bluuebunny/crossref_metadata_2025_split huggingface dataset:
The genomic and cellular basis of biosynthetic innovation in rove beetles
Authors: Kitchen Sheila A. , Naragon Thomas H. , Brückner Adrian , Ladinsky Mark S. , Quinodoz Sofia A. , Badroos Jean M. , Viliunas Joani W. , Wagner Julian M. , Miller David R. , Yousefelahiyeh Mina , Antoshechkin Igor A. , Eldredge K. Taro , Pirro Stacy , Guttman Mitchell , Davis Steven R. , Aardema Matthew L. , Parker Joseph 
Published: May 2023

AbstractHow evolution at the cellular level potentiates change at the macroevolutionary level is a major question in evolutionary biology. With >66,000 described species, rove beetles (Staphylinidae) comprise the largest metazoan family. Their exceptional radiation has been coupled to pervasive biosynthetic innovation whereby numerous lineages bear defensive glands with diverse chemistries. Here, we combine comparative genomic and single-cell transcriptomic data from across the largest rove beetle clade, Aleocharinae. We retrace the functional evolution of two novel secretory cell types that together comprise the tergal gland—a putative catalyst behind Aleocharinae’s megadiversity. We identify key genomic contingencies that were critical to the assembly of each cell type and their organ-level partnership in manufacturing the beetle’s defensive secretion. This process hinged on evolving a mechanism for regulated production of noxious benzoquinones that appears convergent with plant toxin release systems, and synthesis of an effective benzoquinone solvent that weaponized the total secretion. We show that this cooperative biosynthetic system arose at the Jurassic-Cretaceous boundary, and that following its establishment, both cell types underwent ∼150 million years of stasis, their chemistry and core molecular architecture maintained almost clade-wide as Aleocharinae radiated globally into tens of thousands of lineages. Despite this deep conservation, we show that the two cell types have acted as substrates for the emergence of adaptive, biochemical novelties—most dramatically in symbiotic lineages that have infiltrated social insect colonies and produce host behavior-manipulating secretions. Our findings uncover genomic and cell type evolutionary processes underlying the origin, functional conservation and evolvability of a chemical innovation in beetles.
Brain Dissection: fMRI-trained Networks Reveal Spatial Selectivity in the Processing of Natural Images
Authors: Sarch Gabriel H. , Tarr Michael J. , Fragkiadaki Katerina , Wehbe Leila 
Published: May 2023

AbstractThe alignment between deep neural network (DNN) features and cortical responses currently provides the most accurate quantitative explanation for higher visual areas [1, 2, 3, 4]. At the same time, these model features have been critiqued as uninterpretable explanations, trading one black box (the human brain) for another (a neural network). In this paper, we train networks to directly predict, from scratch, brain responses to images from a large-scale dataset of natural scenes [5]. We then use “network dissection” [6], an explainable AI technique used for enhancing neural network interpretability by identifying and localizing the most significant features in images for individual units of a trained network, and which has been used to study category selectivity in the human brain [7]. We adapt this approach to create a hypothesis-neutral model that is then used to explore the tuning properties of specific visual regions beyond category selectivity, which we call “brain dissection”. We use brain dissection to examine a range of ecologically important, intermediate properties, including depth, surface normals, curvature, and object relations across sub-regions of the parietal, lateral, and ventral visual streams, and scene-selective regions. Our findings reveal distinct preferences in brain regions for interpreting visual scenes, with ventro-lateral areas favoring closer and curvier features, medial and parietal areas opting for more varied and flatter 3D elements, and the parietal region uniquely preferring spatial relations. Scene-selective regions exhibit varied preferences, as the retrosplenial complex prefers distant and outdoor features, while the occipital and parahippocampal place areas favor proximity, verticality, and in the case of the OPA, indoor elements. Such findings show the potential of using explainable AI to uncover spatial feature selectivity across the visual cortex, contributing to a deeper, more fine-grained understanding of the functional characteristics of human visual cortex when viewing natural scenes.
Ten years and a million links: building a global taxonomic library connecting persistent identifiers for names, publications and people
Authors: Page Roderic D. M. 
Published: May 2023

AbstractA major gap in the biodiversity knowledge graph is a connection between taxonomic names and the taxonomic literature. While both names and publications often have persistent identifiers (PIDs), such as Life Science Identifiers (LSIDs) or Digital Object Identifiers (DOIs), LSIDs for names are rarely linked to DOIs for publications. This article describes efforts to make those connections across three large taxonomic databases: Index Fungorum, International Plant Names Index (IPNI), and the Index of Organism Names (ION). Over a million names have been matched to DOIs or other persistent identifiers for taxonomic publications. This represents approximately 36% of names for which publication data is available. The mappings between LSIDs and publication PIDs are made available through ChecklistBank. Applications of this mapping are discussed, including a web app to locate the citation of a taxonomic name, and a knowledge graph that uses data on researcher’s ORCID ids to connect taxonomic names and publications to authors of those names.
ChromaX: a fast and scalable breeding program simulator
Authors: Younis Omar G. , Turchetta Matteo , Suarez Daniel Ariza , Yates Steven , Studer Bruno , Athanasiadis Ioannis N. , Krause Andreas , Buhmann Joachim M. , Corinzia Luca 
Published: May 2023

AbstractSummaryChromaX is a Python library that enables the simulation of genetic recombination, genomic estimated breeding value calculations, and selection processes. By utilizing GPU processing, it can perform these simulations up to two orders of magnitude faster than existing tools with standard hardware. This offers breeders and scientists new opportunities to simulate genetic gain and optimize breeding schemes.Availability and ImplementationThe documentation is available athttps://chromax.readthedocs.ioThe code is available athttps://github.com/kora-labs/chromaxContactomargallalaly.younis@inf.ethz.ch,luca.corinzia@inf.ethz.ch,matteo.turchetta@inf.ethz.ch
Caspase-2 is essential for proliferation and self-renewal of nucleophosmin-mutated acute myeloid leukemia
Authors: Sakthivel Dharaniya , Brown-Suedel Alexandra N. , Keane Francesca , Huang Shixia , Sherry Kenneth Mc , Charendoff Chloé I. , Dunne Kevin P. , Robichaux Dexter J. , Le BaoChau , Shin Crystal S. , Carisey Alexandre F. , Flanagan Jonathan M. , Bouchier-Hayes Lisa 
Published: May 2023

AbstractMutation in nucleophosmin (NPM1) causes relocalization of this normally nucleolar protein to the cytoplasm (NPM1c+). Despite NPM1 mutation being the most common driver mutation in cytogenetically normal adult acute myeloid leukemia (AML), the mechanisms of NPM1c+-induced leukemogenesis remain unclear. Caspase-2 is a pro-apoptotic protein activated by NPM1 in the nucleolus. Here, we show that caspase-2 is also activated by NPM1c+ in the cytoplasm, and DNA damage-induced apoptosis is caspase-2-dependent inNPM1c+AML but not inNPM1wtcells. Strikingly, inNPM1c+cells, loss of caspase-2 results in profound cell cycle arrest, differentiation, and down-regulation of stem cell pathways that regulate pluripotency including impairment in the AKT/mTORC1 and Wnt signaling pathways. In contrast, there were minimal differences in proliferation, differentiation, or the transcriptional profile ofNPM1wtcells with and without caspase-2. Together, these results show that caspase-2 is essential for proliferation and self-renewal of AML cells that have mutated NPM1. This study demonstrates that caspase-2 is a major effector of NPM1c+ function and may even be a druggable target to treatNPM1c+AML and prevent relapse.
METASPACE-ML: Context-specific metabolite annotation for imaging mass spectrometry using machine learning
Authors: Wadie Bishoy , Stuart Lachlan , Rath Christopher M. , Drotleff Bernhard , Mamedov Sergii , Alexandrov Theodore 
Published: May 2023

AbstractImaging mass spectrometry is a powerful technology enabling spatial metabolomics, yet metabolites can be assigned only to a fraction of the data generated. METASPACE-ML is a machine learning-based approach addressing this challenge which incorporates new scores and computationally-efficient False Discovery Rate estimation. For training and evaluation, we use a comprehensive set of 1,710 datasets from 159 researchers from 47 labs encompassing both animal and plant-based datasets representing multiple spatial metabolomics contexts derived from the METASPACE knowledge base. Here we show that, METASPACE-ML outperforms its rule-based predecessor, exhibiting higher precision, increased throughput, and enhanced capability in identifying low-intensity and biologically-relevant metabolites.
Body posture, gaze, and predator detection: how stalking behaviour may influence colour vision evolution
Authors: de Moraes Pedro Z. , Diniz Pedro , Pessoa Daniel M. A. 
Published: May 2023

AbstractThe success of a predatory attack is related to how much a predator manages to approach a prey without being detected. Some carnivore mammals use environmental objects as visual obstacles during stalking behaviour, allowing them to get closer to their prey while only showing parts of their coat or faces during movement or visual monitoring. Here, we investigate the influence of carnivores’ body postures and gaze on their detection by potential prey. To do so, we photographed taxidermized carnivore models (cougar, ocelot and lesser grison) in natural scenes and presented them to human dichromats (i.e., colourblind) and trichromats (i.e., normal colour vision). Our findings highlight the importance of predators’ complete body outline and gaze as search images during predator detection tasks. We also demonstrate how the coat and facial colour pattern of predators may camouflage their body outline and gaze, hampering predator detection. Furthermore, we observed that carnivore coat colour patterns may serve as an additional cue for trichromats, particularly in hidden carnivore detection tasks that proved to be more difficult for dichromats. We discuss our results within the context of a predator-prey arms race scenario, considering the evolutionary processes that may have generated the evidence presented in this study.
Synaptic architecture of leg and wing premotor control networks inDrosophila
Authors: Lesser Ellen , Azevedo Anthony W. , Phelps Jasper S. , Elabbady Leila , Cook Andrew , Syed Durafshan Sakeena , Mark Brandon , Kuroda Sumiya , Sustar Anne , Moussa Anthony , Dallmann Chris J. , Agrawal Sweta , Lee Su-Yee J. , Pratt Brandon , Skutt-Kakaria Kyobi , Gerhard Stephan , Lu Ran , Kemnitz Nico , Lee Kisuk , Halageri Akhilesh , Castro Manuel , Ih Dodam , Gager Jay , Tammam Marwan , Dorkenwald Sven , Collman Forrest , Schneider-Mizell Casey , Brittain Derrick , Jordan Chris S. , Macrina Thomas , Dickinson Michael , Lee Wei-Chung Allen , Tuthill John C. 
Published: May 2023

AbstractAnimal movement is controlled by motor neurons (MNs), which project out of the central nervous system to activate muscles. MN activity is coordinated by complex premotor networks that allow individual muscles to contribute to many different behaviors. Here, we use connectomics to analyze the wiring logic of premotor circuits controlling theDrosophilaleg and wing. We find that both premotor networks cluster into modules that link MNs innervating muscles with related functions. Within most leg motor modules, the synaptic weights of each premotor neuron are proportional to the size of their target MNs, establishing a circuit basis for hierarchical MN recruitment. In contrast, wing premotor networks lack proportional synaptic connectivity, which may allow wing steering muscles to be recruited with different relative timing. By comparing the architecture of distinct limb motor control systems within the same animal, we identify common principles of premotor network organization and specializations that reflect the unique biomechanical constraints and evolutionary origins of leg and wing motor control.
Mechanisms of memory storage and retrieval in hippocampal area CA3
Authors: Li Yiding , Briguglio John J. , Romani Sandro , Magee Jeffrey C. 
Published: May 2023

AbstractHippocampal area CA3 is thought to play a central role in memory formation and retrieval. Although various network mechanisms have been hypothesized to mediate these computations, direct evidence is lacking. Using intracellular membrane potential recordings from CA3 neurons and optogenetic manipulations in behaving mice we found that place field activity is produced by a symmetric form of Behavioral Timescale Synaptic Plasticity (BTSP) at recurrent synaptic connections among CA3 principal neurons but not at synapses from the dentate gyrus (DG). Additional manipulations revealed that excitatory input from the entorhinal cortex (EC) but not DG was required to update place cell activity based on the animal’s movement. These data were captured by a computational model that used BTSP and an external updating input to produce attractor dynamics under online learning conditions. Additional theoretical results demonstrate the enhanced memory storage capacity of such networks, particularly in the face of correlated input patterns. The evidence sheds light on the cellular and circuit mechanisms of learning and memory formation in the hippocampus.One Sentence SummaryEvidence from behaving mice points to cellular and circuit mechanisms that underlie observed attractor dynamics in area CA3.
AutoUnmix: an autoencoder-based spectral unmixing method for multi-color fluorescence microscopy imaging
Authors: Jiang Yuan , Sha Hao , Liu Shuai , Qin Peiwu , Zhang Yongbing 
Published: May 2023

AbstractMultiplexed fluorescence microscopy imaging is widely used in biomedical applications. However, simultaneous imaging of multiple fluorophores can result in spectral leaks and overlapping, which greatly degrades image quality and subsequent analysis. Existing popular spectral unmixing methods are mainly based on computational intensive linear models and the performance is heavily dependent on the reference spectra, which may greatly preclude its further applications. In this paper, we propose a deep learning-based blindly spectral unmixing method, termed AutoUnmix, to imitate the physical spectral mixing process. A tranfer learning framework is further devised to allow our AutoUnmix adapting to a variety of imaging systems without retraining the network. Our proposed method has demonstrated real-time unmixing capabilities, surpassing existing methods by up to 100-fold in terms of unmixing speed. We further validate the reconstruction performance on both synthetic datasets and biological samples. The unmixing results of AutoUnmix achieve a highest SSIM of 0.99 in both three- and four-color imaging, with nearly up to 20% higher than other popular unmixing methods. Due to the desirable property of data independency and superior blind unmixing performance, we believe AutoUnmix is a powerful tool to study the interaction process of different organelles labeled by multiple fluorophores.
Progressive excitability changes in the medial entorhinal cortex in the 3xTg mouse model of Alzheimer’s disease pathology
Authors: Chen Lingxuan , Christenson Wick Zoé , Vetere Lauren M. , Vaughan Nick , Jurkowski Albert , Galas Angelina , Diego Keziah S. , Philipsberg Paul , Cai Denise J. , Shuman Tristan 
Published: May 2023

ABSTRACTAlzheimer’s disease (AD) is a chronic neurodegenerative disorder that is characterized by memory loss and progressive cognitive impairments. In mouse models of AD pathology, studies have found neuronal and synaptic deficits in the hippocampus, but less is known about what happens in the medial entorhinal cortex (MEC), which is the primary spatial input to the hippocampus and an early site of AD pathology. Here, we measured the neuronal intrinsic excitability and synaptic activity in MEC layer II (MECII) stellate cells, MECII pyramidal cells, and MEC layer III (MECIII) excitatory neurons at early (3 months) and late (10 months) time points in the 3xTg mouse model of AD pathology. At 3 months of age, prior to the onset of memory impairments, we found early hyperexcitability in MECII stellate and pyramidal cells’ intrinsic properties, but this was balanced by a relative reduction in synaptic excitation (E) compared to inhibition (I), suggesting intact homeostatic mechanisms regulating activity in MECII. Conversely, MECIII neurons had reduced intrinsic excitability at this early time point with no change in the synaptic E/I ratio. By 10 months of age, after the onset of memory deficits, neuronal excitability of MECII pyramidal cells and MECIII excitatory neurons was largely normalized in 3xTg mice. However, MECII stellate cells remained hyperexcitable and this was further exacerbated by an increased synaptic E/I ratio. This observed combination of increased intrinsically and synaptically generated excitability suggests a breakdown in homeostatic mechanisms specifically in MECII stellate cells at this post-symptomatic time point. Together, these data suggest that the breakdown in homeostatic excitability mechanisms in MECII stellate cells may contribute to the emergence of memory deficits in AD.
Nest-building using place cells for spatial navigation in an artificial neural network
Authors: Portegys Thomas E. 
Published: May 2023

AbstractAn animal behavior problem is presented in the form of a nest-building task that involves two cooperating birds, a male and female. The female builds a nest into which she lays an egg. The male’s job is to forage in a forest for food for both himself and the female. In addition, the male must fetch stones from a nearby desert for the female to use as nesting material. The task is completed when the nest is built and an egg is laid in it. A goal-seeking neural network and a recurrent neural network were trained and tested with little success. The goal-seeking network was then enhanced with “place cells”, allowing the birds to spatially navigate the world, building the nest while keeping themselves fed. Place cells are neurons in the hippocampus that map space.
Lipid bilayer strengthens the cooperative network of membrane proteins
Authors: Muhammednazaar Shaima , Yao Jiaqi , Necelis Matthew R. , Park Yein C. , Shen Zhongtian , Bridges Michael D. , Guo Ruiqiong , Swope Nicole , Rhee May S. , Kim Miyeon , Kim Kelly H. , Hubbell Wayne L. , Fleming Karen G. , Columbus Linda , Kang Seung-gu , Hong Heedeok 
Published: May 2023

AbstractAlthough membrane proteins fold and function in a lipid bilayer constituting cell membranes, their structure and functionality can be recapitulated in diverse amphiphilic assemblies whose compositions deviate from native membranes. It remains unclear how various hydrophobic environments can stabilize membrane proteins and whether lipids play any role therein. Here, using the evolutionary unrelated α-helical and β-barrel membrane proteins ofEscherichia coli, we find that the hydrophobic thickness and the strength of amphiphile– amphiphile packing are critical environmental determinants of membrane protein stability. Lipid solvation enhances stability by facilitating residue burial in the protein interior and strengthens the cooperative network by promoting the propagation of local structural perturbations. This study demonstrates that lipids not only modulate membrane proteins’ stability but also their response to external stimuli.
Intra- and Inter-host Evolution of Human Norovirus in Healthy Adults
Authors: Ramani Sasirekha , Javornik Cregeen Sara J. , Surathu Anil , Neill Frederick H. , Muzny Donna M. , Doddapaneni Harsha , Menon Vipin K. , Hoffman Kristi L. , Ross Matthew C. , Metcalf Ginger , Opekun Antone R. , Graham David Y. , Gibbs Richard A. , Petrosino Joseph F. , Estes Mary K. , Atmar Robert L. 
Published: May 2023

ABSTRACTBackgroundHuman noroviruses are a leading cause of acute and sporadic gastroenteritis worldwide. The evolution of human noroviruses in immunocompromised persons has been evaluated in many studies. Much less is known about the evolutionary dynamics of human norovirus in healthy adults.MethodsWe used sequential samples collected from a controlled human infection study with GI.1/Norwalk/US/68 virus to evaluate intra- and inter-host evolution of a human norovirus in healthy adults. Up to 12 samples from day 1 to day 56 post-challenge were sequenced using a norovirus-specific capture probe method.ResultsComplete genomes were assembled, even in samples that were below the limit of detection of standard RT-qPCR assays, up to 28 days post-challenge. Analysis of 123 complete genomes showed changes in the GI.1 genome in all persons, but there were no conserved changes across all persons. Single nucleotide variants resulting in non-synonymous amino acid changes were observed in all proteins, with the capsid VP1 and nonstructural protein NS3 having the largest numbers of changes.ConclusionsThese data highlight the potential of a new capture-based sequencing approach to assemble human norovirus genomes with high sensitivity and demonstrate limited conserved immune pressure-driven evolution of GI.1 virus in healthy adults.
Proximal Molecular Probe Transfer (PROMPT), a new approach for identifying sites of protein/nucleic acid interaction in cells by correlated light and electron microscopy
Authors: Castillon Guillaume A , Phan Sebastien , Hu Junru , Boassa Daniela , Adams Stephen R , Ellisman Mark H 
Published: May 2023

ABSTRACTThe binding and interaction of proteins with nucleic acids such as DNA and RNA constitutes a fundamental biochemical and biophysical process in all living organisms. Identifying and visualizing such temporal interactions in cells is key to understanding their function. To image sites of these events in cells across scales, we developed a method, named PROMPT for PROximal Molecular Probe Transfer, which is applicable to both light and correlative electron microscopy. This method relies on the transfer of a bound photosensitizer from a protein known to associate with specific nucleic acid sequence, allowing the marking of the binding site on DNA or RNA in fixed cells. The method produces a fluorescent mark at the site of their interaction, that can be made electron dense and reimaged at high resolution in the electron microscope. As proof of principle, we labeledin situthe interaction sites between the histone H2B and nuclear DNA. As an example of application for specific RNA localizations we labeled different nuclear and nucleolar fractions of the protein Fibrillarin to mark and locate where it associates with RNAs, also using electron tomography. While the current PROMPT method is designed for microscopy, with minimal variations, it can be potentially expanded to analytical techniques.