bluuebunny/crossref_metadata_2025_split huggingface dataset:
Lonely in the dark: trauma memory and sex-specific dysregulation of amygdala reactivity to fear signals
Authors: Morr Mitjan , Noell Jeanine , Sassin Daphne , Daniels Jule , Philipsen Alexandra , Becker Benjamin , Stoffel-Wagner Birgit , Hurlemann René , Scheele Dirk 
Published: November 2021

AbstractLoneliness exacerbates psychological distress and increases the risk of psychopathology after trauma exposure. The prevalence of trauma-associated disorders varies substantially between sexes, and accumulating evidence indicates sex-specific effects of loneliness. However, it is still unclear whether a lack of social connectedness affects trauma-induced intrusions and the neural processing of fear signals. Moreover, it is uncertain, whether loneliness plays a different role in women and men. We used a prestratification strategy and recruited n=47 (n=20 women) healthy individuals with high loneliness and n=35 controls (n=18 women). Participants were exposed to an experimental trauma and evoked intrusive thoughts in daily life were monitored for three consecutive days. Functional magnetic resonance imaging was used to assess neural habituation to fearful faces and fear learning (conditioning and extinction) prior to trauma exposure. The total number of intrusions and amygdala reactivity in neural fear processing served as the primary study outcomes. Our results revealed a significant interaction between loneliness and sex such that loneliness was associated with more intrusions in men, but not in women. A similar pattern emerged at the neural level, with both reduced amygdala habituation to repeated fearful faces and amygdala hyperreactivity during the conditioning of fear signals in lonely men, but not in women. Our findings indicate that loneliness may confer vulnerability to intrusive memories after trauma exposure in healthy men and that this phenotype relates to altered limbic processing of fear signals. Collectively, interventions targeting social connectedness may mitigate the sequelae of traumatic experiences.
Marker-free characterization of single live circulating tumor cell full-length transcriptomes
Authors: Poonia Sarita , Goel Anurag , Chawla Smriti , Bhattacharya Namrata , Rai Priyadarshini , Lee Yi Fang , Yap Yoon Sim , West Jay , Bhagat Ali Asgar , Tayal Juhi , Mehta Anurag , Ahuja Gaurav , Majumdar Angshul , Ramalingam Naveen , Sengupta Debarka 
Published: November 2021

AbstractThe identification and characterization of circulating tumor cells (CTCs) are important for gaining insights into the biology of metastatic cancers, monitoring disease progression, and medical management of the disease. The limiting factor that hinders enrichment of purified CTC populations is their sparse availability, heterogeneity, and altered phenotypic traits relative to the tumor of origin. Intensive research both at the technical and molecular fronts led to the development of assays that ease CTC detection and identification from the peripheral blood. Most CTC detection methods use a mix of size selection, immune marker based white blood cells (WBC) depletion, and positive enrichment antibodies targeting tumor-associated antigens. However, the majority of these methods either miss out on atypical CTCs or suffer from WBC contamination. Single-cell RNA sequencing (scRNA-Seq) of CTCs provides a wealth of information about their tumors of origin as well as their fate and is a potent method of enabling unbiased identification of CTCs. We present unCTC, an R package for unbiased identification and characterization of CTCs from single-cell transcriptomic data. unCTC features many standard and novel computational and statistical modules for various analysis tasks. These include a novel method of scRNA-Seq clustering, namedDeepDictionaryLearning usingK-means clustering cost (DDLK), expression based copy number variation (CNV) inference, and combinatorial, marker-based verification of the malignant phenotypes. DDLK enables robust segregation of CTCs and WBCs in the pathway space, as opposed to the gene expression space. We validated the utility of unCTC on scRNA-Seq profiles of breast CTCs from six patients, captured and profiled using an integrated ClearCell®FX and PolarisTMworkflow that works by the principles of size-based separation of CTCs and marker based WBC depletion.
Highly variable response of hard coral taxa to successive coral bleaching events (2019-2020) and rising ocean temperatures in Northeast Peninsular Malaysia
Authors: Szereday Sebastian , Amri Affendi Yang 
Published: November 2021

AbstractDue to current greenhouse gas emissions, Malaysian coral reefs are predicted to experience severe annual coral bleaching events by 2043, threatening the survival of coral reefs within this century. However, there is no field data on how Malaysian coral reefs respond to successive events of coral bleaching. Despite the notion that many scleractinian taxa exhibit increased thermal tolerance over the last decade, it remains unresolved whether these changes are a result of ‘weeding out’ thermally susceptible species and actually ameliorate accelerating warming rates and increasing frequencies of heat disturbances. Moreover, complex interaction of environmental and biological factors that underlie differences in the bleaching response necessitate conducting studies at the within-reef scale (i.e., leeward shallow, windward shallow). Here, we studied two successive thermal stress events starting during the 2019 El Niño Southern Oscillation (ENSO), and determined bleaching trajectories of 29 hard coral taxa across fine spatio-temporal gradients in Northeast Peninsular Malaysia. Analysis of climate trajectories affirms accelerating warming rates (0.17°C per decade) and higher return-frequency of heat disturbance. Despite high annual maximum temperatures above the putative bleaching threshold (31.07°C and 31.74°C, respectively), accumulated thermal stress was low during both bleaching episodes (Degree Heating Weeks of 1.05°C-weeks and 0.18°C-weeks, respectively), suggesting widespread thermal sensitivity of hard coral taxa (55.21% and 26.63% bleaching incidence in 2019 and 2020, respectively). However, significant discrepancies between satellite and in-situ temperature data were found (0.63°C; SD±0.26). Bleaching severity was highly taxon-specific, varied across and within reef scales due to wind exposure and depth (e.g., less bleaching at shallow windward sites), and partially contrasted historical bleaching observations (e.g., Acropora and Montipora were less susceptible, Cyphastrea, Echinopora, Goniastrea, Heliopora and Porites were highly susceptible). While bleaching severity was higher in 2019, Galaxea and Leptastrea were bleaching more in 2020 despite lower heat stress, suggesting negative legacy effects of the 2019 bleaching event on these taxa. In conclusion, hard corals were subjected to more frequent heat stress during the last decade and remain highly vulnerable to marine heatwaves across all biophysical reef scales. Annual coral bleaching impacted all hard coral taxa and reduced thermal tolerance in at least two taxa.
Genetic polymorphisms in COMT and BDNF influence synchronization dynamics of human neuronal oscillations
Authors: Simola Jaana , Siebenhühner Felix , Myrov Vladislav , Kantojärvi Katri , Paunio Tiina , Palva J. Matias , Brattico Elvira , Palva Satu 
Published: November 2021

SummaryNeuronal oscillations, their inter-areal synchronization, and scale-free dynamics constitute fundamental mechanisms for cognition by regulating communication in neuronal networks. These oscillatory dynamics have large inter-individual variability that is partly heritable. However, the genetic underpinnings of oscillatory dynamics have remained poorly understood. We recorded resting-state magnetoencephalography (MEG) from 82 healthy participants and investigated whether oscillation dynamics were influenced by genetic polymorphisms in Catechol-O-methyltransferase (COMT) Val158Met and brain-derived neurotrophic factor (BDNF) Val66Met. Both COMT and BDNF polymorphisms influenced local oscillation amplitudes and their long-range temporal correlations (LRTCs), while only BDNF polymorphism affected the strength of large-scale synchronization. Our findings demonstrate that COMT and BDNF genetic polymorphisms contribute to inter-individual variability in local and large-scale synchronization dynamics of neuronal oscillations. Comparison of these results to computational modelling of near-critical synchronization dynamics further suggested that COMT and BDNF polymorphisms influenced local oscillations by modulating the excitation-inhibition balance according to the brain criticality framework.
Reversible inactivation of ferret auditory cortex impairs spatial and non-spatial hearing
Authors: Town Stephen M. , Poole Katarina C. , Wood Katherine C. , Bizley Jennifer K. 
Published: November 2021

AbstractA key question in auditory neuroscience is to what extent are brain regions functionally specialized for processing specific sound features such as sound location and identity. In auditory cortex, correlations between neural activity and sounds support both the specialization of distinct cortical subfields, and encoding of multiple sound features within individual cortical areas. However, few studies have tested the contribution of auditory cortex to hearing in multiple contexts. Here we determined the role of ferret primary auditory cortex in both spatial and non-spatial hearing by reversibly inactivating the middle ectosylvian gyrus during behavior using cooling (n=2) or optogenetics (n=1). In optogenetic experiments, we utilized the mDLx promoter to express Channelrhodopsin 2 in GABAergic interneurons and confirmed both viral expression (n=2) and light-driven suppression of spiking activity in auditory cortex, recorded using Neuropixels under anesthesia (n=465 units from 2 additional untrained ferrets). Cortical inactivation impaired vowel discrimination in co-located noise, but not in clean conditions, or when the temporally coincident vowel and noise were spatially separated by 180°. Testing the ferrets implanted with cooling loops in a sound localization task confirmed that deficits in spatial hearing arose from inactivation of the same region of auditory cortex that was implicated in vowel discrimination in noise. Our results are consistent with single unit recordings in primary auditory cortex showing mixed selectivity for spatial and non-spatial features of sound and suggest a contribution of this region to multiple forms of hearing necessary for auditory scene analysis.Significance StatementNeurons in primary auditory cortex are often sensitive to the location and identity of sounds. Here we inactivated auditory cortex during spatial and non- spatial listening tasks using cooling, or optogenetics. Auditory cortical inactivation impaired multiple behaviors, demonstrating a role in both the analysis of sound location and identity and confirming a functional contribution of mixed selectivity observed in neural activity. Parallel optogenetic experiments in two additional untrained ferrets linked behavior to physiology by demonstrating that expression of Channelrhodopsin 2 permitted rapid light-driven suppression of auditory cortical activity recorded under anesthesia.
Whole genome sequencing uncovers the structural and transcriptomic landscape of hexaploid wheat/Ambylopyrum muticum introgression lines
Authors: Coombes Benedict , Fellers John P. , Grewal Surbhi , Rusholme-Pilcher Rachel , Hubbart-Edwards Stella , Yang Caiyun , Joynson Ryan , King Ian P. , King Julie , Hall Anthony 
Published: November 2021

AbstractWheat is a globally vital crop, but its limited genetic variation creates a challenge for breeders aiming to maintain or accelerate agricultural improvements over time. Introducing novel genes and alleles from wheat’s wild relatives into the wheat breeding pool via introgression lines is an important component of overcoming this low variation but is constrained by poor genomic resolution and limited understanding of the genomic impact of introgression breeding programmes. By sequencing 17 hexaploid wheat/Ambylopyrum muticum introgression lines and the parent lines, we have precisely pinpointed the borders of introgressed segments, most of which occur within genes. We report a genome assembly and annotation of Am. muticum that has facilitated the identification of Am. muticum resistance genes commonly introgressed in lines resistant to stripe rust. Our analysis has identified an abundance of structural disruption and homoeologous pairing across the introgression lines, likely caused by the suppressed Ph1 locus. mRNAseq analysis of six of these introgression lines revealed that novel introgressed genes are rarely expressed and those that directly replace a wheat orthologue have a tendency towards downregulation, with no discernible compensation in the expression of homoeologous copies. This study explores the genomic impact of introgression breeding and provides a schematic that can be followed to characterise introgression lines and identify segments and candidate genes underlying the phenotype. This will facilitate more effective utilisation of introgression pre-breeding material in wheat breeding programmes.
Dosage-sensitivity shapes how genes transcriptionally respond to allopolyploidy and homoeologous exchange in resynthesized Brassica napus
Authors: Bird Kevin A. , Pires J. Chris , VanBuren Robert , Xiong Zhiyong , Edger Patrick P. 
Published: November 2021

AbstractThe Gene Balance Hypothesis (GBH) proposes that selection acts on the dosage (i.e. copy number) of genes within dosage-sensitive portions of networks, pathways, and protein complexes to maintain balanced stoichiometry of interacting proteins, because perturbations to stoichiometric balance can result in reduced fitness. This selection has been called dosage balance selection. Dosage balance selection is also hypothesized to constrain expression responses to dosage changes, making dosage-sensitive genes (those encoding members of interacting proteins) experience more similar expression changes. In allopolyploids, where whole-genome duplication involves hybridization of diverged lineages, organisms often experience homoeologous exchanges (HEs) that recombine, duplicate, and delete homoeologous regions of the genome and alter the expression of homoeologous gene pairs. Although the GBH makes predictions about the expression response to HEs, they have not been empirically tested. We used genomic and transcriptomic data from six resynthesized, isogenicBrassica napuslines over ten generations to identify HEs, analyzed expression responses, and tested for patterns of genomic imbalance. Groups of dosage-sensitive genes had less variable expression responses to HEs than dosage-insensitive genes, a sign that their relative dosage is constrained. This difference was absent for homoeologous pairs whose expression was biased toward the BnA subgenome. Finally, the expression response to HEs was more variable than the response to WGD, suggesting HEs create genomic imbalance. These findings expand our knowledge of the impact of dosage balance selection on genome evolution and potentially connect patterns in polyploid genomes over time; from homoeolog expression bias to duplicate gene retention.
The Prevalence of Litter Foraging Among UK Birds Lessons Learned From A Citizen Science Project
Authors: Schalz Sabrina , Horrod-Wilson Warren D. , Chauhan Keir 
Published: November 2021

1.AbstractAnthropogenic food sources, such as litter, are readily available to birds in urban areas. As an overly anthropogenic diet can have negative health consequences for wildlife, monitoring the frequency of foraging in litter compared to natural food resources can be an important component of wildlife conservation efforts. To understand how common litter foraging is among different bird species, we conducted a citizen science project with volunteers across the UK. Through this project, we also tried to engage people in birdwatching and bird surveys who would not normally participate in these activities. A particular focus was on recruiting respondents from underrepresented groups, and the methodology was designed to accommodate people without any background knowledge of birds. While we did not receive enough observations to draw conclusions about the litter foraging rates of different bird species across the UK, we report the submissions we received, as well as the demographic composition of the volunteer group. We successfully reached volunteers who did not participate in birdwatching or BTO bird surveys before, as well as some young volunteers, but were unsuccessful in reaching respondents from diverse socioeconomic backgrounds. We hope that the successes and failures of our methods reported here can be useful to others designing citizen science studies, so that birdwatching and volunteering for bird surveys will be equally accessible to all in the future.
Stimulus-induced narrow-band gamma oscillations in humans can be recorded using open-hardware low-cost EEG amplifier
Authors: Pattisapu Srividya , Ray Supratim 
Published: November 2021

AbstractStimulus-induced narrow-band gamma oscillations (30–70 Hz) in human electro - encephalograph (EEG) have been linked to attentional and memory mechanisms and are abnormal in mental health conditions such as autism, schizophrenia and Alzheimer’s Disease. This suggests that gamma oscillations could be valuable both as a research tool and an inexpensive, non-invasive biomarker for disease evaluation. However, since the absolute power in EEG decreases rapidly with increasing frequency following a “1/f” power law, and the gamma band includes line noise frequency, these oscillations are highly susceptible to instrument noise. Previous studies that recorded stimulus-induced gamma oscillations used expensive research-grade EEG amplifiers to address this issue. While low-cost EEG amplifiers have become popular in Brain Computer Interface applications that mainly rely on low-frequency oscillations (< 30 Hz) or steady-state-visually-evoked-potentials, whether they can also be used to measure stimulus-induced gamma oscillations is unknown. We recorded EEG signals using a low-cost, open-source amplifier (OpenBCI) and a traditional, research-grade amplifier (Brain Products GmbH) in male (N = 6) and female (N = 5) subjects (22–29 years) while they viewed full-screen static gratings that are known to induce gamma oscillations. OpenBCI recordings showed gamma response in almost all the subjects who showed a gamma response in Brain Products recordings, and the spectral and temporal profiles of these responses in alpha (8–13 Hz) and gamma bands were highly correlated between OpenBCI and Brain Products recordings. These results suggest that low-cost amplifiers can potentially be used in stimulus induced gamma response detection, making its research, and application in medicine more accessible.
Localized delivery of β-NGF via injectable microrods accelerates endochondral fracture repair
Authors: Rivera Kevin O. , Cuylear Darnell L. , Duke Victoria , O’Hara Kelsey Marie , Kharbikar Bhushan N. , Kryger Alex N. , Miclau Theodore , Bahney Chelsea S. , Desai Tejal A. 
Published: November 2021

AbstractCurrently, there are no biological approaches to accelerate bone fracture repair. Osteobiologics that promote endochondral ossification are an exciting alternative to surgically implanted bone grafts, however, the translation of osteobiologics remains elusive because of the need for localized and sustained delivery that is both safe and effective. In this regard, an injectable system composed of hydrogel-based microparticles designed to release osteobiologics in a controlled and localized manner is ideal in the context of bone fracture repair. Here, we describe poly (ethylene glycol) dimethacrylate (PEGDMA)-based microparticles, in the form of microrods, engineered to be loaded with beta nerve growth factor (β-NGF) for use in a murine tibial fracture model. In-vitro studies demonstrated that protein-loading efficiency is readily altered by varying PEGDMA macromer concentration and that β-NGF loaded onto PEGDMA microrods exhibited sustained release over a period of 7 days. In-vitro bioactivity of β-NGF was confirmed using a tyrosine receptor kinase A (Trk-A) expressing cell line, TF-1. Moreover, TF-1 cell proliferation significantly increased when incubated with β-NGF loaded PEGDMA microrods versus β-NGF in media. In-vivo studies show that PEGDMA microrods injected into the fracture calluses of mice remained in the callus for over 7 days. Importantly, a single injection of β-NGF-loaded PEGDMA microrods resulted in significantly improved fracture healing as indicated by significant increases in bone volume, trabecular connective density, and bone mineral density and a significant decrease in cartilage despite a remarkably lower dose (∼111 fold) than the β-NGF in media. In conclusion, we demonstrate a novel and translational method of delivering β-NGF via injectable PEGDMA microrods to improve bone fracture repair.
Phylogenomic analyses of Alismatales shed light into adaptations to aquatic environments
Authors: Chen Ling-Yun , Lu Bei , Morales-Briones Diego F. , Moody Michael L. , Liu Fan , Hu Guang-Wan , Huang Chien-Hsun , Chen Jin-Ming , Wang Qing-Feng 
Published: November 2021

AbstractLand plants first evolved from freshwater algae, and flowering plants returned to water as early as the Cretaceous and multiple times subsequently. Alismatales is the largest clade of aquatic angiosperms including all marine angiosperms, as well as terrestrial plants. We used Alismatales to explore plant adaptation to aquatic environments by analyzing a data set that included 95 samples (89 Alismatales species) covering four genomes and 91 transcriptomes (59 generated in this study). To provide a basis for investigating adaptation, we assessed phylogenetic conflict and whole-genome duplication (WGD) events in Alismatales. We recovered a relationship for the three main clades in Alismatales as (Tofieldiaceae, Araceae) + core Alismatids. We also found phylogenetic conflict among the backbone of the three main clades that could be explained by incomplete lineage sorting and introgression. Overall, we identified 18 putative WGD events across Alismatales. One of them occurred at the most recent common ancestor of core Alismatids, and three occurred at seagrass lineages. We also found that lineage and life-form were both important for different evolutionary patterns for the genes related to freshwater and marine adaptation. For example, several light or ethylene-related genes were lost in the seagrass Zosteraceae, but are present in other seagrasses and freshwater species. Stomata-related genes were lost in both submersed freshwater species and seagrasses. Nicotianamine synthase genes, which are important in iron intake, expanded in both submersed freshwater species and seagrasses. Our results advance the understanding of the adaptation to aquatic environments and whole-genome duplications using phylogenomics.
A multiplexed cell-free assay to screen for antimicrobial peptides in double emulsion droplets
Authors: Nuti Nicola , Rottmann Philipp , Stucki Ariane , Koch Philipp , Panke Sven , Dittrich Petra S. 
Published: November 2021

AbstractThe global surge in bacterial resistance against traditional antibiotics triggered intensive research for novel compounds, with antimicrobial peptides (AMPs) identified as a promising candidate. Automated methods to systematically generate and screen AMPs according to their membrane preference, however, are still lacking. We introduce a novel microfluidic system for the simultaneous cell-free production and screening of AMPs for their membrane specificity. On our device, AMPs are cell-free produced within water-in-oil-in-water double emulsion droplets, generated at high frequency. Within each droplet, the peptides can interact with different classes of co-encapsulated liposomes, generating a membrane-specific fluorescent signal. The double emulsions can be incubated and observed in a hydrodynamic trapping array or analysed via flow cytometry. Our approach provides a valuable tool for the discovery and development of membrane-active antimicrobials.