bluuebunny/crossref_metadata_2025_split huggingface dataset:
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

Abstract

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

Abstract

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&lt;5 or AHI≤10 events/hr with &gt;50% AHI reduction), 11 were partial responders (&gt;50% AHI reduction but AHI&gt;10 events/hr), and 27 nonresponders (AHI reduction&lt;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 (&gt; 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

Abstract
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

Abstract
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.
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

AbstractThe 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

AbstractWildlife 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

AbstractThe 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 paragraphThe 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

AbstractExcessive 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

AbstractBread 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

AbstractConventional 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

AbstractTraditionally, 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

AbstractMachine 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.