estimation, localization, and path planning. We combine the full suite of modern perception sensors, including high-resolution fisheye cameras, 3D dense LiDAR, differential GPS, and an inertial measurement unit, with ecological metadata of the area, including stand age, diameter, exact 3D position, and species. The dataset consists of three hand held measurement series taken from sensors mounted on a UAV during each of three seasons: winter, spring, and early summer. This enables new research opportunities and paves the way for testing forest environment 3D perception tasks and mission set automation for robotics.
Physical modeling and geometric shape simulation for one-dimensional flexible objects with cylindrical surface constraints
Authors: Mei Yuhang , Du Hongwang , Jiang Qinwen , Xiong Wei 
Published: March 2023

AbstractThis study develops forces equilibrium differential equations for the geometric modeling of 1D flexible objects with surface constraints. These second-order equations are an extension of the Cosserat elastic rod theory and include both bending and torsion. Variables were established for the centerline and attitude in the Cartesian coordinate system of the cross section. This paper specifically investigates the case of a 1D flexible object constrained by a cylindrical surface. To solve this problem, a novel hybrid semi-analytical numerical method is proposed. In this process, a Hamiltonian function and an initial integral operator are introduced in a cylindrical coordinate system. The analytical solution, decoupled in polar coordinates, is then derived. The improved finite difference method was then used to obtain three cylindrical coordinates, which ensured numerical stability and efficiency. The results of a geometric shape simulation with differing boundary conditions demonstrate that this proposed method is capable of real-time modeling. As such, this technique could be a promising new tool for use in graphics simulations of elongated structures, such as DNA molecules, drill pipes, and submarine cables.
Homologous recombination deficiency signatures in gastrointestinal and thoracic cancers correlate with platinum therapy duration
Authors: Tsang Erica S. , Csizmok Veronika , Williamson Laura M. , Pleasance Erin , Topham James T. , Karasinska Joanna M. , Titmuss Emma , Schrader Intan , Yip Stephen , Tessier-Cloutier Basile , Mungall Karen , Ng Tony , Sun Sophie , Lim Howard J. , Loree Jonathan M. , Laskin Janessa , Marra Marco A. , Jones Steven J. M. , Schaeffer David F. , Renouf Daniel J. 
Published: March 2023

AbstractThere is emerging evidence about the predictive role of homologous recombination deficiency (HRD), but this is less defined in gastrointestinal (GI) and thoracic malignancies. We reviewed whole genome (WGS) and transcriptomic (RNA-Seq) data from advanced GI and thoracic cancers in the Personalized OncoGenomics trial (NCT02155621) to evaluate HRD scores and single base substitution (SBS)3, which is associated withBRCA1/2mutations and potentially predictive of defective HRD. HRD scores were calculated by sum of loss of heterozygosity, telomeric allelic imbalance, and large-scale state transitions scores. Regression analyses examined the association between HRD and time to progression on platinum (TTPp). We included 223 patients with GI (n = 154) or thoracic (n = 69) malignancies. TTPp was associated with SBS3 (p < 0.01) but not HRD score in patients with GI malignancies, whereas neither was associated with TTPp in thoracic malignancies. Tumors with gBRCA1/2mutations and a somatic second alteration exhibited high SBS3 and HRD scores, but these signatures were also present in several tumors with germline but no somatic second alterations, suggesting silencing of the wild-type allele orBRCA1/2haploinsufficiency. Biallelic inactivation of an HR gene, including loss ofXRCC2andBARD1, was identified inBRCA1/2wild-type HRD tumors and these patients had prolonged response to platinum. Thoracic cases with high HRD score were associated with highRECQL5expression (p ≤ 0.025), indicating another potential mechanism of HRD. SBS3 was more strongly associated with TTPp in patients with GI malignancies and may be complementary to using HRD andBRCAstatus in identifying patients who benefit from platinum therapy.
Prediction model for drug response of acute myeloid leukemia patients
Authors: Trac Quang Thinh , Pawitan Yudi , Mou Tian , Erkers Tom , Östling Päivi , Bohlin Anna , Österroos Albin , Vesterlund Mattias , Jafari Rozbeh , Siavelis Ioannis , Bäckvall Helena , Kiviluoto Santeri , Orre Lukas M. , Rantalainen Mattias , Lehtiö Janne , Lehmann Sören , Kallioniemi Olli , Vu Trung Nghia 
Published: March 2023

AbstractDespite some encouraging successes, predicting the therapy response of acute myeloid leukemia (AML) patients remains highly challenging due to tumor heterogeneity. Here we aim to develop and validate MDREAM, a robust ensemble-based prediction model for drug response in AML based on an integration of omics data, including mutations and gene expression, and large-scale drug testing. Briefly, MDREAM is first trained in the BeatAML cohort (n = 278), and then validated in the BeatAML (n = 183) and two external cohorts, including a Swedish AML cohort (n = 45) and a relapsed/refractory acute leukemia cohort (n = 12). The final prediction is based on 122 ensemble models, each corresponding to a drug. A confidence score metric is used to convey the uncertainty of predictions; among predictions with a confidence score >0.75, the validated proportion of good responders is 77%. The Spearman correlations between the predicted and the observed drug response are 0.68 (95% CI: [0.64, 0.68]) in the BeatAML validation set, –0.49 (95% CI: [–0.53, –0.44]) in the Swedish cohort and 0.59 (95% CI: [0.51, 0.67]) in the relapsed/refractory cohort. A web-based implementation of MDREAM is publicly available at https://www.meb.ki.se/shiny/truvu/MDREAM/.
Preadapted to adapt: underpinnings of adaptive plasticity revealed by the downy brome genome
Authors: Revolinski Samuel R. , Maughan Peter J. , Coleman Craig E. , Burke Ian C. 
Published: March 2023

AbstractBromus tectorum L. is arguably the most successful invasive weed in the world. It has fundamentally altered arid ecosystems of the western United States, where it now found on an excess of 20 million hectares. Invasion success is related to avoidance of abiotic stress and human management. Early flowering is a heritable trait utilized by B. tectorum, enabling the species to temporally monopolize limited resources and outcompete the native plant community. Thus, understanding the genetic underpinning of flowering time is critical for the design of integrated management strategies. To study flowering time traits in B. tectorum, we assembled a chromosome scale reference genome for B. tectorum. To assess the utility of the assembled genome, 121 diverse B. tectorum accessions are phenotyped and subjected to a genome wide association study (GWAS). Candidate genes, representing homologs of genes that have been previously associated with plant height or flowering phenology traits in related species are located near QTLs we identified. This study uses a high-resolution GWAS to identify reproductive phenology genes in a weedy species and represents a considerable step forward in understanding the mechanisms underlying genetic plasticity in one of the most successful invasive weed species.
Direct reprogramming of human fibroblasts into insulin-producing cells using transcription factors
Authors: Fontcuberta-PiSunyer Marta , García-Alamán Ainhoa , Prades Èlia , Téllez Noèlia , Alves-Figueiredo Hugo , Ramos-Rodríguez Mireia , Enrich Carlos , Fernandez-Ruiz Rebeca , Cervantes Sara , Clua Laura , Ramón-Azcón Javier , Broca Christophe , Wojtusciszyn Anne , Montserrat Nuria , Pasquali Lorenzo , Novials Anna , Servitja Joan-Marc , Vidal Josep , Gomis Ramon , Gasa Rosa 
Published: March 2023

AbstractDirect lineage reprogramming of one somatic cell into another without transitioning through a progenitor stage has emerged as a strategy to generate clinically relevant cell types. One cell type of interest is the pancreatic insulin-producing β cell whose loss and/or dysfunction leads to diabetes. To date it has been possible to create β-like cells from related endodermal cell types by forcing the expression of developmental transcription factors, but not from more distant cell lineages like fibroblasts. In light of the therapeutic benefits of choosing an accessible cell type as the cell of origin, in this study we set out to analyze the feasibility of transforming human skin fibroblasts into β-like cells. We describe how the timed-introduction of five developmental transcription factors (Neurog3, Pdx1, MafA, Pax4, and Nkx2-2) promotes conversion of fibroblasts toward a β-cell fate. Reprogrammed cells exhibit β-cell features including β-cell gene expression and glucose-responsive intracellular calcium mobilization. Moreover, reprogrammed cells display glucose-induced insulin secretion in vitro and in vivo. This work provides proof-of-concept of the capacity to make insulin-producing cells from human fibroblasts via transcription factor-mediated direct reprogramming.
Common seed dispersers contribute most to the persistence of a fleshy-fruited tree
Authors: Rehling Finn , Jongejans Eelke , Schlautmann Jan , Albrecht Jörg , Fassbender Hubert , Jaroszewicz Bogdan , Matthies Diethart , Waldschmidt Lina , Farwig Nina , Schabo Dana G. 
Published: March 2023

AbstractMutualistic interactions are by definition beneficial for each contributing partner. However, it is insufficiently understood how mutualistic interactions influence partners throughout their lives. Here, we used animal species-explicit, microhabitat-structured integral projection models to quantify the effect of seed dispersal by 20 animal species on the full life cycle of the treeFrangula alnusin Białowieża Forest, Eastern Poland. Our analysis showed that animal seed dispersal increased population growth by 2.5%. The effectiveness of animals as seed dispersers was strongly related to the interaction frequency but not the quality of seed dispersal. Consequently, the projected population decline due to simulated species extinction was driven by the loss of common rather than rare mutualist species. Our results support the notion that frequently interacting mutualists contribute most to the persistence of the populations of their partners, underscoring the role of common species for ecosystem functioning and nature conservation.
A comprehensive molecular profiling approach reveals metabolic alterations that steer bone tissue regeneration
Authors: Löffler Julia , Noom Anne , Ellinghaus Agnes , Dienelt Anke , Kempa Stefan , Duda Georg N. 
Published: March 2023

AbstractBone regeneration after fracture is a complex process with high and dynamic energy demands. The impact of metabolism on bone healing progression and outcome, however, is so far understudied. Our comprehensive molecular profiling reveals that central metabolic pathways, such as glycolysis and the citric acid cycle, are differentially activated between rats with successful or compromised bone regeneration (young versus aged female Sprague-Dawley rats) early in the inflammatory phase of bone healing. We also found that the citric acid cycle intermediate succinate mediates individual cellular responses and plays a central role in successful bone healing. Succinate induces IL-1β in macrophages, enhances vessel formation, increases mesenchymal stromal cell migration, and potentiates osteogenic differentiation and matrix formation in vitro. Taken together, metabolites—here particularly succinate—are shown to play central roles as signaling molecules during the onset of healing and in steering bone tissue regeneration.
Host-driven temperature dependence of Deformed wing virus infection in honey bee pupae
Authors: Palmer-Young Evan C. , Ryabov Eugene V. , Markowitz Lindsey M. , Boncristiani Dawn L. , Grubbs Kyle , Pawar Asha , Peterson Raymond , Evans Jay D. 
Published: March 2023

AbstractThe temperature dependence of infection reflects changes in performance of parasites and hosts. High temperatures often mitigate infection by favoring heat-tolerant hosts over heat-sensitive parasites. Honey bees exhibit endothermic thermoregulation—rare among insects—that can favor resistance to parasites. However, viruses are heavily host-dependent, suggesting that viral infection could be supported—not threatened—by optimum host function. To understand how temperature-driven changes in performance of viruses and hosts shape infection, we compared the temperature dependence of isolated viral enzyme activity, three honey bee traits, and infection of honey bee pupae. Viral enzyme activity varied <2-fold over a > 30 °C interval spanning temperatures typical of ectothermic insects and honey bees. In contrast, honey bee performance peaked at high (≥ 35 °C) temperatures and was highly temperature-sensitive. Although these results suggested that increasing temperature would favor hosts over viruses, the temperature dependence of pupal infection matched that of pupal development, falling only near pupae’s upper thermal limits. Our results reflect the host-dependent nature of viruses, suggesting that infection is accelerated—not curtailed—by optimum host function, contradicting predictions based on relative performance of parasites and hosts, and suggesting tradeoffs between infection resistance and host survival that limit the viability of bee ‘fever’.
Interspecies interaction reduces selection for antibiotic resistance in Escherichia coli
Authors: Nair Ramith R. , Andersson Dan I. 
Published: March 2023

AbstractEvolution of microbial traits depends on the interaction of a species with its environment as well as with other coinhabiting species. However, our understanding of the evolution of specific microbial traits, such as antibiotic resistance in complex environments is limited. Here, we determine the role of interspecies interactions on the dynamics of nitrofurantoin (NIT) resistance selection among Escherichia coli. We created a synthetic two-species community comprised of two variants of E. coli (NIT susceptible and resistant) and Bacillus subtilis in minimal media with glucose as the sole carbon source. We show that the presence of B. subtilis significantly slows down the selection for the resistant E. coli mutant when NIT is present and that this slowdown is not due to competition for resources. Instead, the dampening of NIT resistance enrichment is largely mediated by extracellular compounds produced by B. subtilis with the peptide YydF playing a significant role. Our results not only demonstrate the impact of interspecies interactions on the evolution of microbial traits but also show the importance of using synthetic microbial systems in unravelling relevant interactions and mechanisms affecting the evolution of antibiotic resistance. This finding implies that interspecies interactions should be considered to better understand and predict resistance evolution in the clinic as well as in nature.
Rising water-use efficiency in European grasslands is driven by increased primary production
Authors: Poppe Terán Christian , Naz Bibi S. , Graf Alexander , Qu Yuquan , Hendricks Franssen Harrie-Jan , Baatz Roland , Ciais Phillipe , Vereecken Harry 
Published: March 2023

AbstractWater-use efficiency is the amount of carbon assimilated per water used by an ecosystem and a key indicator of ecosystem functioning, but its variability in response to climate change and droughts is not thoroughly understood. Here, we investigated trends, drought response and drivers of three water-use efficiency indices from 1995–2018 in Europe with remote sensing data that considered long-term environmental effects. We show that inherent water-use efficiency decreased by −4.2% in Central Europe, exhibiting threatened ecosystem functioning. In European grasslands it increased by +24.2%, by regulated transpiration and increased carbon assimilation. Further, we highlight modulation of water-use efficiency drought response by hydro-climate and the importance of adaptive canopy conductance on ecosystem function. Our results imply that decoupling carbon assimilation from canopy conductance and efficient water management strategies could make the difference between threatened and well-coping ecosystems with ongoing climate change, and provide important insights for land surface model development.
Linking prokaryotic genome size variation to metabolic potential and environment
Authors: Rodríguez-Gijón Alejandro , Buck Moritz , Andersson Anders F , Izabel-Shen Dandan , Nascimento Francisco J A , Garcia Sarahi L 
Published: March 2023

Abstract
While theories and models have appeared to explain genome size as a result of evolutionary processes, little work has shown that genome sizes carry ecological signatures. Our work delves into the ecological implications of microbial genome size variation in benthic and pelagic habitats across environmental gradients of the brackish Baltic Sea. While depth is significantly associated with genome size in benthic and pelagic brackish metagenomes, salinity is only correlated to genome size in benthic metagenomes. Overall, we confirm that prokaryotic genome sizes in Baltic sediments (3.47 Mbp) are significantly bigger than in the water column (2.96 Mbp). While benthic genomes have a higher number of functions than pelagic genomes, the smallest genomes coded for a higher number of module steps per Mbp for most of the functions irrespective of their environment. Some examples of this functions are amino acid metabolism and central carbohydrate metabolism. However, we observed that nitrogen metabolism was almost absent in pelagic genomes and was mostly present in benthic genomes. Finally, we also show that Bacteria inhabiting Baltic sediments and water column not only differ in taxonomy, but also in their metabolic potential, such as the Wood-Ljungdahl pathway or the presence of different hydrogenases. Our work shows how microbial genome size is linked to abiotic factors in the environment, metabolic potential and taxonomic identity of Bacteria and Archaea within aquatic ecosystems.
A novel technique for texture description and image classification based in RGB compositions
Authors: Leyferman Carlos Eduardo Padilla , Bonilla José Trinidad Guillen , Gutiérrez Juan Carlos Estrada , Rodríguez Maricela Jiménez 
Published: March 2023

AbstractAt present, facial recognition entertains great importance in performing authentication processes, because it prevents unauthorized access to devices and places. Additionally, it allows for the identification of persons. Henceforth, this paper proposes a novel texture descriptor called Cyclical Chroma and a new classification technique, which takes in consideration the sub‐pixel values of 0–255 for each RGB (Red, Green, Blue) channel that conforms the image. To verify the effectiveness of the proposed techniques, tests were performed with a database of images in a controlled environment and in one under uncontrolled conditions; additionally, Cyclical Chroma was tested with a different classifier, denominated the Multiclass Classifier, and the results were compared against other descriptors, including GLCM, SHDH, LQP, and CCR, demonstrating the effectiveness of the proposed techniques with 100% efficiency with controlled images and 78% effectiveness under uncontrolled conditions prior to the application of an equalization technique, increasing the efficiency to 100%.
Research and implementation of modulation recognition based on cascaded feature fusion
Authors: Qian Lei , Wu Hao , Zhang Tao , Yang Xiaomeng 
Published: March 2023

AbstractAiming at the problems of weak robustness of single feature and limited recognition range in modulation recognition, this paper proposes a modulation recognition algorithm based on cascaded feature fusion and multi‐classifier combination, in which time‐frequency map and instantaneous amplitude spectral density features are extracted from low intermediate frequency (IF) signal, constellation map and high‐order cumulant features are extracted from zero IF signal, and a three‐level recognition algorithm is designed through the decision fusion of decision tree, convolutional neural network, and support vector machine. In order to verify the performance of the algorithm, a modulation recognition system is designed and built based on USRP2974. The low IF and zero IF modulation signals are received through two channels, and the RF signals are received and processed in real time with the help of the built‐in CPU of the receiver. The recognition of 13 kinds of analog modulation and digital modulation signals is realized. Under the condition of wireless reception, the recognition rate of this system is more than 93% at 5 to 10 dB.