bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Framework for Fast, Large-scale, Semi-Automatic Inference of Animal Behavior from Monocular Videos
Authors: Price Eric , Khandelwal Pranav C. , Rubenstein Daniel I. , Ahmad Aamir 
Published: August 2023

AbstractAn automatic, quick, accurate, and scalable method for animal behavior inference using only videos of animals offers unprecedented opportunities to understand complex biological phenomena and answer challenging ecological questions. The advent of sophisticated machine learning techniques now allows the development and implementation of such a method. However, apart from developing a network model that infers animal behavior from video inputs, the key challenge is to obtain sufficient labeled (annotated) data to successfully train that network - a laborious task that needs to be repeated for every species and/or animal system. Here, we propose solutions for both problems, i) a novel methodology for rapidly generating large amounts of annotated data of animals from videos and ii) using it to reliably train deep neural network models to infer the different behavioral states of every animal in each frame of the video. Our method’s workflow is bootstrapped with a relatively small amount of manually-labeled video frames. We develop and implement this novel method by building upon the open-source tool Smarter-LabelMe, leveraging deep convolutional visual detection and tracking in combination with our behavior inference model to quickly produce large amounts of reliable training data. We demonstrate the effectiveness of our method on aerial videos of plains and Grévy’s Zebras (Equus quaggaandEquus grevyi). We fully open-source the code1of our method as well as provide large amounts of accurately-annotated video datasets2of zebra behavior using our method. A video abstract of this paper is available here3.
Modeling individual variability in habitat selection and movement using integrated step-selection analyses
Authors: Chatterjee Nilanjan , Wolfson David , Kim Dongmin , Velez Juliana , Freeman Smith , Bacheler Nathan M. , Shertzer Kyle , Taylor J. Christopher , Fieberg John 
Published: August 2023

Abstract1. Integrated step-selection analyses(ISSAs) are frequently used to study habitat selection using animal movement data. Methods for incorporating random effects in ISSAs have been developed, making it possible to quantify variability among animals in their space-use patterns. Although it is possible to model variability in both habitat selection and movement parameters, applications to date have focused on the former despite the widely acknowledged and important role that movement plays in determining ecological processes from the individual to ecosystem level. One potential explanation for this omission is the absence of readily-available software or examples demonstrating methods for estimating movement parameters in ISSAs with random effects.2. We demonstrated methods for characterizing among-individual variability in both movement and habitat-selection parameters using a simulated data set and by fitting two models to an acoustic telemetry data set containing locations of 35 red snapper (Lutjanus campechanus). Movement kernels were assumed to depend on either the type of benthic reef habitat in which the fish was located (model 1) or the distance between the fish’s current location and nearest edge habitat (model 2). In both models, we also quantified habitat selection for different benthic habitat classes and distance to edge habitat, and we allowed for individual variability in movement and habitat-selection parameters using random effects.3. The simulation example highlights the benefits of a mixed effects specification, namely we can increase precision when estimating individual-specific movement parameters by borrowing information across like individuals. In our applied example, we found substantial among-individual variability in both habitat selection and movement parameters. Nonetheless, most red snapper selected for hardbottom habitat and for locations nearer to edge habitat. They also moved less when in hardbottom habitat. Turn angles were frequently near ±π, but were more dispersed when fish were far away from edge habitat.4. We provide code templates and functions for quantifying variability in movement and habitat-selection parameters when implementing ISSAs with random effects. In doing so, we hope to encourage ecologists conducting ISSAs to take full advantage of their ability to model among-individual variability in both habitat-selection and movement patterns.
How do Cicadas Emerge Together? Thermophysical Aspects of Their Collective Decision-Making
Authors: Goldstein Raymond E. , Jack Robert L. , Pesci Adriana I. 
Published: August 2023

AbstractCertain periodical cicadas exhibit life cycles with durations of 13 or 17 years, and it is now generally accepted that such large prime numbers arise evolutionarily to avoid synchrony with predators. Less well explored is the question ofhow, in the face of intrinsic biological and environmental noise, insects within a brood emerge together in large successive swarms from underground during springtime warming. Here we consider the decision-making process of underground cicada nymphs experiencing random but spatially-correlated thermal microclimates like those in nature. Introducing short-range communication between insects leads to a model of consensus building that maps on to the statistical physics of an Ising model with a quenched, spatially correlated random magnetic field and annealed site dilution, which displays the kinds of collective swarms seen in nature.
Sea butterflies in a pickle: Reliable biomarkers and seasonal sensitivity of pteropods to ocean acidification in the Gulf of Maine
Authors: Maas Amy E. , Lawson Gareth L. , Bergan Alexander J. , Wang Zhaohui Aleck , Tarrant Ann M. 
Published: August 2023

AbstractThe passive dissolution of anthropogenically produced CO2into the ocean system is reducing ocean pH and changing a suite of chemical equilibria, with negative consequences for some marine organisms, in particular those that bear calcium carbonate shells. Although our monitoring of these chemical changes has improved, we have not developed effective tools to translate observations, which are typically of the pH and carbonate saturation state, into ecologically relevant predictions of biological risks. One potential solution is to develop bioindicators: biological variables with a clear relationship to environmental risk factors that can be used for assessment and management. Thecosomatous pteropods, a group of pelagic shelled marine gastropods, whose biological responses to CO2have been suggested as potential bioindicators of OA owing to their sensitivity to acidification in both laboratory and the natural environment. Using five CO2exposure experiments, occurring across 4 seasons and running for up to 15 days, we describe a consistent relationship between saturation state, shell transparency, and duration of exposure, as well as identify a suite of genes that could be used for biological monitoring. We clarify variations in thecosome responses due to seasonality, resolving prior uncertainties and demonstrating the range of their phenotypic plasticity. These biomarkers of acidification stress can be implemented into ecosystem models and monitoring programs in regions where pteropods are found, while the approach will serve as an example for other regions on how to bridge the gap between point-based chemical monitoring and biologically relevant assessments of ecosystem health.Summary StatementDespite seasonal variability, pteropods exposed to acidification over multiple seasons reveal consistent patterns in gene expression and shell condition that can be used as bioindicators of ocean acidification stress.
NetActivity enhances transcriptional signals by combining gene expression into robust gene set activity scores through interpretable autoencoders
Authors: Ruiz-Arenas Carlos , Marín-Goñi Irene , Wang Liewei , Ochoa Idoia , Pérez-Jurado Luis A , Hernaez Mikel 
Published: August 2023

AbstractGrouping gene expression into gene set activity scores (GSAS) provides better biological insights than studying individual genes. However, existing gene set projection methods cannot return representative, robust, and interpretable GSAS. We developedNetActivity, a framework based on a sparsely-connected autoencoder and a three-tier training that yields robust and interpretable GSAS.NetActivitywas trained with 1,518 well-known gene sets and all GTEx samples, returning GSAS representative of the original transcriptome and assigning higher importance to more biologically relevant genes. Moreover,NetActivityreturns GSAS with a more consistent definition than GSVA and hipathia, state-of-the-art gene set projection methods. Finally,NetActivityenables combining bulk RNA-seq and microarray datasets in a meta-analysis of prostate cancer progression, highlighting gene sets related to cell division. When applied to metastatic prostate cancer, gene sets associated with cancer progression were also altered due to drug resistance, while a classical enrichment analysis identified gene sets irrelevant to the phenotype.
Mitochondrial Ca2+uniporter (MCU) variants form plasma-membrane channels
Authors: Polina Iuliia , Mishra Jyotsna , Cypress Michael W , Landherr Maria , Valkov Nedyalka , Chaput Isabel , Nieto Bridget , Mende Ulrike , Zhang Peng , Jhun Bong Sook , O-Uchi Jin 
Published: August 2023

AbstractMCU is widely recognized as a responsible gene for encoding a pore-forming subunit of highly mitochondrial-specific and Ca2+-selective channel, mitochondrial Ca2+uniporter complex (mtCUC). Here, we report a novel short variant derived from the MCU gene (termed MCU-S) which lacks mitochondria-targeted sequence and forms a Ca2+- permeable channel outside of mitochondria. MCU-S was ubiquitously expressed in all cell-types/tissues, with particularly high expression in human platelets. MCU-S formed Ca2+channels at the plasma membrane, which exhibited similar channel properties to those observed in mtCUC. MCU-S channels at the plasma membrane served as an additional Ca2+influx pathway for platelet activation. Our finding is completely distinct from the originally reported MCU gene function and provides novel insights into the molecular basis of MCU variant-dependent cellular Ca2+handling.
The axes of biology: a novel axes-based network embedding paradigm to decipher the functional mechanisms of the cell
Authors: Doria-Belenguer Sergio , Xenos Alexandros , Ceddia Gaia , Malod-Dognin Noël , Pržulj Nataša 
Published: August 2023

AbstractCommon approaches for deciphering biological networks involve network embedding algorithms. These approaches strictly focus on clustering the genes’ embedding vectors and interpreting such clusters to reveal the hidden information of the networks. However, the difficulty in interpreting the genes’ clusters and the limitations of the functional annotations’ resources hinder the identification of the currently unknown cell’s functioning mechanisms. Thus, we propose a new approach that shifts this functional exploration from the embedding vectors of genes in space to the axes of the space itself. Our methodology better disentangles biological information from the embedding space than the classic gene-centric approach. Moreover, it uncovers new data-driven functional interactions that are unregistered in the functional ontologies, but biologically coherent. Furthermore, we exploit these interactions to define new higher-level annotations that we term Axes-Specific Functional Annotations and validate them through literature curation. Finally, we leverage our methodology to discover evolutionary connections between cellular functions and the evolution of species.
Local population structure in Cambridgeshire during the Roman occupation
Authors: Scheib Christiana L. , Hui Ruoyun , Rose Alice K. , Solnik Anu , D’Atanasio Eugenia , Inskip Sarah A. , Cessford Craig , Griffith Samuel J. , Wiseman Rob , Neil Benjamin , Biers Trish , Harknett Sarah-Jane , Sasso Stefania , Biagini Simone A. , Runfeldt Göran , Duhig Corinne , Evans Christopher , O’Connell Tamsin C. , Metspalu Mait , Millett Martin J. , Robb John E. , Kivisild Toomas 
Published: August 2023

AbstractThe Roman period saw the empire expand across Europe and the Mediterranean, including much of what is today the United Kingdom. While there is written evidence of high mobility into and out of Britain for administrators, traders and the military, the impact of imperialism on local population structure is invisible in the textual record. The extent of genetic change that occurred in Britain before the Early Medieval Period and how closely linked by genetic kinship the local populations were, remains underexplored. Here, using genome-wide data from 52 ancient individuals from Cambridgeshire, we show low levels of genetic ancestry differentiation between Romano-British sites and lower levels of runs of homozygosity over 4 centimorgans (cM than in the Bronze Age and Neolithic. We find fourteen cases of genetic relatedness within and one between sites without evidence of patrilineal dominance and one case of temporary mobility within a family unit during the Late Romano-British period. We also show that the modern patterns of genetic ancestry composition in Modern Britain emerged after the Roman period.
Thinner is not always better: Optimising cryo lamellae for subtomogram averaging
Authors: Tuijtel Maarten W. , Kreysing Jan Philipp , Welsch Sonja , Hummer Gerhard , Beck Martin , Turoňová Beata 
Published: August 2023

AbstractCryo-electron tomography (cryo-ET) is a powerful method to elucidate subcellular architecture and to structurally analyse biomoleculesin situby subtomogram averaging (STA). Specimen thickness is a key factor affecting cryo-ET data quality. Cells that are too thick for transmission imaging can be thinned by cryo-focused-ion-beam (cryo-FIB) milling. However, optimal specimen thickness for cryo-ET on lamellae has not been systematically investigated. Furthermore, the ions used to ablate material can cause damage in the lamellae, thereby reducing STA resolution. Here, we systematically benchmark the resolution depending on lamella thickness and the depth of the particles within the sample. Up to ca. 180 nm, lamella thickness does not negatively impact resolution. This shows that there is no need to generate very thin lamellae and thickness can be chosen such that it captures major cellular features. Furthermore, we show that gallium-ion-induced damage extends to depths of up to 30 nm from either lamella surface.
Dynamic proximity interaction profiling suggests that YPEL2 is involved in cellular stress surveillance
Authors: Turan Gizem , Olgun Çağla Ece , Ayten Hazal , Toker Pelin , Ashyralyyev Annageldi , Savaş Büşra , Karaca Ezgi , Muyan Mesut 
Published: August 2023

ABSTRACTYPEL2 is a member of the evolutionarily conserved YPEL family involved in cellular proliferation, mobility, differentiation as well as senescence and death. However, the mechanism by which YPEL2, or YPEL proteins, mediates its effects is yet unknown. Proteins perform their functions in a network of proteins whose identities, amounts, and compositions change spatiotemporally in a lineage-specific manner in response to internal and external stimuli. We here explored interaction partners of YPEL2 by using dynamic TurboID-coupled mass spectrometry analyses to infer a function for the protein. Our results using inducible transgene expressions in COS7 cells indicate that proximity interaction partners of YPEL2 are largely involved in RNA and mRNA metabolic processes, ribonucleoprotein complex biogenesis, regulation of gene silencing by miRNA, and cellular responses to stress. We showed that YPEL2 interacts with RNA binding protein ELAVL1 and selective autophagy receptor SQSTM1. We also found that YPEL2 participates in events associated with the formation/disassembly of stress granules in response to sodium arsenite an oxidative stress inducer. Establishing a point of departure in the delineation of structural/functional features of YPEL2, our results suggest that YPEL2 may be involved in stress surveillance mechanisms.
Hidden in plain sight: the invasive macroalgaCaulerpa proliferaevades detection by environmental DNA methods due to negligible shedding
Authors: Waters Tanner , Langlois Kylie , Gold Zack , Theroux Susanna , Eagle Robert A. 
Published: August 2023

AbstractThe macroalgaeCaulerpa proliferais considered an invasive species in many environments and can colonize large patches of seafloor, reduce native species, and alter ecosystem functioning. Environmental managers need a rapid and cost-effective monitoring tool for tracking the spread of this invasive species. We developed a digital PCR assay for detection ofC. proliferafrom environmental DNA seawater samples. We demonstrate, in both field and laboratory experiments, that the invasive algaeC. proliferais undetectable in practical applications of eDNA due to its minimal shedding. To test why, we conducted tank-based shedding experiments for two California invasive algae species,C. proliferaandSargassum horneri. Copy numbers ofC. proliferaeDNA detected in the experimental tanks were found to be two orders of magnitude lower thanS. horneri. A meta-analysis of steady state eDNA produced by aquatic organisms reported in the literature showC. proliferato have the lowest recorded steady state concentrations of eDNA in the water column. We attributeC. proliferalow eDNA shedding to its unique biology as a unicellular, multinucleate, macroscopic siphonous algae which reduces the possible modes of eDNA release compared to multicellular organisms. Our results highlight the value of benchmarking and validating eDNA surveys in both field and laboratory settings and potential limits of eDNA approaches for some applications. These results also emphasize the importance of organismal physiology in eDNA shedding rates, variations in mechanisms of eDNA shedding between organisms, and characterizing shedding rates for accurate interpretation of eDNA results.
DePARylation is critical for S phase progression and cell survival
Authors: Nie Litong , Wang Chao , Huang Min , Liu Xiaoguang , Feng Xu , Tang Mengfan , Li Siting , Hang Qinglei , Teng Hongqi , Shen Xi , Ma Li , Gan Boyi , Chen Junjie 
Published: August 2023

AbstractPoly(ADP-ribose)ylation or PARylation by PAR polymerase 1 (PARP1) and dePARylation by poly(ADP-ribose) glycohydrolase (PARG) are equally important for the dynamic regulation of DNA damage response. PARG, the most active dePARylation enzyme, is recruited to sites of DNA damage via pADPr-dependent and PCNA-dependent mechanisms. Targeting dePARylation is considered an alternative strategy to overcome PARP inhibitor resistance. However, precisely how dePARylation functions in normal unperturbed cells remains elusive. To address this challenge, we conducted multiple CRISPR screens and revealed that dePARylation of S phase pADPr by PARG is essential for cell viability. Loss of dePARylation activity initially induced S phase-specific pADPr signaling, which resulted from unligated Okazaki fragments and eventually led to uncontrolled pADPr accumulation and PARP1/2-dependent cytotoxicity. Moreover, we demonstrated that proteins involved in Okazaki fragment ligation and/or base excision repair regulate pADPr signaling and cell death induced by PARG inhibition. In addition, we determined that PARG expression is critical for cellular sensitivity to PARG inhibition. Additionally, we revealed that PARG is essential for cell survival by suppressing pADPr. Collectively, our data not only identify an essential role for PARG in normal proliferating cells but also provide a potential biomarker for the further development of PARG inhibitors in cancer therapy.
Opsin gene expression plasticity and spectral sensitivity in male damselflies could mediate female colour morph detection
Authors: Roberts Natalie S. , Svensson Erik I. , Liénard Marjorie A. 
Published: August 2023

ABSTRACTThe visual systems of Odonata are characterized by many opsin genes, which form the primary light-sensitive photopigments of the eye. Female-limited colour polymorphisms are also common in Odonata, with one morph typically exhibiting male-like (androchrome) colouration and one or two morphs exhibiting female-specific colouration (gynochromes). These colour polymorphisms are thought to be maintained by frequency-dependent sexual conflict, in which males form search images for certain morphs, causing disproportionate mating harassment. Here, we investigate opsin sensitivity and gene expression plasticity in mate-searching males of the damselflyIschnura elegansduring adult maturation and across populations with different female morph frequencies. We find evidence for opsin-specific plasticity in relative and proportional opsin mRNA expression, suggesting changes in opsin regulation and visual sensitivity during sexual maturation. In particular, expression of the long-wavelength sensitive opsin LWF2 changed over development and varied between populations with different female morph frequencies. UV-Vis analyses indicate that short- and long-wavelength opsins absorb wavelength of light between 350 and 650 nm. Assuming opponency between photoreceptors with distinct short- and long-wavelength sensitivities, these sensitivities suggest male spectral visual discrimination ability of andromorph and gynomorph females. Overall, our results suggest that opsin sensitivity and expression changes contribute to visual tuning that could impact conspecific discrimination.
A robust method for measuring aminoacylation through tRNA-Seq
Authors: Davidsen Kristian , Sullivan Lucas B 
Published: August 2023

AbstractCurrent methods to quantify the fraction of aminoacylated tRNAs, also known as the tRNA charge, are limited by issues with either low throughput, precision, and/or accuracy. Here, we present an optimized charge tRNA-Seq method that combines previous developments with newly described approaches to establish a protocol for precise and accurate tRNA charge measurements. We verify that this protocol provides robust quantification of tRNA aminoacylation and we provide an end-to-end method that scales to hundreds of samples including software for data processing. Additionally, we show that this method supports measurements of relative tRNA expression levels and can be used to infer tRNA modifications through reverse transcription misincorporations, thereby supporting multipurpose applications in tRNA biology.