bluuebunny/crossref_metadata_2025 huggingface dataset:
i-Motif formation and spontaneous deletions in human cells
Authors: Martella Marianna , Pichiorri Flavia , Chikhale Rupesh V , Abdelhamid Mahmoud A S , Waller Zoë A E , Smith Steven S
Published: February 2022

Concatemers of d(TCCC) that were first detected through their association with deletions at the RACK7 locus, are widespread throughout the human genome. Circular dichroism spectra show that d(GGGA)n sequences form G-quadruplexes when n > 3, while i-motif structures form at d(TCCC)n sequences at neutral pH when n ≥ 7 in vitro. In the PC3 cell line, deletions are observed only when the d(TCCC)n variant is long enough to form significant levels of unresolved i-motif structure at neutral pH. The presence of an unresolved i-motif at a representative d(TCCC)n element at RACK7 was suggested by experiments showing that that the region containing the d(TCCC)9 element was susceptible to bisulfite attack in native DNA and that d(TCCC)9 oligo formed an i-motif structure at neutral pH. This in turn suggested that that the i-motif present at this site in native DNA must be susceptible to bisulfite mediated deamination even though it is a closed structure. Bisulfite deamination of the i-motif structure in the model oligodeoxynucleotide was confirmed using mass spectrometry analysis. We conclude that while G-quadruplex formation may contribute to spontaneous mutation at these sites, deletions actually require the potential for i-motif to form and remain unresolved at neutral pH.
In Reply
Authors: Rai Karan , Brooks Gabriel
Published: February 2022

This letter to the editor responds to Morelli et al, continuing the discussion on the implementation of DPYD genotyping.
COP1 positively regulates ABA signaling during Arabidopsis seedling growth in darkness by mediating ABA-induced ABI5 accumulation
Authors: Peng Jing , Wang Meijiao , Wang Xiaoji , Qi Lijuan , Guo Can , Li Hong , Li Cong , Yan Yan , Zhou Yun , Terzaghi William , Li Zhen , Song Chun-Peng , Qin Feng , Gong Zhizhong , Li Jigang
Published: February 2022

CONSTITUTIVELY PHOTOMORPHOGENIC1 (COP1), a well-characterized E3 ubiquitin ligase, is a central repressor of seedling photomorphogenic development in darkness. However, whether COP1 is involved in modulating abscisic acid (ABA) signaling in darkness remains largely obscure. Here, we report that COP1 is a positive regulator of ABA signaling during Arabidopsis seedling growth in the dark. COP1 mediates ABA-induced accumulation of ABI5, a transcription factor playing a key role in ABA signaling, through transcriptional and post-translational regulatory mechanisms. We further show that COP1 physically interacts with ABA-hypersensitive DCAF1 (ABD1), a substrate receptor of the CUL4-DDB1 E3 ligase targeting ABI5 for degradation. Accordingly, COP1 directly ubiquitinates ABD1 in vitro, and negatively regulates ABD1 protein abundance in vivo in the dark but not in the light. Therefore, COP1 promotes ABI5 protein stability post-translationally in darkness by destabilizing ABD1 in response to ABA. Interestingly, we reveal that ABA induces the nuclear accumulation of COP1 in darkness, thus enhancing its activity in propagating the ABA signal. Together, our study uncovers that COP1 modulates ABA signaling during seedling growth in darkness by mediating ABA-induced ABI5 accumulation, demonstrating that plants adjust their ABA signaling mechanisms according to their light environment.
The evolutionary history of small RNAs in Solanaceae
Authors: Baldrich Patricia , Bélanger Sébastien , Kong Shuyao , Pokhrel Suresh , Tamim Saleh , Teng Chong , Schiebout Courtney , Gurazada Sai Guna Ranjan , Gupta Pallavi , Patel Parth , Razifard Hamid , Nakano Mayumi , Dusia Ayush , Meyers Blake C , Frank Margaret H
Published: February 2022

The Solanaceae or “nightshade” family is an economically important group with remarkable diversity. To gain a better understanding of how the unique biology of the Solanaceae relates to the family’s small RNA (sRNA) genomic landscape, we downloaded over 255 publicly available sRNA data sets that comprise over 2.6 billion reads of sequence data. We applied a suite of computational tools to predict and annotate two major sRNA classes: (1) microRNAs (miRNAs), typically 20- to 22-nucleotide (nt) RNAs generated from a hairpin precursor and functioning in gene silencing and (2) short interfering RNAs (siRNAs), including 24-nt heterochromatic siRNAs typically functioning to repress repetitive regions of the genome via RNA-directed DNA methylation, as well as secondary phased siRNAs and trans-acting siRNAs generated via miRNA-directed cleavage of a polymerase II-derived RNA precursor. Our analyses described thousands of sRNA loci, including poorly understood clusters of 22-nt siRNAs that accumulate during viral infection. The birth, death, expansion, and contraction of these sRNA loci are dynamic evolutionary processes that characterize the Solanaceae family. These analyses indicate that individuals within the same genus share similar sRNA landscapes, whereas comparisons between distinct genera within the Solanaceae reveal relatively few commonalities.
The Neck Disability Index Reflects Allodynia and Headache Disability but Not Cervical Musculoskeletal Dysfunction in Migraine
Authors: Liang Zhiqi , Thomas Lucy , Jull Gwendolen , Treleaven Julia
Published: February 2022

Objective

The Neck Disability Index (NDI) is a self-rated disability tool originally developed for whiplash-associated disorders and validated in cervical musculoskeletal conditions. It is now commonly used to assess neck disability in migraine, but it is unknown whether NDI scores relate to migraine and hypersensitivity, cervical musculoskeletal dysfunction, or both. This single-blinded observational study aimed to determine whether the presence of cervical musculoskeletal dysfunction, migraine features, and hypersensitivity predict NDI scores and whether alternate versions of the NDI (NDI-physical, NDI-8, NDI-5) relate more to cervical musculoskeletal dysfunction.

Methods

Migraine and neck pain features, the Headache Impact Test (HIT-6), NDI, Allodynia Symptom Checklist (ASC12), and pressure pain thresholds were assessed in 104 participants with migraine and neck pain, 45 previously identified with cervical musculoskeletal dysfunction and 59 without. The NDI score was regressed on the presence or absence of cervical dysfunction, migraine features, HIT-6, total pressure pain threshold, and ASC12 while accounting for neck pain features. The presence of cervical dysfunction was regressed on the scores of NDI versions.

Results

The ASC12 (standardized ß = 0.20) and HIT-6 (standardized ß = 0.18) were significantly predictive of total NDI score, as were neck pain intensity (standardized ß = 0.32) and frequency (standardized ß = 0.44). No scores from alternate NDI versions related to cervical dysfunction.

Conclusion

The NDI score is a complex measure of neck disability influenced by migraine disability and hypersensitivity beyond the presence of cervical musculoskeletal dysfunction. This has implications for the clinical interpretation of NDI scores in patients with migraine.

Impact

Many patients with migraine and neck pain report neck disability; therefore, it is important to understand if migraine impacts neck disability. The results of this study indicate that clinicians need to consider migraine-related disability and hypersensitivity when managing neck disability in this population.
The relationship between mandibular advancement, tongue movement, and treatment outcome in obstructive sleep apnea
Authors: Jugé Lauriane , Knapman Fiona L , Humburg Peter , Burke Peter G R , Lowth Aimee B , Brown Elizabeth , Butler Jane E , Eckert Danny J , Ngiam Joachim , Sutherland Kate , Cistulli Peter A , Bilston Lynne E
Published: February 2022

Study Objectives

To characterize how mandibular advancement enlarges the upper airway via posterior tongue advancement in people with obstructive sleep apnea (OSA) and whether this is associated with mandibular advancement splint (MAS) treatment outcome.

Methods

One-hundred and one untreated people with OSA underwent a 3T magnetic resonance (MRI) scan. Dynamic mid-sagittal posterior tongue and mandible movements during passive jaw advancement were measured with tagged MRI. Upper airway cross-sectional areas were measured with the mandible in a neutral position and advanced to 70% of maximum advancement. Treatment outcome was determined after a minimum of 9 weeks of therapy.

Results

Seventy-one participants completed the study: 33 were responders (AHI<5 or AHI≤10 events/hr with >50% AHI reduction), 11 were partial responders (>50% AHI reduction but AHI>10 events/hr), and 27 nonresponders (AHI reduction<50% and AHI≥10 events/hr). Responders had the greatest naso- and oropharyngeal tongue anterior movement (0.40 ± 0.08 and 0.47 ± 0.13 mm, respectively) and oropharyngeal cross-sectional area enlargement (6.41 ± 2.12%) per millimeter of mandibular advancement. A multivariate model that included tongue movement and percentage of airway enlargement per millimeter of mandibular advancement along with baseline AHI correctly classified 69.2% (5-fold cross-validated 62.5%, n = 39) of participants in response categories when the jaw was advanced in the range that would usually be regarded as sufficient for clinical efficacy (> 4 mm). In comparison, a model using only baseline AHI correctly classified 50.0% of patients (5-fold cross-validated 52.5%, n = 40).

Conclusions

Tongue advancement and upper airway enlargement with mandibular advancement in conjunction with baseline AHI improve treatment response categorization to a satisfactory level (69.2%, 5-fold cross-validated 62.5%).
Impact of chronic sleep restriction on sleep continuity, sleep structure, and neurobehavioral performance
Authors: Xin Qilong , Yuan Robin K , Zitting Kirsi-Marja , Wang Wei , Purcell Shaun M , Vujovic Nina , Ronda Joseph M , Quan Stuart F , Williams Jonathan S , Buxton Orfeu M , Duffy Jeanne F , Czeisler Charles A
Published: February 2022

Chronic sleep restriction (CSR) has been associated with adverse effects including cognitive impairment and increased risk of diabetes and cardiovascular disease. Yet, sleep restriction therapy is an essential component of most behavioral treatments for insomnia. Moreover, little is known about the impact of CSR on sleep continuity and structure in healthy people whose need for sleep is satiated. We investigated the impact of CSR on sleep continuity and structure in nine healthy participants. They had 4 nights of sleep extension, 2 nights of post-extension sleep, 21 nights of CSR (5/5.6-hour time-in-bed), and 9 nights of recovery sleep. Compared to postextension sleep, during CSR sleep duration was reduced by 95.4 ± 21.2 min per night, Slow-Wave Activity was significantly increased, and sleep was more consolidated. During recovery, sleep duration was increased by 103.3 ± 23.8 min compared to CSR, and the CSR-induced increase in Slow-Wave Activity persisted, particularly after the 5-hour exposure. Yet, we found that sustained vigilant attention was not fully recovered even after nine nights of recovery sleep. Our results suggest that CSR improves traditional metrics of sleep quality and may have a persistent impact on sleep depth, which is consistent with the reported benefits on sleep continuity and structure of sleep restriction therapy. However, these improvements in traditional metrics of sleep quality were associated with deterioration rather than improvement in neurobehavioral performance, demonstrating that sleep duration should be included in assessments of sleep quality. These results have implications for the long-term use of sleep restriction in the behavioral treatment of insomnia. Clinical Trial Registration: Impact of Chronic Circadian Disruption vs. Chronic Sleep Restriction on Metabolism (https://clinicaltrials.gov/ct2/show/; #NCT02171273).
SAHA Enhances Differentiation of CD34+CD45+ Hematopoietic Stem and Progenitor Cells from Pluripotent Stem Cells Concomitant with an Increase in Hemogenic Endothelium
Authors: Shim Seon-Hui , Tufa Dejene , Woods Renee , George Trahan D , Shank Tyler , Yingst Ashley , Lake Jessica , Cobb Laura , Jones Dallas , Jones Kenneth , Verneris Michael R
Published: February 2022

Epigenetic modification is an important process during hematopoietic cell differentiation. Histone deacetylase (HDAC) inhibitors have previously been shown to enhance expansion of umbilical cord blood-derived hematopoietic stem cells (HSCs). However, the effect of HDAC inhibitors on pluripotent stem cells (PSCs) in this context is less understood. For years, investigators have considered PSC-derived natural killer (NK) and T-cell therapies. These “off-the-shelf” cellular therapies are now entering the clinic. However, the in vitro commitment of PSCs to the hematopoietic lineage is inefficient and represents a major bottleneck. We investigated whether HDAC inhibitors (HDACi) influence human PSC differentiation into CD34+CD45+ hematopoietic stem and progenitor cells (HSPCs), focusing on hemogenic endothelium (HE). Pluripotent stem cells cultured in the presence of HDACi showed a 2-5 times increase in HSPCs. Concurrent with this, HDACi-treated PSCs increased expression of 7 transcription factors (HOXA5, HOXA9, HOXA10, RUNX1, ERG, SPI1, and LCOR) recently shown to convert HE to HSPCs. ChIP-qPCR showed that SAHA upregulated acetylated-H3 at the promoter region of the above key genes. SAHA-treated human PSC-derived CD34+CD45+ cells showed primary engraftment in immunodeficient mice, but not serial transplantation. We further demonstrate that SAHA-derived HSPCs could differentiate into functional NK cells in vitro. The addition of SAHA is an easy and effective approach to overcoming the bottleneck in the transition from PSC to HSPCs for “off-the-shelf” cellular immunotherapy.
American Cochlear Implant Alliance Task Force Guidelines for Determining Cochlear Implant Candidacy in Children
Authors: Warner-Czyz Andrea D. , Roland J. Thomas , Thomas Denise , Uhler Kristin , Zombek Lindsay
Published: February 2022

This article summarizes the available evidence on pediatric cochlear implantation to provide current guidelines for clinical protocols and candidacy recommendations in the United States. Candidacy determination involves specification of audiologic and medical criteria per guidelines of the Food and Drug Administration. However, recommendations for a cochlear implant evaluation also should maintain flexibility and consider a child’s skill progression (i.e., month-for-month progress in speech, language, and auditory development) and quality of life with appropriately fit hearing aids. Moreover, evidence supports medical and clinical decisions based on other factors, including (a) ear-specific performance, which affords inclusion of children with asymmetric hearing loss and single-sided deafness as implant candidates; (b) ear-specific residual hearing, which influences surgical technique and device selection to optimize hearing; and (c) early intervention to minimize negative long-term effects on communication and quality of life related to delayed identification of implant candidacy, later age at implantation, and/or limited commitment to an audiologic rehabilitation program. These evidence-based guidelines for current clinical protocols in determining pediatric cochlear implant candidacy encourage a team-based approach focused on the whole child and the family system.
The Challenge of Studying Long COVID: An Updated Review
Authors: Zimmermann Petra , Pittet Laure F. , Curtis Nigel
Published: February 2022

Accurately determining the risk of long COVID is challenging. Existing studies in children and adolescents have considerable limitations and distinguishing long-term SARS-CoV-2 infection-associated symptoms from pandemic-related symptoms is difficult. Over half of individuals in this age group, irrespective of COVID-19, report physical and psychologic symptoms, highlighting the impact of the pandemic. More robust data is needed to inform policy decisions.
SARS-CoV-2 Associated Respiratory Failure in a Preterm Infant and the Outcome after Remdesivir Treatment
Authors: Sarhan Mohammed A. , Casalino Maria , Paopongsawan Pongsatorn , Gryn David , Kulkarni Tapas , Bitnun Ari , Gauda Estelle B.
Published: February 2022

Severe coronavirus disease 2019 (COVID-19) occurs in approximately 10% of neonates infected with severe acute respiratory syndrome coronavirus 2. Guidelines for optimal management of severe COVID-19 in neonates do not exist. In this report, we describe a late-preterm neonate with severe COVID-19, requiring invasive mechanical ventilation who recovered following treatment with remdesivir and high dose dexamethasone.
Automated Analysis Pipeline For Extracting Saccade, Pupil, and Blink Parameters Using Video-Based Eye Tracking
Authors: Coe Brian C. , Huang Jeff , Brien Donald C. , White Brian J. , Yep Rachel , Munoz Douglas P.
Published: February 2022

The tremendous increase of video-based eye tracking has made it possible to collect data from thousands of participants. Traditional manual detection and classification procedures for saccades and trial categorization is not viable for the large data sets being collected. Additionally, high-speed video-based eye trackers now allow for the novel analysis of pupil responses and blink behavior. Here we present a detailed description of our pipeline for collecting data, storing data, organizing participant codes, and cleaning data, which are fairly lab-specific but nonetheless important precursory steps in establishing standardized pipelines. More importantly, we also include descriptions of the automated detection and classification of saccades, blinks, ‘blincades’ (blinks occurring during saccades), and boomerang saccades (two saccades in opposite directions that occur almost simultaneously so that speed-based algorithms fail to split them), which are almost entirely task-agnostic and can be used on a wide variety of data. We additionally describe novel findings about post-saccadic oscillations, and provide a method to get more accurate estimates for end-points of saccades. Lastly, we describe the automated behavior classification for the Interleaved Pro- and Anti-Saccade Task (IPAST), a well-known task that probes voluntary and inhibitory control. This pipeline was evaluated using data collected from 592 human participants between 5 and 93 years of age, making it robust enough to handle large clinical patient data sets as well. In sum, this pipeline has been optimized to consistently handle large data sets obtained from diverse study cohorts (i.e., development, aging, clinical), and collected across multiple laboratory sites.
Highly divergent white-tailed deer SARS-CoV-2 with potential deer-to-human transmission
Authors: Pickering Bradley , Lung Oliver , Maguire Finlay , Kruczkiewicz Peter , Kotwa Jonathon D. , Buchanan Tore , Gagnier Marianne , Guthrie Jennifer L. , Jardine Claire M. , Marchand-Austin Alex , Massé Ariane , McClinchey Heather , Nirmalarajah Kuganya , Aftanas Patryk , Blais-Savoie Juliette , Chee Hsien-Yao , Chien Emily , Yim Winfield , Banete Andra , Griffin Bryan D. , Yip Lily , Goolia Melissa , Suderman Matthew , Pinette Mathieu , Smith Greg , Sullivan Daniel , Rudar Josip , Adey Elizabeth , Nebroski Michelle , Goyette Guillaume , Finzi Andrés , Laroche Geneviève , Ariana Ardeshir , Vahkal Brett , Côté Marceline , McGeer Allison J. , Nituch Larissa , Mubareka Samira , Bowman Jeff
Published: February 2022

Wildlife reservoirs of SARS-CoV-2 may enable viral adaptation and spillback from animals to humans. In North America, there is evidence of unsustained spillover of SARS-CoV-2 from humans to white-tailed deer (Odocoileus virginianus), but no evidence of transmission from deer to humans. Through a biosurveillance program in Ontario, Canada we identified a new and highly divergent lineage of SARS-CoV-2 in white-tailed deer. This lineage is the most divergent SARS-CoV-2 lineage identified to date, with 76 consensus mutations (including 37 previously associated with non-human animal hosts) and signatures of considerable evolution and transmission within wildlife. Phylogenetic analysis also revealed an epidemiologically linked human case. Together, our findings represent the first clear evidence of sustained evolution of SARS-CoV-2 in white-tailed deer and of deer-to-human transmission.
New insights into 4,000 years of resource economy across Greenland using ancient DNA
Authors: Seersholm Frederik V. , Harmsen Hans , Gotfredsen Anne Birgitte , Madsen Christian Koch , Jensen Jens Fog , Hollesen Jørgen , Meldgaard Morten , Bunce Michael , Hansen Anders J.
Published: February 2022

The success and failure of past cultures across the Arctic was tightly coupled to the ability of past people to exploit the full range of resources available to them, and to adapt to fluctuations in resource availability. There is substantial evidence for the hunting of birds, caribou and a wide range of marine mammals in pre-historic Greenland from bone remains preserved in ancient middens. However, the extent to which these communities relied on marine resources such as fish and large cetaceans is understudied because of the taphonomic processes and bias that affect how these taxa present themselves in the archaeological record. To address this, we analyse DNA from bulk bone samples from 12 archaeological sites across Greenland dating from Paleo-Inuit to Neo-Inuit periods. Using a combination of metabarcoding and shotgun metagenomics we identify an assemblage of 43 species consisting of birds, fish, and both marine and terrestrial mammals. We find genetic evidence of five different whale species, of which the bowhead whale (Balaena mysticetus) was the most commonly detected. Furthermore, we detect nine fish species, of which four have not previously been identified in any of the studied sites. Lastly, we identify a novel haplotype in caribou (Rangifer tarandus) at the 3,000-year-old site Itinnera, suggesting the presence of a distinct lineage of (now extinct) dwarfed caribou that colonised Greenland after the last ice age 9,000 years ago. Collectively, these findings provide a rare insight into whaling and fishing practices in Greenland and demonstrate that prehistoric Greenlandic communities had the social and technological capacity to target the largest whales available in the waters around them.
Dynamic Synchronization between Hippocampal Spatial Representations and the Stepping Rhythm
Authors: Joshi Abhilasha , Denovellis Eric , Mankili Abhijith , Meneksedag Yagiz , Davidson Thomas , Gillespie Anna K. , Guidera Jennifer Ann , Roumis Demetris , Frank Loren M.
Published: February 2022

Summary paragraph

The hippocampus is a vertebrate brain structure that expresses spatial representations1 and is critical for navigation2,3. Navigation in turn intricately depends on locomotion; however, current accounts suggest a dissociation between hippocampal spatial representations and the details of locomotor processes. Specifically, the hippocampus is thought to primarily represent higher-order cognitive and locomotor variables like position, speed, and direction of movement4–7, while the limb movements that propel the animal are thought to be computed and represented primarily in subcortical circuits, including the spinal cord, brainstem, and cerebellum8–11. Whether hippocampal representations are actually decoupled from the detailed structure of locomotor processes remains unknown. To address this question, we simultaneously monitored hippocampal spatial representations and ongoing limb movements underlying locomotion at fast timescales. We found that the forelimb stepping cycle in freely behaving rats is rhythmic and peaks at ~8 Hz during movement, matching the ~8 Hz organization of information processing in the hippocampus during locomotion12. We also discovered precisely timed coordination between the time at which the forelimbs touch the ground (‘plant’ times of the stepping cycle) and the hippocampal representation of space. Notably, plant times coincide with hippocampal representations closest to the actual position of the animal, while in-between these plant times, the hippocampal representation progresses towards possible future locations. This synchronization was specifically detectable when animals approached upcoming spatial decisions. Taken together, our results reveal profound and dynamic coordination on a timescale of tens of milliseconds between central cognitive representations and peripheral motor processes. This coordination engages and disengages rapidly in association with cognitive demands and is well suited to support rapid information exchange between cognitive and sensory-motor circuits.
The Development, but not Expression, of Alcohol Front-loading in C57BL/6J Mice Maintained on LabDiet 5001 is Abolished by Maintenance on Teklad 2920x Rodent Diet
Authors: Maphis Nicole M. , Huffman Tameryn Radcliff , Linsenbardt David N.
Published: February 2022

Excessive alcohol (ethanol) consumption, such as binge-drinking, is extremely commonplace and represents a major health concern. Through modeling excessive drinking in rodents, we are beginning to uncover the neurobiological and neurobehavioral causes and consequences of this pattern of ethanol intake. One important factor for modeling binge drinking in mice is that subjects reliably drink to blood ethanol concentrations (BECs) of 80 mg/dl or higher. Drinking-in-the-dark (DID) is a commonly used mouse model of binge drinking, and we have shown these methods reliably result in robust ethanol front-loading and binge-level BECs in C57BL/6J (B6) mice as well as other ethanol-preferring mouse strains/lines. However, establishing the DID model in a new vivarium space forced us to consider the use of rodent diet formulations we had not previously used. The current set of experiments were designed to investigate the role of two standard rodent diet formulations on binge drinking and the development of ethanol front-loading using DID. We found that BECs in animals maintained on LabDiet 5001 (LD01) were double those found in mice maintained on Teklad 2920x (TL20). Interestingly, this effect was paralleled by differences in the degree of front-loading, such that LD01-fed mice consumed approximately twice as much ethanol in the first 15 minutes of the 2-hour DID sessions compared to TL20-fed mice. Surprisingly however, mice that developed front-loading during maintenance on the LD01 diet continued to display front-loading behavior after being switched to the TL20 diet. These data emphasize the importance of choosing and reporting diet formulations when conducting voluntary drinking studies and support the need for further investigation into the mechanisms behind diet-induced differences in binge drinking, particularly front-loading.
Wheat Panache - a pangenome graph database representing presence/absence variation across 16 bread wheat genomes
Authors: Bayer Philipp E. , Petereit Jakob , Durant Éloi , Monat Cécile , Rouard Mathieu , Hu Haifei , Chapman Brett , Li Chengdao , Cheng Shifeng , Batley Jacqueline , Edwards David
Published: February 2022

Bread wheat is one of humanity’s most important staple crops, characterized by a large and complex genome with a high level of gene presence/absence variation between cultivars, hampering genomic approaches for crop improvement. With the growing global population and the increasing impact of climate change on crop yield, there is an urgent need to apply genomic approaches to accelerate wheat breeding. With recent advances in DNA sequencing technology, a growing number of high-quality reference genomes are becoming available, reflecting the genetic content of a diverse range of cultivars. However, information on the presence or absence of genomic regions has been hard to visualize and interrogate due to the size of these genomes and the lack of suitable bioinformatics tools. To address this limitation, we have produced a wheat pangenome graph maintained within an online database to facilitate interrogation and comparison of wheat cultivar genomes. The database allows users to visualize regions of the pangenome to assess presence/absence variation between bread wheat genomes.

Database URL:http://www.appliedbioinformatics.com.au/wheat_panache
High coverage of single cell genomes by T7-assisted enzymatic methyl-sequencing
Authors: Wang Juan , Fang Yitong , Chen WenFang , Zhang Chen , Chen Zhichao , Xie Zhe , Weng Zhe , Chen Weitian , Ruan Fengying , Xie Yeming , Sun Yuxin , Guo Mei , Li Yaning , Tang Chong
Published: February 2022

Conventional approaches to studying 5mC marks in single cells or samples with picogram input DNA amounts usually suffer from low genome coverage due to DNA degradation. Many methods have been developed to optimize the library construction efficiency for bisulfite-treated DNA. However, most of these approaches ignored the amplification bias of bisulfite-treated DNA, which leads to shallow genome coverage. In this study, we developed the T7-assisted enzymatic methyl-sequencing method (TEAM-seq), which adopts enzymatic conversion to minimize DNA degradation and T7 polymerase-assisted unbiased amplification. We demonstrate that TEAM-seq delivered, to the best of our knowledge, the highest reported coverage(70% for 100pg, 35% for 20pg) of single cell genomes in whole-genome 5mC sequencing.
Interaction of human keratinocytes and nerve fiber terminals at the neuro-cutaneous unit
Authors: Erbacher Christoph , Britz Sebastian , Dinkel Philine , Klein Thomas , Sauer Markus , Stigloher Christian , Üçeyler Nurcan
Published: February 2022

Traditionally, peripheral sensory neurons hold the monopole of transducing external stimuli. Current research moves epidermal keratinocytes into focus as sensors and transmitters of nociceptive and non-nociceptive sensations, tightly interacting with intraepidermal nerve fibers at the neuro-cutaneous unit. In animal models, epidermal cells establish close contacts and ensheath sensory neurites. However, ultrastructural morphological and mechanistic data examining the human keratinocyte-nociceptor interface are sparse. We investigated this exact interface in human skin applying super-resolution array tomography, expansion microscopy, and structured illumination microscopy. We show keratinocyte ensheathment of nociceptors and connexin 43 plaques at keratinocyte-nociceptor contact sites in healthy native skin. We further derived a fully human co-culture system, modeling ensheathment and connexin 43 plaques in vitro. Unraveling human intraepidermal nerve fiber ensheathment and interaction sites marks a milestone in research at the neuro-cutaneous unit. These findings are mind-changers on the way to decipher the mechanisms of cutaneous nociception.
Performance reserves in brain-imaging-based phenotype prediction
Authors: Schulz Marc-Andre , Bzdok Danilo , Haufe Stefan , Haynes John-Dylan , Ritter Kerstin
Published: February 2022

Machine learning studies have shown that various phenotypes can be predicted from structural and functional brain images. However, in most such studies, prediction performance ranged from moderate to disappointing. It is unclear whether prediction performance will substantially improve with larger sample sizes or whether insufficient predictive information in brain images impedes further progress. Here, we systematically assess the effect of sample size on prediction performance using sample sizes far beyond what is possible in common neuroimaging studies. We project 3-9 fold improvements in prediction performance for behavioral and mental health phenotypes when moving from one thousand to one million samples. Moreover, we find that moving from single imaging modalities to multimodal input data can lead to further improvements in prediction performance, often on par with doubling the sample size. Our analyses reveal considerable performance reserves for neuroimaging-based phenotype prediction. Machine learning models may benefit much more from extremely large neuroimaging datasets than currently believed.
Methods in Cognitive Pupillometry: Design, Preprocessing, and Statistical Analysis
Authors: Mathôt Sebastiaan , Vilotijević Ana
Published: February 2022

Cognitive pupillometry is the measurement of pupil size to investigate cognitive processes such as attention, mental effort, working memory, and many others. Currently, there is no commonly agreed-upon methodology for conducting cognitive-pupillometry experiments, and approaches vary widely between research groups and even between different experiments from the same group. This lack of consensus makes it difficult to know which factors to consider when conducting a cognitive-pupillometry experiment. Here we provide a comprehensive, hands-on guide to methods in cognitive pupillometry, with a focus on trial-based experiments in which the measure of interest is the task-evoked pupil response to a stimulus. We cover all methodological aspects of cognitive pupillometry: experimental design; preprocessing of pupil-size data; and statistical techniques to deal with multiple comparisons when testing pupil-size data. In addition, we provide code and toolboxes (in Python) for preprocessing and statistical analysis, and we illustrate all aspects of the proposed workflow through an example experiment and example scripts.
The estrous cycle modulates early-life adversity effects on mouse avoidance behavior through progesterone signaling
Authors: Laham Blake J. , Murthy Sahana S. , Hanani Monica , Clappier Mona , Boyer Sydney , Vasquez Betsy , Gould Elizabeth
Published: February 2022

Early-life adversity (ELA) predisposes individuals to develop neuropsychiatric conditions, which are more prevalent in women than men. Efforts to model this sex difference in rodents have produced mixed results, with some studies paradoxically showing stronger phenotypes in males than females. Since changes in reproductive hormone levels can increase the likelihood of anxiety disorders in women, we examined the effects of ELA on adult female mice across the estrous cycle. We found that during diestrus, when the ratio of progesterone to estrogen is relatively high, ELA mice exhibit increased avoidance behavior, altered activity levels in specific contexts, and increased theta oscillation power in the ventral hippocampus. Ovariectomy, which eliminates circulating estrogen but not progesterone, unexpectedly preserved some of the effects present in diestrus ELA mice. Progesterone receptor antagonism in diestrus normalized avoidance behavior in ELA mice, while treatment with a negative allosteric modulator of the progesterone metabolite allopregnanolone promoted avoidance behavior in control mice. These results suggest that altered progesterone and allopregnanolone signaling during diestrus increases avoidance behavior in ELA mice
Age-Related Central Gain with Degraded Neural Synchrony in the Auditory Brainstem of Mice and Humans
Authors: Rumschlag Jeffrey A. , McClaskey Carolyn M. , Dias James W. , Kerouac Lilyana B. , Noble Kenyaria V. , Panganiban Clarisse , Lang Hainan , Harris Kelly C.
Published: February 2022

Aging is associated with auditory nerve (AN) functional deficits and decreased inhibition in the central auditory system, amplifying central responses in a process known as central gain. Although central gain enhances response amplitudes, central gain may not restore disrupted response timing. In this translational study, we measured responses from the AN and auditory midbrain in younger and older mice and humans. We hypothesized that older mice and humans exhibit central gain without an improvement in inter-trial synchrony in the midbrain. Our data demonstrated greater age-related deficits in AN response amplitudes than auditory midbrain response amplitudes, as shown by significant interactions between neural generator and age group, indicating central gain in auditory midbrain. However, synchrony decreases with age in both the AN and midbrain responses. These results reveal age-related central gain without concomitant improvements in synchrony, consistent with those predictions based on decreases in inhibition. Persistent decreases in synchrony may contribute to auditory processing deficits in older mice and humans.
Olfactory responses ofDrosophilaare encoded in the organization of projection neurons
Authors: Choi Kiri , Kim Won Kyu , Hyeon Changbong
Published: February 2022

The projection neurons (PNs), reconstructed from electron microscope (EM) images of theDrosophilaolfactory system, offer a detailed view of neuronal anatomy, providing glimpses into information flow in the brain. About 150 uPNs constituting 58 glomeruli in the antennal lobe (AL) are bundled together in the axonal extension, routing the olfactory signal received at AL to mushroom body (MB) calyx and lateral horn (LH). Here we quantify the neuronal organization by inter-PN distances and examine its relationship with the odor types sensed byDrosophila. The homotypic uPNs that constitute glomeruli are tightly bundled and stereotyped in position throughout the neuropils, even though the glomerular PN organization in AL is no longer sustained in the higher brain center. Instead, odor-type dependent clusters consisting of multiple homotypes innervate the MB calyx and LH. Pheromone-encoding and hygro/thermo-sensing homotypes are spatially segregated in MB calyx, whereas two distinct clusters of food-related homotypes are found in LH in addition to the segregation of pheromone-encoding and hygro/thermo-sensing homotypes. We find that there are statistically significant associations between the spatial organization among a group of homotypic uPNs and certain stereotyped olfactory responses. Additionally, the signals from some of the tightly bundled homotypes converge to a specific group of lateral horn neurons (LHNs), which indicates that homotype (or odor type) specific integration of signals occurs at the synaptic interface between PNs and LHNs. Our findings suggest that before neural computation in the inner brain, some of the olfactory information are already encoded in the spatial organization of uPNs, illuminating that a certain degree of labeled-line strategy is at work in theDrosophilaolfactory system.
KIAA1109 is required for survival and for normal development and function of the neuromuscular junction in mice
Authors: Liu Yun , Lin Weichun
Published: February 2022

KIAA1109 (4932438A13Rik) is a novel gene linked to Alkuraya-Kucinska Syndrome, an autosomal recessive disorder with severe brain malformations and arthrogryposis in humans. The role of KIAA1109 in mammalian development and function remains poorly understood. Here, we characterize mutant mice deficient in Kiaa1109 (Kiaa1109−/−). We report that Kiaa1109−/− mice died during perinatal stages. These Kiaa1109−/− embryos exhibited impaired intramuscular nerve growth and reduced sizes of the neuromuscular junction (NMJ) compared with their littermate controls. Electrophysiological analysis further revealed defects in neuromuscular synaptic transmission in Kiaa1109−/− embryos. Notably, the frequency of spontaneous neurotransmitter release was markedly increased, whereas evoked neurotransmitter release and quantal content were reduced. Furthermore, neuromuscular synapses in Kiaa1109−/− embryos failed to respond to a repetitive, low frequency stimulation (10Hz). These results demonstrate that KIAA1109 is required for survival in mice and for proper development and function of the NMJ.

Significance Statement

This is the first report characterizing the phenotype of mutant mice deficient in KIAA1109 (4932438A13Rik), a novel gene in mammals. We show that KIAA1109 is required for survival in mice and that KIAA1109 plays important roles in normal development and function of the NMJ in mice.
A Geometric View of Signal Sensitivity Metrics in multi-echo fMRI
Authors: Liu Thomas T. , Li Bochao , Fernandez Brice , Banerjee Suchandrima
Published: February 2022

In multi-echo fMRI (ME-fMRI), two metrics have been widely used to measure the performance of various acquisition and analysis approaches. These are temporal SNR (tSNR) and differential contrast-to-noise ratio (dCNR). A key step in ME-fMRI is the weighted combination of the data from multiple echoes, and prior work has examined the dependence of tSNR and dCNR on the choice of weights. However, most studies have focused on only one of these two metrics, and the relationship between the two metrics has not been examined. In this work, we present a geometric view that offers greater insight into the relation between the two metrics and their weight dependence. We identify three major regimes: (1) a tSNR robust regime in which tSNR is robust to the weight selection with most weight variants achieving close to optimal performance, whereas dCNR shows a pronounced dependence on the weights with most variants achieving suboptimal performance; (2) a dCNR robust regime in which dCNR is robust to the weight selection with most weight variants achieving close to optimal performance, while tSNR exhibits a strong dependence on the weights with most variants achieving significantly lower than optimal performance; and (3) a within-type robust regime in which both tSNR and dCNR achieve nearly optimal performance when the form of the weights are variants of their respective optimal weights and exhibit a moderate decrease in performance for other weight variants. Insight into the behavior observed in the different regimes is gained by considering spherical representations of the weight dependence of the components used to form each metric. For multi-echo acquisitions, dCNR is shown to be more directly related than tSNR to measures of CNR and signal-to-noise ratio (SNR) for both task-based and resting-state fMRI scans, respectively.
Single-deletion-mutant, third-generation rabies viral vectors allow nontoxic retrograde targeting of projection neurons with greatly increased efficiency
Authors: Jin Lei , Sullivan Heather A. , Zhu Mulangma , Lea Nicholas E. , Lavin Thomas K. , Fu Xin , Matsuyama Makoto , Hou YuanYuan , Feng Guoping , Wickersham Ian R.
Published: February 2022

Rabies viral vectors have become important components of the systems neuroscience toolkit, allowing both direct retrograde targeting of projection neurons and monosynaptic tracing of inputs to defined postsynaptic populations, but the rapid cytotoxicity of first-generation (ΔG) vectors limits their use to short-term experiments. We recently introduced second-generation, double-deletion-mutant (ΔGL) rabies viral vectors, showing that they efficiently retrogradely infect projection neurons and express recombinases effectively but with little to no detectable toxicity; more recently, we have shown that ΔGL viruses can be used for monosynaptic tracing with far lower cytotoxicity than the first-generation system. Here we introduce third-generation (ΔL) rabies viral vectors, which, like first-generation vectors, have only a single gene deleted from their genomes (in this case the viral polymerase gene L) but which appear to be as nontoxic as second-generation ones, based onin vivolongitudinal structural and functional two-photon imaging andex vivoelectrophysiology. Although third-generation vectors are therefore phenotypically very similar to second-generation ones, we show that they have the major advantage of growing to much higher titers, and this key difference results in significantly increased numbers of retrogradely labeled neuronsin vivo. These ΔL rabies viral vectors therefore constitute a new state of the art for minimally perturbative, pathway-specific expression of recombinases and transactivators in mammalian neurons selected on the basis of their axonal projections. Because replication of deletion-mutant rabies viruses within complementing cells is precisely the process that underlies monosynaptic tracing, the higher replication efficiency of this new class of rabies viral vectors furthermore suggests the potential to provide the foundation of an improved nontoxic monosynaptic tracing system.
A real-world evaluation of the implementation of NLP technology in abstract screening of a systematic review
Authors: Perlman-Arrow Sara , Loo Noel , Bobrovitz Niklas , Yan Tingting , Arora Rahul K.
Published: February 2022

The laborious and time-consuming nature of systematic review production hinders the dissemination of up-to-date evidence synthesis. Well-performing natural language processing (NLP) tools for systematic reviews have been developed, showing promise to improve efficiency. However, the feasibility and value of these technologies have not been comprehensively demonstrated in a real-world review. We developed an NLP-assisted abstract screening tool that provides text inclusion recommendations, keyword highlights, and visual context cues. We evaluated this tool in a living systematic review on SARS-CoV-2 seroprevalence, conducting a quality improvement assessment of screening with and without the tool. We evaluated changes to abstract screening speed, screening accuracy, characteristics of included texts, and user satisfaction. The tool improved efficiency, reducing screening time per abstract by 45.9% and decreasing inter-reviewer conflict rates. The tool conserved precision of article inclusion (positive predictive value; 0.92 with tool vs 0.88 without) and recall (sensitivity; 0.90 vs 0.81). The summary statistics of included studies were similar with and without the tool. Users were satisfied with the tool (mean satisfaction score of 4.2/5). We evaluated an abstract screening process where one human reviewer was replaced with the tool’s votes, finding that this maintained recall (0.92 one-person, one-tool vs 0.90 two tool-assisted humans) and precision (0.91 vs 0.92) while reducing screening time by 70%. Implementing an NLP tool in this living systematic review improved efficiency, maintained accuracy, and was well-received by researchers, demonstrating the real-world effectiveness of NLP in expediting evidence synthesis.
Examining the Association between the Gastrointestinal Microbiota and Gulf War Illness: A Prospective Cohort Study
Authors: Kates Ashley , Keating Julie , Baubie Kelsey , Putman-Buehler Nathan , Watson Lauren , Godfrey Jared , Deblois Courtney L. , Suen Garret , Cook Dane B. , Rabago David , Gangnon Ronald , Safdar Nasia
Published: February 2022

Gulf War Illness (GWI) affects 25-35% of the 1991 Gulf War Veteran population. Patients with GWI experience pain, fatigue, cognitive impairments, gastrointestinal dysfunction, skin disorders, and respiratory issues. In longitudinal studies, many patients with GWI have shown little to no improvement in symptoms since diagnosis. The gut microbiome and diet play an important role in human health and disease, and preliminary studies suggest it may play a role in GWI. To examine the relationship between the gut microbiota, diet, and GWI, we conducted an eight-week prospective cohort study collecting stool samples, medications, health history, and dietary data. Sixty-nine participants were enrolled into the study, 36 of which met the case definition for GWI. The gut microbiota of participants, determined by 16S rRNA sequencing of stool samples, was stable over the duration of the study and showed no within person (alpha diversity) differences. Between group analyses (beta diversity) identified statistically significant different between those with and without GWI. Several taxonomic lineages were identified as differentially abundant between those with and without GWI (n=9) including a greater abundance of Lachnospiraceae and Ruminococcaceae in those without GWI. Additionally, there were taxonomic differences between those with high and low HEI scores including a greater abundance of Ruminococcaceae in those with higher HEI scores. This longitudinal cohort study of GWVs found that participants with GWI had significantly different microbiomes from those without GWI. Further studies are needed to determine the role these differences may play in the development and treatment of GWI.