bluuebunny/crossref_metadata_2025 huggingface dataset:
Sea lice(Lepeophtherius salmonis)detection and quantification around aquaculture installations using environmental DNA
Authors: Krolicka Adriana , Nilsen Mari Mæland , Provan Fiona , Hansen Brian Klitgaard , Jacobsen Magnus Wulf , Baussant Thierry
Published: August 2021

The naturally occurring ectoparasite salmon lice (Lepeophtherirus salmonis) poses a great challenge for the salmon farming industry, as well as for wild salmonids in the Northern hemisphere. To better control the infestation pressure and protect the production, there is a need to provide fish farmers with sensitive and efficient tools for rapid early detection and monitoring of the parasitic load. This can be achieved by targetingL. salmonisDNA in environmental samples. Here, we developed and tested a newL. salmonisspecific DNA-based assay (qPCR assay) for detection and quantification from seawater samples using an analytical pipeline compatible with the Environmental Sample Processor (ESP) for autonomous water sample analysis of gene targets. Specificity of the L. salmonis qPCR assay was demonstrated through in-silico DNA analyses covering sequences of differentL. salmonisisolates. Seawater was spiked with known numbers of nauplii and copepodite free-swimming (planktonic) stages ofL. salmonisto investigate the relationship with the number of marker gene copies (MGC). Finally, field samples collected at different times of the year in the vicinity of a salmon production farm in Western Norway were analyzed forL. salmonisdetection and quantification. The assay specificity was high and a high correlation between MGC and planktonic stages ofL. salmoniswas established in the laboratory conditions. In the field,L. salmonisDNA was consequently detected, but with MGC number below that expected for one copepodite or nauplii. We concluded that onlyL. salmonistissue or eDNA residues were detected. This novel study opens for a fully automatizedL. salmonisDNA quantification using ESP robotic to monitor the parasitic load, but the challenge remains the adequate sampling of a volume of seawater sufficiently large to be representative of outbreaks and load around fish farms.
Rapid 3D-STORM imaging of diverse molecular targets in tissue
Authors: Albrecht Nicholas E. , Jiang Danye , Hobson Robert , Speer Colenso M. , Samuel Melanie A.
Published: August 2021

The precise organization of fine scale molecular architecture is critical for the nervous system and other biological functions and would benefit from nanoscopic imaging methods with improved accessibility, throughput, and native tissue compatibility. Here, we report RAIN-STORM, a rapid and scalable imaging approach that enables three-dimensional nanoscale target visualization for multiple subcellular and intracellular targets within tissue at depth. RAIN-STORM utilizes conventional tissue samples, readily available reagents in optimized formulas, requires no specialized sample handling, and is suitable for commercial instrumentation. To illustrate RAIN-STORM’s ability for quantitative high-resolution nanoscopic tissue imaging, we utilized the well-organized but structurally complex retina. We show that RAIN-STORM is rapid and versatile, enabling 3D nanoscopic imaging of over 20 distinct targets to reveal known and novel nanoscale features of synapses, neurons, glia, and vascular. Further, imaging parameters are compatible with a wide range of tissue sources and molecular targets across a spectrum of biological structures. Finally, we show that this method can be applied to clinically derived samples and reveal the nanoscale distribution of molecular targets within human samples. RAIN-STORM thus enables rapid 3D imaging for a range of molecules, paving the way for high throughput studies of nanoscopic molecular features in intact tissue from diverse sources.
Control of invasive Phragmites australis (European common reed) alters macroinvertebrate communities
Authors: Robichaud C.D. , Basso J.V. , Rooney R.C.
Published: August 2021

Wetland restoration often involves invasive plant species suppression to encourage the recovery of native-dominated vegetation communities. However, assessment of recovery is usually focused only on vegetation and the response of other critical wetland biota, such as macroinvertebrates, is seldom assessed. We characterized the aquatic, semi-aquatic, and terrestrial macroinvertebrate communities in remnant, uninvaded marsh to identify restoration targets and compared this to the communities in Phragmites australis-invaded marsh, and in formerly invaded marsh that was treated with the herbicide glyphosate in 2016 to simultaneously evaluate the effects of invasion and of invasive species suppression. We sampled invertebrates in 2017 and 2018 to track two years following herbicide treatment. The invertebrate community composition captured by the emergence traps was similar between P. australis and remnant marsh, suggesting invasion has little effect on macroinvertebrate community structure. There was also high concordance between the aquatic and emerging invertebrate communities in the invaded and uninvaded habitats. In contrast, herbicide-treated sites had a unique community composition, characterized by very high densities of Chironomidae (Diptera) and low taxa richness and evenness. Herbicide-treated sites also exhibited low concordance between the aquatic and emerging invertebrate communities, potentially attributable to the sparse emerging vegetation cover providing limited substrates for emergence. Herbicide-based invasive species control results in considerable changes to the macroinvertebrate community in freshwater marshes for at least two years after treatment, which may have consequences for aquatic food webs and species that rely on macroinvertebrates as prey.
Instructions and experiential learning have similar impacts on pain and pain-related brain responses but produce dissociations in value-based reversal learning
Authors: Atlas Lauren Y. , Dildine Troy C. , Palacios-Barrios Esther E. , Yu Qingbao , Reynolds Richard C. , Banker Lauren A. , Grant Shara S. , Pine Daniel S.
Published: August 2021

Recent data suggest that interactions between systems involved in higher order knowledge and associative learning drive responses during appetitive and aversive learning. However, it is unknown how these systems impact subjective responses, such as pain. We tested how instructions and reversal learning influence pain and pain-evoked brain activation. Healthy volunteers (n = 40) were either instructed about contingencies between cues and aversive outcomes or learned through experience in a paradigm where contingencies reversed three times. We measured predictive cue effects on pain and heat-evoked brain responses using functional magnetic resonance imaging. Predictive cues dynamically modulated pain perception as contingencies changed, regardless of whether participants received contingency instructions. Heat-evoked responses in the insula, anterior cingulate, and putamen updated as contingencies changed, whereas the periaqueductal gray and thalamus responded to initial contingencies throughout the task. Quantitative modeling revealed that expected value was shaped purely by instructions in the Instructed Group, whereas expected value updated dynamically in the Uninstructed Group as a function of error-based learning. These differences were accompanied by dissociations in the neural correlates of value-based learning in the rostral anterior cingulate, medial prefrontal cortex, and orbitofrontal cortex. These results show how predictions impact subjective pain. Moreover, imaging data delineate three types of networks involved in pain generation and value-based learning: those that respond to initial contingencies, those that update dynamically during feedback-driven learning as contingencies change, and those that are sensitive to instruction. Together, these findings provide multiple points of entry for therapies designs to impact pain.
Spatial Analysis of Neural Cell Proteomic Profiles following Ischemic Stroke in Mice using High-Plex Digital Spatial Profiling
Authors: Noll Jessica M. , Augello Catherine J. , Kürüm Esra , Pan Liuliu , Pavenko Anna , Nam Andy , Ford Byron D.
Published: August 2021

Stroke is ranked as the fifth leading cause of death and the leading cause of adult disability. The progression of neuronal damage after stroke is recognized to be a complex integration of glia, neurons, and the surrounding extracellular matrix, therefore potential treatments must target the detrimental effects created by these interactions. In this study, we examined the spatial cellular and neuroinflammatory mechanisms occurring early after ischemic stroke utilizing Nanostring Digital Spatial Profiling (DSP) technology. Male C57bl/6 mice were subjected to photothrombotic middle cerebral artery occlusion (MCAO) and sacrificed at three-days post-ischemia. Spatial distinction of the ipsilateral hemisphere was studied according to the regions of interest: the ischemic core, peri-infarct tissues, and peri-infarct normal tissue (PiNT) in comparison to the contralateral hemisphere. We demonstrated that the ipsilateral hemisphere initiates distinct spatial regulatory proteomic profiles with DSP technology that can be identified consistently with the immunohistochemical markers, FJB, GFAP, and Iba-1. The core border profile demonstrated an induction of neuronal death, apoptosis, autophagy, immunoreactivity, and early degenerative proteins. Most notably, the core border resulted in a decrease of the neuronal proteins Map2 and NeuN, an increase in the autophagy proteins BAG3 and CTSD, an increase in the microglial and peripheral immune invasion proteins Iba1, CD45, CD11b, and CD39, and an increase in the neurodegenerative proteins BACE1, APP, αβ 1-42, ApoE, and hyperphosphorylated tau protein S-199. The peri-infarct region demonstrated increased astrocytic immunoreactivity, apoptotic, and neurodegenerative proteomic profile, with an increase in BAG3, GFAP, and hyperphosphorylated tau protein S-199. The PiNT region displayed minimal changes compared to the contralateral cortex with only an increase in GFAP. Overall, our data highlight the importance of identifying ischemic mechanisms in a spatial manner to understand the complex, dynamic interactions throughout ischemic progression and repair as well to introduce potential targets for successful therapeutic interventions.
A large-sample crisis? Exaggerated false positives by popular differential expression methods
Authors: Li Yumei , Ge Xinzhou , Peng Fanglue , Li Wei , Li Jingyi Jessica
Published: August 2021

We report a surprising phenomenon about identifying differentially expressed genes (DEGs) from population-level RNA-seq data: two popular bioinformatics methods, DESeq2 and edgeR, have unexpectedly high false discovery rates (FDRs). Via permutation analysis on an immunotherapy RNA-seq dataset, we observed that DESeq2 and edgeR identified even more DEGs after samples’ condition labels were randomly permuted. Motivated by this, we evaluated six DEG identification methods (DESeq2, edgeR, limma-voom, NOISeq, dearseq, and the Wilcoxon rank-sum test) on population-level RNA-seq datasets. We found that the FDR control was often failed by the three popular parametric methods—DESeq2, edgeR, and limma-voom— and the new non-parametric method dearseq. In particular, the actual FDRs of DESeq2 and edgeR sometimes exceeded 20% when the target FDR threshold was only 5%. Although NOISeq, a non-parametric method used by GTEx, controlled the FDR better than the other four methods did, its power was much lower than that of the Wilcoxon rank-sum test, a classic nonparametric test that consistently controlled the FDR and achieved good power in our evaluation. Based on these results, for population-level RNA-seq studies, we recommend the Wilcoxon rank-sum test.
Erytra Blood Group Analyser and Kode Technology testing of SARS-CoV-2 antibodies among convalescent patients and vaccinated individuals
Authors: Weinstock Christof , Flegel Willy A , Srivastava Kshitij , Kaiser Sabine , Schrezenmeier Hubert , Tsamadou Chrysanthi , Ludwig Carolin , Jahrsdörfer Bernd , Bovin Nicolai V , Henry Stephen M
Published: August 2021

Surveillance of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic requires tests to monitor antibody formation and prevalence. We detected SARS-CoV-2 antibodies using red cells coated by Kode technology with short peptides derived from the SARS-CoV-2 spike protein. Such modified red cells, called C19-kodecytes, can be used as reagent cells in any manual or automated column agglutination assay. We investigated the presence of SARS-CoV-2 antibodies in 130 samples from COVID-19 convalescent plasma donors using standard manual technique, two FDA authorized ELISA assays and a virus neutralisation assay. The sensitivity of the C19-kodecyte assay was 88%, comparable to the anti-SP and anti-NCP ELISAs (86% and 83%) and the virus neutralisation assay (88%). The specificity of the C19-kodecyte assay was 90% (anti-SP 100% and anti-NCP 97%). Likewise, 231 samples from 73 vaccinated individuals were tested with an automated analyser and we monitored the appearance and persistence of SARS-CoV-2 antibodies. The C19-kodecyte assay is a robust tool for SARS-CoV-2 antibody detection. Automated blood group analyser use enables large-scale SARS-CoV-2 antibody testing for vaccination monitoring in population surveys.
Differentials and determinants of immunization coverage among children aged 12-36 months in India: Analysis of nationally-representative, population-based survey data
Authors: Naaz Eram , Akhtar Saddaf Naaz , Malik Manzoor Ahmad , Pradhan Jalandhar
Published: August 2021

Introduction

Immunization coverage among children is still a major public health concern in India and other low-middle income countries. Low coverage likely risks the health of children and therefore impacts their overall growth. We therefore examined the immunization coverage rates among children aged 12-36 months in India and its states. We also explored the associated factors affecting immunization coverage among children aged 12-36 in India.

Methods

We used data from 75th round of the National Sample Survey Organizations (NSSO), collected from July 2017 to June 2018. The analytical sample of children aged 12-36 months information cases was 15887. Immunization coverage rates of India and its states were calculated. We evaluated the immunization coverage rate by background characteristics in India and its states. We performed multinomial logistic regression analysis to estimate the factors associated with the immunization coverage in India.

Results

About 61.95% were fully immunized, 35.62% were partially immunized and the rest 2.43% had not received any vaccine. The children aged 21-28 months (0.50; p<0.01) & 29-36 months (0.35; p<0.01), belonging to North-Eastern regions (0.60; p<0.01) were found to be significantly less likely to receive fully immunization. Likewise, urban children are (1.26; p<0.1) found to be more likely to receive fully immunization. The lowest fully immunization has been seen in Daman and Diu (1.73%) followed by Nagaland (6.93%), NCT Delhi (34.71%), and Tripura (46.33%).

Conclusions

Child immunization is a key public health concern and vital challenge to be addressed. Socio-economic characteristics play a key role in immunization coverage. Therefore necessary policy measures must be taken to address the challenges of poor immunization coverage and its impact on health and wellbeing of children
Characterisation of type 2 diabetes subgroups and their association with ethnicity and clinical outcomes: a UK real-world data study using the East London Database
Authors: Mathur Rohini , Hull Sally A , Hodgson Sam , Finer Sarah
Published: August 2021

Background

Subgroups of type 2 diabetes (T2DM) have been well characterised in experimental studies. However, it is unclear whether T2DM subgroups can be identified in UK based real-world populations and if they impact clinical outcomes.

Aim

To derive T2DM subgroups using primary care data from a multi-ethnic population, evaluate associations with glycaemic control, treatment initiation and vascular outcomes, and understand how these vary by ethnicity.

Design and setting

An observational cohort study in the East London Primary Care Database from 2008-2018.

Method

Latent class analysis using age, sex, glycated haemoglobin, and body mass index at diagnosis was used to derive T2DM subgroups in White, South Asian, and Black groups. Time to treatment initiation and vascular outcomes was estimated using multivariable Cox-proportional hazards regression.

Results

31,931 adults with T2DM were included: 47% south Asian, 25% White, 20% Black. We replicated two previously described subgroups, ‘Mild Age-Related Diabetes’ (MARD), ‘Mild Obesity-related Diabetes (MOD), and characterised a third ‘Severe Hyperglycaemic Diabetes’ (SHD). Compared to MARD, SHD had the poorest long term glycaemic control, fastest initiation of antidiabetic treatment (HR 2.02, 1.76-2.32), and highest risk of microvascular complications (HR 1.38, 1.28-1.49). MOD had the highest risk of macrovascular complications (HR 1.50, 1.23-1.83). Subgroup differences in treatment initiation were most pronounced for the White group, and vascular complications for the Black group.

Conclusions

Clinically useful T2DM subgroups, identified at diagnosis, can be generated in routine real-world multi-ethnic populations, and may offer a pragmatic means to develop stratified primary care pathways and improve healthcare resource allocation.

How this fits in

Previous studies of predominantly White European populations have identified four T2DM subgroups. In the UK the clinical measures necessary to replicate these subgroups are only available in secondary care data, limiting their usefulness for diabetes management in primary care settings. In this study, we demonstrate how clinically meaningful T2DM subgroups can be pragmatically generated using real-world primary care data. Furthermore, we highlight important differences between T2DM subgroups with respect to vascular outcomes, treatment initiation, and HbA1c control. Diabetes subgroups are a useful heuristic for helping clinician decision-making which, in turn, this can lead to a more personalised design of diabetes care focussed on more intensive management of subgroups most at risk of complications, such as those with severe hyperglycaemia at time of diagnosis.
Nurse-physician Communication around Identifying Palliative Care Needs in Nursing Home Residents
Authors: van der Steen Jenny T. , Jongen Esmée A. , Dekker Natashe Lemos , Bagchus Lotje , Pasman H. Roeline W. , Onwuteaka-Philipsen Bregje D. , Achterberg Wilco P.
Published: August 2021

Objective

To assess experiences of medical practitioners who are on the staff of nursing homes with communication with nursing staff about identifying emerging and changing (palliative) care needs of residents of nursing homes in the Netherlands.

Design

Qualitative interview study.

Setting and Participants

Fifteen physicians and two nurse practitioners employed by eight care organizations in the western urbanized region of the Netherlands.

Methods

We conducted individual semi-structured interviews in 2018 informed by a topic list that was based on a qualitative dataset about facilitators to palliative care in dementia reported by elderly care physicians. The interviews were recorded, transcribed verbatim and analysed with Atlas.ti. We used both deductive and inductive coding adding refined codes related to communication.

Results

All interviewees expressed appreciation for nursing staff on whom they relied to communicate palliative care needs, yet they reported a variety of communication challenges around important changes in resident’s condition which were covered by two themes. (1) Teamwork was facilitated or impeded by team size and structure, quality of relationships and clarity in hierarchical relationships. (2) Continuity of information was affected by (in)effective routes of consultation and (lack of) detail in communicating observations.

Conclusions and Implications

Also in the case of on-staff physicians, functioning of the multidisciplinary team and accurate sharing of observed changes in nursing home residents’ condition are crucial for physicians to be able to address palliative care needs. The physicians’ expressions of how they would favor nursing staff to communicate can inspire interprofessional training, such as reporting objective observations and phrasing a clear request for help while avoiding overly demanding appeals.
Silent Hypoxia in Coronavirus disease-2019: Is it more dangerous?-A retrospective cohort study
Authors: Sirohiya Prashant , Elavarasi Arunmozhimaran , Raju Sagiraju Hari Krishna , Baruah Madhusmita , Gupta Nishkarsh , Garg Rohit Kumar , Paul Saurav Sekhar , Ratre Brajesh Kumar , Singh Ram , Kumar Balbir , Vig Saurabh , Pandit Anuja , Kumar Abhishek , Garg Rakesh , Meena Ved Prakash , Mittal Saurabh , Pahuja Saurabh , Das Nupur , Dwivedi Tanima , Gupta Ritu , Kumar Sunil , Pandey Manisha , Mishra Abhinav , Matharoo Karanvir Singh , Mohan Anant , Guleria Randeep , Bhatnagar Sushma
Published: August 2021

Background

Hypoxia in patients with COVID-19 is one of the strongest predictors of mortality. Silent hypoxia is characterized by the presence of hypoxia without dyspnea.. Silent hypoxia has been shown to affect the outcomes in previous studies.

Research Question

Are the outcomes in patients presenting with silent hypoxia different from those presenting with dyspneic hypoxia?

Study design and Methods

This was a retrospective study of a cohort of patients with SARS-CoV-2 infection who were hypoxic at presentation. Clinical, laboratory, and treatment parameters in patients with silent hypoxia and dyspneic hypoxia were compared. Multivariate logistic regression models were fitted to identify the factors predicting mortality.

Results

Among 2080 patients with COVID-19 admitted to our hospital, 811 patients were hypoxic with SpO2<94% at the time of presentation. 174 (21.45%) did not have dyspnea since the onset of COVID-19 symptoms. 5.2% of patients were completely asymptomatic for COVID-19 and were found to be hypoxic only on pulse oximetry. The case fatality rate in patients with silent hypoxia was 45.4% as compared to 40.03% in dyspneic hypoxic patients (P=0.202). The odds ratio of death was 1.1 (95% CI 0.41-2.97) in the patients with silent hypoxia after adjusting for baseline characteristics, laboratory parameters, treatment, and in-hospital complications, which did not reach statistical significance (P=0.851).

Interpretation

Silent hypoxia may be the only presenting feature of COVID-19. Since the case fatality rate is comparable between silent and dyspneic hypoxia, it should be recognized early and treated as aggressively. Since home isolation is recommended in patients with COVID-19, it is essential to use pulse oximetry at the home setting to identify these patients.
A computational optimization approach for the automatic generation of Gamma Knife radiosurgery treatment plans
Authors: Walker Matthew R. , Malekmohammadi Mehrdad , Coolens Catherine , Laperriere Normand , Heaton Robert , Sheikholeslami Ali , Hodaie Mojgan
Published: August 2021

Gamma Knife (GK) radiosurgery is a non-invasive treatment modality which allows single fraction delivery of focused radiation to one or more brain targets. Treatment planning mostly involves manual placement and shaping of shots to conform the prescribed dose to a surgical target. This process can be time consuming and labour intensive. An automated method is needed to determine the optimum combination of treatment parameters to decrease planning time and chance for operator-related error. Recent advancements in hardware platforms which employ parallel computational methods with stochastic optimization schemes are well suited to solving such combinatorial optimization problems efficiently. We present a method of generating optimized GK radiosurgery treatment plans using these techniques, which we name ROCKET (Radiosurgical Optimization Configuration Kit for Enhanced Treatments). Our approach consists of two phases in which shot isocenter positions are generated based on target geometry, followed by optimization of sector collimator parameters. Using this method, complex treatment plans can be generated, on average, in less than one minute, a substantial decrease relative to manual planning. Our results also demonstrate improved selectivity and treatment safety through decreased exposure to nearby organs-at-risk (OARs), compared to manual reference plans with matched coverage. Stochastic optimization is therefore shown to be a robust and efficient clinical tool for the automatic generation of GK radiosurgery treatment plans.
A Large-Scale Investigation of White Matter Microstructural Associations with Reading Ability
Authors: Meisler Steven L. , Gabrieli John D.E.
Published: August 2021

Reading involves the functioning of a widely distributed brain network, and white matter tracts are responsible for transmitting information between constituent network nodes. Several studies have analyzed fiber bundle microstructural properties to shed insights into the neural basis of reading abilities and disabilities. Findings have been inconsistent, potentially due to small sample sizes and varying methodology. To address this, we analyzed a large data set of 686 children ages 5-18 using state-of-the-art neuroimaging acquisitions and processing techniques. We searched for associations between fractional anisotropy (FA) and single-word and single-nonword reading skills in children with diverse reading abilities across multiple tracts previously thought to contribute to reading. We also looked for group differences in tract FA between typically reading children and children with reading disabilities. FA of the white matter increased with age across all participants. There were no significant correlations between overall reading abilities and tract FAs across all children, and no significant group differences in tract FA between children with and without reading disabilities. There were associations between FA and nonword reading ability in older children (ages 9 and above). Higher FA in the right superior longitudinal fasciculus (SLF) and left inferior cerebellar peduncle (ICP) correlated with better nonword reading skills. These results suggest that letter-sound correspondence skills, as measured by nonword reading, are associated with greater white matter coherence among older children in these two tracts, as indexed by higher FA.
Allele expression biases in mixed-ploid sugarcane accessions
Authors: Correr Fernando Henrique , Furtado Agnelo , Garcia Antonio Augusto Franco , Henry Robert James , Margarido Gabriel Rodrigues Alves
Published: August 2021

Allele-specific expression (ASE) represents differences in the magnitude of expression between alleles of the same gene. This is not straightforward for polyploids, especially autopolyploids, as knowledge about the dose of each allele is required for accurate estimation of ASE. This is the case for the genomically complex Saccharum species, characterized by high levels of ploidy and aneuploidy. We used a Beta-Binomial model to test for allelic imbalance in Saccharum, with adaptations for mixed-ploid organisms. The hierarchical Beta-Binomial model was used to test if allele expression followed the expectation based on genomic allele dosage. The highest frequencies of ASE occurred in sugarcane hybrids, suggesting a possible influence of interspecific hybridization in these genotypes. For all accessions, ASEGs were less frequent than those with balanced allelic expression. These genes were related to a broad range of processes, mostly associated with general metabolism, organelles, responses to stress and responses to stimuli. In addition, the frequency of ASEGs in high-level functional terms was similar among the genotypes, with a few genes associated with more specific biological processes. We hypothesize that ASE in Saccharum is largely a genotype-specific phenomenon, as a large number of ASEGs were exclusive to individual accessions.
The brain selectively tunes to unfamiliar voices during sleep
Authors: Ameen Mohamed S. , Heib Dominik PJ , Blume Christine , Schabus Manuel
Published: August 2021

The brain continues to respond selectively to environmental stimuli even during sleep. However, the functional role of such responses, and whether they reflect information processing or rather sensory inhibition is not fully understood.

Here, we presented 17 human sleepers (14 females) with their own name and two unfamiliar first names, spoken by either a familiar voice (FV) or an unfamiliar voice (UFV), while recording polysomnography during a full night’s sleep. We detected K-complexes, sleep spindles, and micro-arousals, and then assessed event-related potentials, oscillatory power as well as intertrial phase synchronization in response to the different stimuli presented during non-rapid eye movement (NREM) sleep.

We show that UFVs evoke more K-complexes and micro-arousals than FVs. When both stimuli evoke a K-complex, we observed larger evoked potentials, higher oscillatory power in the high beta (>16Hz) frequency range, and stronger time-locking in the delta band (1-4 Hz) in response to UFVs relative to FVs. Crucially, these differences in brain responses disappear when no K-complexes are evoked by the auditory stimuli.

Our findings highlight discrepancies in brain responses to auditory stimuli based on their relevance to the sleeper and propose a key role for K-complexes in the modulation of sensory processing during sleep. We argue that such content-specific, dynamic reactivity to external sensory information enables the brain to enter a ‘sentinel processing mode’ in which it engages in the many important processes that are ongoing during sleep while still maintaining the ability to process vital information in the surrounding.

Significance statement

Previous research has shown that sensory processing continues during sleep. Here, we studied the capacity of the sleeping brain to extract and process relevant sensory information. We presented sleepers with their own names and unfamiliar names spoken by either a familiar (FV) or an unfamiliar voice (UFV). During non-rapid eye movement (NREM) sleep, UFVs elicited more K-complexes and micro-arousals than FVs. By contrasting stimuli which evoked K-complexes, we demonstrate that UFVs triggered larger evoked potentials, stronger time-locking in the delta (1-4Hz) band, and higher oscillatory power (>16Hz) relative to FVs. These differences in brain responses disappeared when no K-complexes were evoked. Our results suggest a pivotal role for K-complexes in the selective processing of relevant information during NREM sleep.
Infection-Induced Dermal Lymphatic Zippering Restricts Viral Dissemination from Skin and Promotes Anti-Viral CD8+ T Cell Expansion
Authors: Churchill Madeline J. , du Bois Haley , Heim Taylor A. , Mudianto Tenny , Steele Maria M. , Nolz Jeffrey C. , Lund Amanda W.
Published: August 2021

Lymphatic vessels are often considered passive conduits that rapidly flush antigenic material, pathogens, and cells to draining lymph nodes. Recent evidence, however, suggests that lymphatic vessels actively regulate diverse processes from antigen transport to leukocyte trafficking and dietary lipid absorption. Here we tested the hypothesis that dermal lymphatic transport is dynamic and contributes to innate host defense during viral infection. We demonstrate that cutaneous vaccinia virus infection activates the tightening of lymphatic interendothelial junctions, termed zippering, in a VEGFA/VEGFR2-dependent manner. Both antibody-mediated blockade of VEGFA/VEGFR2 and lymphatic-specific deletion of Vegfr2 impaired lymphatic capillary zippering and increased fluid flux out of tissue. Strikingly, inhibition of lymphatic zippering allows viral dissemination to draining lymph nodes independent of dendritic cell migration and impairs CD8+ T cell priming. These data indicate that infection-induced dermal lymphatic capillary zippering is a context-dependent, active mechanism of innate host defense that limits interstitial fluid and virion flux and promotes protective, anti-viral CD8+ T cell responses.

Cutaneous infection with vaccinia virus induces VEGFR2-dependent dermal lymphatic capillary zippering. This tightening of lymphatic junctions exacerbates tissue edema, sequesters virus, and promotes anti-viral CD8+ T cell responses. Dermal lymphatic capillaries are therefore an active component of innate host defense.
KLF4 induces Mesenchymal - Epithelial Transition (MET) by suppressing multiple EMT-inducing transcription factors
Authors: Subbalakshmi Ayalur Raghu , Sahoo Sarthak , McMullen Isabelle , Saxena Aaditya Narayan , Venugopal Sudhanva Kalasapura , Somarelli Jason , Jolly Mohit Kumar
Published: August 2021

Epithelial-Mesenchymal Plasticity (EMP) refers to reversible dynamic processes where cells can transition from epithelial to mesenchymal (EMT) or from mesenchymal to epithelial (MET) phenotypes. Both these processes are modulated by multiple transcription factors acting in concert. While EMT-inducing transcription factors (TFs) – TWIST1/2, ZEB1/2, SNAIL1/2/3, GSC, FOXC2 – are well-characterized, the MET-inducing TFs are relatively poorly understood (OVOL1/2, GRHL1/2). Here, using mechanism-based mathematical modeling, we show that the transcription factor KLF4 can delay the onset of EMT by suppressing multiple EMT-TFs. Our simulations suggest that KLF4 overexpression can promote phenotypic shift toward a more epithelial state, an observation suggested by negative correlation of KLF4 with EMT-TFs and with transcriptomic based EMT scoring metrics in cancer cell lines. We also show that the influence of KLF4 in modulating EMT dynamics can be strengthened by its ability to inhibit cell-state transitions at an epigenetic level. Thus, KLF4 can inhibit EMT through multiple parallel paths and can act as a putative MET-TF. KLF4 associates with patient survival metrics across multiple cancers in a context-specific manner, highlighting the complex association of EMP with patient survival.
Extensive incorporation, polarisation and improved maturation of transplanted human cones in a murine cone degeneration model
Authors: Gasparini Sylvia J , Tessmer Karen , Reh Miriam , Wieneke Stephanie , Carido Madalena , Völkner Manuela , Borsch Oliver , Swiersy Anka , Zuzic Marta , Goureau Olivier , Kurth Thomas , Busskamp Volker , Zeck Günther , Karl Mike O , Ader Marius
Published: August 2021

Once human photoreceptors die, they do not regenerate, thus photoreceptor transplantation has emerged as a potential treatment approach for blinding diseases. Improvements in transplant organization, donor cell maturation and synaptic connectivity to the host will be critical in advancing this technology to clinical practice. Unlike the unstructured grafts of prior cell suspension transplantations into end-stage degeneration models, we describe extensive incorporation of iPSC retinal organoid-derived human photoreceptors into mice with cone dysfunction. This incorporative phenotype was validated in both cone-only as well as pan-photoreceptor transplantations. Rather than forming a glial barrier, Müller cells extend throughout the graft, even forming a common outer limiting membrane. Donor-host interaction appears to promote polarisation as well as development of morphological features critical for light detection, namely formation of inner and well stacked outer segments oriented towards the RPE. Putative synapse formation and graft function is evident both at a structural and electrophysiological level. Overall, these results show that human photoreceptors interact readily with a partially degenerated retina. Moreover, incorporation into the host retina appears to be beneficial to graft maturation, polarisation and function.

Highlights

Generation of the first human iPSC cone reporter line

Human cones extensively incorporate into the retina of mice with cone degeneration

Donor cone age and time in vivo are important factors for transplant incorporation

Incorporation into the host retina correlates with graft polarisation

Improved photoreceptor maturation after transplantation in vivo vs. in vitro

Re-establishment of cone-mediated light-responses in the cone deficient mouse
Deep molecular characterization linked to drug response profiling of pancreatic ductal adenocarcinoma using patient-derived organoids
Authors: Le Blanc Solange , Ishaque Naveed , Jabs Julia , Bauer Tobias , Schuth Sebastian , Hu Qing , Debnath Olivia , Ten Foo Wei , Leonhardt Carl-Stephan , König Anna-Katharina , Bieg Matthias , Eckert Christoph , Gaida Matthias M. , Volkmar Michael , Hübschmann Daniel , Schenk Miriam , Offringa Rienk , Giese Nathalia A. , Schlesner Matthias , Büchler Markus W. , Eils Roland , Conrad Christian , Strobel Oliver
Published: August 2021

Pancreatic ductal adenocarcinoma (PDAC) is characterized by high drug resistance and poor prognosis. Novel therapeutic and stratification strategies are urgently needed. Here, we present an integration of in-depth genomic and transcriptomic characterization with drug screening and clinical outcome based on a catalogue of 51 patient-derived tumor organoids (PDOs) from resected PDAC. Known PDAC molecular subtypes and their prognostic value are conserved in organoids. Integration of transcriptomic and drug response profiles suggest a metabolism-mediated modulations of drug resistance. Copy number alterations on chromosome 13q and wild-type status of TP53 emerged as potential novel genomic biomarkers for sensitivity to 5-FU and oxaliplatin treatment, respectively. Functional testing of targeted drugs in PDOs revealed its additional value for genome-driven personalized oncology. Co-deletion of TP53/POLR2A increased vulnerability to RNA polymerase II inhibition, pointing to a promising target for personalized treatment in PDAC.

Significance

Patient-derived PDAC organoids hold great promise as surrogate tumor models for personalized oncology. By integrating highly granular molecular, drug sensitivity and clinical data, we demonstrate that PDOs are valid models for molecular characterization and response prediction that also enable identification of novel drug sensitivity biomarkers and resistance mechanisms in PDAC.
Fluorescence lifetime imaging as anin situand label-free readout for the chemical composition of lignin
Authors: Escamez Sacha , Terryn Christine , Gandla Madhavi Latha , Yassin Zakiya , Scheepers Gerhard , Näsholm Torgny , Sundman Ola , Jönsson Leif J. , Lundberg-Felten Judith , Tuominen Hannele , Niittylä Totte , Paës Gabriel
Published: August 2021

Important structures and functions within living organisms rely on naturally fluorescent polymeric molecules such as collagen, keratin, elastin, resilin, or lignin. Theoretical physics predict that fluorescence lifetime of these polymers is related to their chemical composition. We verified this prediction for lignin, a major structural element in plant cell walls and one of the most abundant components of wood. Lignin is composed of different types of phenylpropanoid units, and its composition affects its properties, biological functions, and the utilization of wood biomass. We carried out fluorescence lifetime imaging microscopy (FLIM) measurements of wood cell wall lignin in a population of 90 hybrid aspen trees genetically engineered to display differences in cell wall chemistry and structure. We also measured wood cell wall composition by classical analytical methods in the wood cell walls of these trees. Using statistical modelling and machine learning algorithms, we identified parameters of fluorescence lifetime that predict the content of S-type and G-type lignin units, the two main types of units in the lignin of angiosperm plants. Finally, we show how quantitative measurements of lignin chemical composition by FLIM can reveal the dynamics of lignin biosynthesis in two different biological contexts, includingin vivowhile lignin is being synthesized in the walls of living cells.
Towards Decoding Selective Attention Through Cochlear Implant Electrodes as Sensors in Subjects with Contralateral Acoustic Hearing
Authors: Aldag Nina , Büchner Andreas , Lenarz Thomas , Nogueira Waldo
Published: August 2021

Objectives

Focusing attention on one speaker in a situation with multiple background speakers or noise is referred to as auditory selective attention. Decoding selective attention is an interesting line of research with respect to future brain-guided hearing aids or cochlear implants (CIs) that are designed to adaptively adjust sound processing through cortical feedback loops. This study investigates the feasibility of using the electrodes and backward telemetry of a CI to record electroencephalography (EEG).

Approach

The study population included 6 normal-hearing (NH) listeners and 5 CI users with contralateral acoustic hearing. Cortical auditory evoked potentials (CAEP) and selective attention were recorded using a state-of-the-art high-density scalp EEG and, in the case of CI users, also using two CI electrodes as sensors in combination with the backward telemetry system of these devices (iEEG).

Main results

The peak amplitudes of the CAEPs recorded with iEEG were lower and the latencies were higher than those recorded with scalp EEG. In the selective attention paradigm with multi-channel scalp EEG the mean decoding accuracy across subjects was 92.0 and 92.5% for NH listeners and CI users, respectively. With single-channel scalp EEG the accuracy decreased to 65.6 and to 75.8% for NH listeners and CI users, respectively, and was above chance level in 9 out of 11 subjects. With the single-channel iEEG, the accuracy for CI users decreased to 70% and was above chance level in 3 out of 5 subjects.

Significance

This study shows that single-channel EEG is suitable for auditory selective attention decoding, even though it reduces the decoding quality compared to a multi-channel approach. CI-based iEEG can be used for the purpose of recording CAEPs and decoding selective attention. However, the study also points out the need for further technical development for the CI backward telemetry regarding long-term recordings and the optimal sensor positions.
Decadal trend of plankton community change and habitat shoaling in the Arctic gateway recorded by planktonic foraminifera
Authors: Greco Mattia , Werner Kirstin , Zamelczyk Katarzyna , Rasmussen Tine L. , Kucera Michal
Published: August 2021

The Fram Strait plays a crucial role in regulating the heat and sea-ice dynamics in the Arctic. In response to the ongoing global warming, the marine biota of this Arctic gateway is experiencing significant changes with increasing advection of Atlantic species. The footprint of this “Atlantification” has been identified in isolated observations across the plankton community, but a systematic, multi-decadal perspective on how regional climate change facilitates the invasion of Atlantic species and affects the ecology of the resident species is lacking. Here we evaluate a series of 51 depth-resolved plankton profiles collected in the Fram Strait during seven surveys between 1985 and 2015, using planktonic foraminifera as a proxy for changes in both the pelagic community composition and species vertical habitat depth. The time series reveals a progressive shift towards more Atlantic species, occurring independently of changes in local environmental conditions. We conclude that this trend is reflecting higher production of the Atlantic species in the “source” region, from where they are advected into the Fram Strait. At the same time, we observe that the ongoing extensive sea-ice export from the Arctic and associated cooling-induced decline in density and habitat shoaling of the subpolarTurborotalita quinqueloba, whereas the residentNeogloboquadrina pachydermapersists. As a result, the planktonic foraminiferal community and vertical structure in the Fram Strait shifts to a new state, driven by both remote forcing of the Atlantic invaders and local climatic changes acting on the resident species. The strong summer export of Arctic sea ice has so far buffered larger plankton transformation. We predict that if the sea-ice export will decrease, the Arctic gateway will experience rapid restructuring of the pelagic community, even in the absence of further warming. Such a large change in the gateway region will likely propagate into the Arctic proper.
Accurate and automated high-coverage identification of chemically cross-linked peptides with MaxLynx
Authors: Yılmaz Şule , Busch Florian , Nagaraj Nagarjuna , Cox Jürgen
Published: August 2021

Cross-linking combined with mass spectrometry (XL-MS) provides a wealth of information about the 3D structure of proteins and their interactions. We introduce MaxLynx, a novel computational proteomics workflow for XL-MS integrated into the MaxQuant environment. It is applicable to non-cleavable and MS-cleavable cross linkers. For both we have generalized the Andromeda peptide database search engine to efficiently identify cross-linked peptides. For non-cleavable peptides, we implemented a novel di-peptide Andromeda score, which is the basis for a computationally efficient N-squared search engine. Additionally, partial scores summarize the evidence for the two constituents of the di-peptide individually. A posterior error probability based on total and partial scores is used to control false discovery rates. For MS-cleavable cross linkers a scoring of signature peaks is combined with the conventional Andromeda score on the cleavage products. The MaxQuant 3D-peak detection was improved to ensure more accurate determination of the monoisotopic peak of isotope patterns for heavy molecules, which cross-linked peptides typically are. A wide selection of filtering parameters can replace manual filtering of identifications, which is often necessary when using other pipelines. On benchmark datasets of synthetic peptides, MaxLynx outperforms all other tested software on data for both types of cross linkers as well as on a proteome-wide dataset of cross-linked D. melanogaster cell lysate. The workflow also supports ion-mobility enhanced MS data. MaxLynx runs on Windows and Linux, contains an interactive viewer for displaying annotated cross-linked spectra and is freely available at https://www.maxquant.org/.
Autophagy in DG engrams mediates Rac1-dependent forgetting via TLR2/4 signals in microglia
Authors: Wang Zhilin , Chen Ruyan , Lin Qing , Jiang Yan , Le Qiumin , Liu Xing , Ma Lan , Wang Feifei
Published: August 2021

BACKGROUND

Engrams are considered to be substrates for memory storage, and the adaptive plasticity remolding that switch engrams to an inaccessible state cause forgetting. The normal function of engrams is ensured by the crosstalk between neurons and microglia, the major immune cells in the brain implicated in synapse remodeling and memory processing. However, the cellular processes and molecular mediators between engrams and microglia underlying forgetting are poorly understood.

METHODS

We utilized doxycycline (Dox)-dependent robust activity marking (RAM) system to label and manipulate DG engrams encoding contexture fear memory in mice. Combining optogenetics, microglia-specific transcriptomics, fluorescence in situ hybridization and spine morphology analysis, we investigated the potential mechanisms of information exchange between engrams and microglia mediating memory forgetting.

RESULTS

The expression of Rac1 in dentate gyrus (DG) engrams upregulated memory encoding. Increased Rac1 activity in DG engrams accelerated forgetting, upregulated autophagy influx and the expression of autophagy protein 7 (Atg7). The elevated ATG7 expression in the engrams activated of DG microglia and promoted forgetting. In addition, the Toll-like receptor (TLR) signal in DG microglia was upregulated when overexpressing ATG7 or activating Rac1 in DG engrams, and mediated the ATG7-dependent synapse remodeling and Rac1-dependent forgetting.

CONCLUSIONS

In this study, we found that Rac1 increases ATG7-dependent autophagy in DG engrams, which activated microglia via TLR2/4, to promote spine remodeling and forgetting. These results unravel a novel pathway mediating memory forgetting, and provide a potential therapeutic strategy in the treatment of cognitive disorders such as Alzheimer’s disease.