bluuebunny/crossref_metadata_2025_split huggingface dataset:
Validation of the Cervical Torsion Test and Head-Neck Differentiation Test in Patients With Peripheral Vestibular Hypofunction
Authors: Nüesch Andrea , Treleaven Julia , Ernst Markus J 
Published: April 2024

Abstract

Objective
This study compared adults with peripheral vestibular hypofunction (VH) to healthy controls and assessed the sensitivity and specificity of the Cervical Torsion Test (CTT) and the Head-Neck Differentiation Test (HNDT). This study aimed to determine whether neck problems affected primary outcomes.

Methods
This cross-sectional study included adults from a specialist consultation for dizziness. VH had been diagnosed with the video Head Impulse Test. Exclusion criteria were conditions following head or neck trauma and diseases of the central nervous system. The sensitivity and specificity of the index tests were calculated, and regression analyses were performed to test for contributing factors.

Results
A total of 19 patients with VH and a historical cohort of 19 matched healthy controls were included. Most patients with VH (84.2%) experienced symptoms in at least 1 test component, compared to 5.2% of the control group. Of patients with VH, 78.9% had symptoms during the HNDT “en bloc” (en bloc = head and trunk rotated together), whereas only 26.3% reported symptoms during the CTT en bloc. The best discriminatory validity was found for the HNDT en bloc, with a sensitivity of 0.79 (95% CI = 0.54–0.94), a specificity of 0.86 (95% CI = 0.65–0.97), and a positive likelihood ratio of 5.79 (95% CI = 1.97–17.00). The number of symptoms of CTT “in torsion” (in torsion = trunk rotated actively with fixed head) was increased by a factor of 1.13 (95% CI = 1.01–1.27) for every additional point on the Neck Disability Index.

Conclusion
The CTT and HNDT can serve as non-laboratory tests for patients with dizziness. The HNDT en bloc has the best discriminatory validity, finding those with and those without VH. Symptom reproduction during torsion may help to identify when neck problems may contribute to dizziness.

Impact
The HNDT en bloc may be useful for ruling VH in or out in patients with dizziness. Positive CTT and HNDT in torsion components may verify the likelihood of additional neck involvement.
Measuring research quality in a more inclusive way: Evidence from the UK Research Excellence Framework
Authors: Hengel Erin , Sevilla Almudena , Smith Sarah 
Published: April 2024

Abstract
Evidence suggests that common metrics of research quality—e.g. journal publications and citations—are systematically biased against certain groups. But does relying solely on them to evaluate quality lead to lower diversity in academia? In this paper, we start to answer this question by analysing data from the UK’s nationwide research assessment exercise, the Research Excellence Framework. We find that narrowly focussed output-based measures of departmental research quality do indeed negatively correlate with the diversity of departmental staff, while measures of research impact and of the quality of the research environment correlate positively. An aggregate measure that incorporates all three components is therefore likely to better promote staff diversity compared to more narrowly defined output-focused measures. More generally, our results suggest that comprehensive definitions of research quality may be more effective at promoting diversity in academia compared to narrower measures. We further argue that funding decisions informed by broader measures result in more efficient resource allocations across the higher education sector.
Do sell-side analysts say “buy” while whispering “sell”?
Authors: Hirshleifer David , Shi Yushui , Wu Weili 
Published: April 2024

Abstract
We study here say-buy/whisper-sell behavior wherein analysts issue optimistic recommendations to attract retail investors while providing more accurate information to fund managers in private, sometimes resulting in fund managers selling the recommended stocks. We test whether fund managers return the favor using their votes for analysts in a Chinese “star analyst” competition. Managers are more likely to vote for analysts who exhibit greater “say-buy/whisper-sell” behavior toward these managers. This suggests that analysts reduce the accuracy of their public recommendations, thereby maintaining the value of their private advice to funds. Our findings help explain several empirical puzzles about analyst public recommendations.
Museum Genomics Reveals the Hybrid Origin of an Extinct Crater Lake Endemic
Authors: Tims Amy R , Unmack Peter J , Hammer Michael P , Brown Culum , Adams Mark , McGee Matthew D 
Published: April 2024

Abstract
Crater lake fishes are common evolutionary model systems, with recent studies suggesting a key role for gene flow in promoting rapid adaptation and speciation. However, the study of these young lakes can be complicated by human-mediated extinctions. Museum genomics approaches integrating genetic data from recently extinct species are, therefore, critical to understanding the complex evolutionary histories of these fragile systems. Here, we examine the evolutionary history of an extinct Southern Hemisphere crater lake endemic, the rainbowfish Melanotaenia eachamensis. We undertook a comprehensive sampling of extant rainbowfish populations of the Atherton Tablelands of Australia alongside historical museum material to understand the evolutionary origins of the extinct crater lake population and the dynamics of gene flow across the ecoregion. The extinct crater lake species is genetically distinct from all other nearby populations due to historic introgression between 2 proximate riverine lineages, similar to other prominent crater lake speciation systems, but this historic gene flow has not been sufficient to induce a species flock. Our results suggest that museum genomics approaches can be successfully combined with extant sampling to unravel complex speciation dynamics involving recently extinct species.
Lytic/Lysogenic Transition as a Life-History Switch
Authors: Roughgarden Joan 
Published: April 2024

Abstract
The transition between lytic and lysogenic life cycles is the most important feature of the life-history of temperate viruses. To explain this transition, an optimal life-history model is offered based a discrete-time formulation of phage/bacteria population dynamics that features infection of bacteria by Poisson sampling of virions from the environment. The time step is the viral latency period. In this model, density-dependent viral absorption onto the bacterial surface produces virus/bacteria coexistence and density dependence in bacterial growth is not needed. The formula for the transition between lytic and lysogenic phases is termed the ‘fitness switch’. According to the model, the virus switches from lytic to lysogenic when its population grows faster as prophage than as virions produced by lysis of the infected cells, and conversely for the switch from lysogenic to lytic. A prophage that benefits the bacterium it infects automatically incurs lower fitness upon exiting the bacterial genome, resulting in its becoming locked into the bacterial genome in what is termed here as a ‘prophage lock’. The fitness switch qualitatively predicts the ecogeographic rule that environmental enrichment leads to microbialization with a concomitant increase in lysogeny, fluctuating environmental conditions promote virus-mediated horizontal gene transfer, and prophage-containing bacteria can integrate into the microbiome of a eukaryotic host forming a functionally integrated tripartite holobiont. These predictions accord more with the ‘Piggyback-the-Winner’ hypothesis than with the ‘Kill-the-Winner’ hypothesis in virus ecology.
Disaster Plant Pathology: Smart Solutions for Threats to Global Plant Health from Natural and Human-Driven Disasters
Authors: Etherton Berea A. , Choudhury Robin A. , Alcalá Briseño Ricardo I. , Mouafo-Tchinda Romaric A. , Plex Sulá Aaron I. , Choudhury Manoj , Adhikari Ashish , Lei Si Lin , Kraisitudomsook Nattapol , Buritica Jacobo Robledo , Cerbaro Vinicius A. , Ogero Kwame , Cox Cindy M. , Walsh Stephen P. , Andrade-Piedra Jorge L. , Omondi Bonaventure Aman , Navarrete Israel , McEwan Margaret A. , Garrett Karen A. 
Published: April 2024

Disaster plant pathology addresses how natural and human-driven disasters impact plant diseases and the requirements for smart management solutions. Local to global drivers of plant disease change in response to disasters, often creating environments more conducive to plant disease. Most disasters have indirect effects on plant health through factors such as disrupted supply chains and damaged infrastructure. There is also the potential for direct effects from disasters, such as pathogen or vector dispersal due to floods, hurricanes, and human migration driven by war. Pulse stressors such as hurricanes and war require rapid responses, whereas press stressors such as climate change leave more time for management adaptation but may ultimately cause broader challenges. Smart solutions for the effects of disasters can be deployed through digital agriculture and decision support systems supporting disaster preparedness and optimized humanitarian aid across scales. Here, we use the disaster plant pathology framework to synthesize the effects of disasters in plant pathology and outline solutions to maintain food security and plant health in catastrophic scenarios. We recommend actions for improving food security before and following disasters, including (i) strengthening regional and global cooperation, (ii) capacity building for rapid implementation of new technologies, (iii) effective clean seed systems that can act quickly to replace seed lost in disasters, (iv) resilient biosecurity infrastructure and risk assessment ready for rapid implementation, and (v) decision support systems that can adapt rapidly to unexpected scenarios. [Formula: see text] Copyright © 2024 The Author(s). This is an open access article distributed under the CC BY 4.0 International license .
Merit-Based Incentive Payment System: How Are Plastic Surgeons Performing?
Authors: Perez Otero Sofia , Diaz Allison L. , Hemal Kshipra , Boyd Carter J. , Lee Wen-Yu , Karp Nolan S. 
Published: April 2024

Background:
The Merit-based Incentive Payment System (MIPS) is a payment model implemented to promote high-value care through performance-based adjustments of Medicare reimbursements. Higher scores indicate superior performance in health care quality, efficiency, and interoperability, which can result in financial advantages. Given the paucity of literature, the authors aimed to characterize plastic surgery performance in MIPS.

Methods:
The Centers for Medicare and Medicaid Services online data repository was queried for data on MIPS performance of plastic surgeons from 2019 to 2021. Descriptive analyses and multivariable logistic regression were conducted to identify predictors of receiving bonus payment for exceptional performance.

Results:
Approximately 1400 surgeons were sampled in each year. The median number of Medicare beneficiaries and percentage of dually eligible beneficiaries—eligible for Medicare and Medicaid—were higher in 2019 (P < 0.001). Beneficiary median hierarchical condition category risk score, which measures expected health care costs and needs based on health status, was lower in 2021 (P < 0.001). The most common reporting schema was reporting as a group. Total MIPS score increased from 2019 to 2020 to 2021 (90.2 versus 96.4 versus 98.3, respectively; P < 0.001), but quality score progressively decreased (98.8 versus 95.5 versus 89.90, respectively; P < 0.001). Fewer physicians received positive adjustment and bonus payments in 2020 and 2021. Predictors of receiving bonus payments were reporting as an alternative payment model, practice size greater than 24, and having 10% to 49% of dually eligible beneficiaries (P < 0.05).

Conclusion:
Understanding performance of plastic surgeons in MIPS can guide future policy direction and ensure that high-quality care translates into improved patient outcomes across all fields and levels of social vulnerability.
Orthognathic Considerations of Maxillary and Mandibular Asymmetry at Skeletal Maturity in Patients with Cleft Lip and Palate
Authors: Salinero Lauren K , Friedman Leigh , Shulkin Jared M , Barrero Carlos E , Wagner Connor S , Pontell Matthew E , Swanson Jordan W , Bartlett Scott P , Nah Hyun-Duck , Taylor Jesse A 
Published: April 2024

Background:
Improving occlusion and aesthetics is the primary objective of orthognathic surgery for patients with cleft lip and palate (CLP). However, these patients often suffer from horizontal, vertical, and rotational asymmetry in addition to maxillary retrusion. This study aims to describe maxillary and mandibular asymmetry in patients with CLP undergoing orthognathic surgery and analyze its anatomic basis.

Methods:
Patients with isolated CLP undergoing CT imaging prior to orthognathic surgery were retrospectively reviewed. Maxillary and mandibular positioning and dimensional symmetry were evaluated. Incidence of clinically significant asymmetry, correlations between areas of asymmetry, and associations with clinical history were analyzed.

Results:
Fifty-eight patients, with mean age 17 years were analyzed, including 32 patients with unilateral CLP and 26 with bilateral CLP. Twenty (34%) patients demonstrated chin deviation ≥4mm and 21 (36%) had a ≥5% discrepancy in mandibular ramus lengths. Horizontal occlusal plane cant of ≥2° was seen in 20 (34%) maxillae and 28 (48%) mandibles, with dental arch yaw ≥2° noted in 32 (55%) of both maxillae and mandibles. Chin deviation correlated with maxillary cant, discrepancy in ramus length, discrepancy in mandibular body length, and discrepancy in condylar volume (p<0.05). Bilateral and unilateral CLP did not show significantly different asymmetry on any measure (p>0.05).

Conclusions:
Both maxillary and mandibular asymmetry is common in skeletally mature patients with CLP and frequently results in notable chin deviation. Preoperative three-dimensional imaging and virtual surgical planning of orthognathic surgery aid in recognition of facial asymmetries and reveal opportunities to optimize results in this population.
Dynamics of Saccade Trajectory Modulation by Distractors: Neural Activity Patterns in the Frontal Eye Field
Authors: Ramezanpour H. , Kehoe D. H. , Schall J. D. , Fallah M. 
Published: April 2024

AbstractThe sudden appearance of a visual distractor shortly before saccade initiation can capture spatial attention and modulate the saccade trajectory in spite of the ongoing execution of the initial plan to shift gaze straight to the saccade target. To elucidate the neural correlates underlying these curved saccades, we recorded from single neurons in the frontal eye field (FEF) of two rhesus monkeys shifting gaze to a target while an isoeccentric distractor appeared either left or right of the target at various delays after target presentation. We found that the population level of pre-saccadic activity encoded the direction of the saccade trajectory. Stronger activity occurred when saccades curved toward the distractor, and weaker when saccades curved away. This relationship held whether the distractor was ipsilateral or contralateral to the recorded neurons. Meanwhile, visually responsive neurons showed asymmetrical patterns of excitatory responses that varied with the location of the distractor and the duration of distractor processing relating to attentional capture and distractor inhibition. During earlier distractor processing, neurons encoded curvature towards the distractor. During later distractor processing, neurons encoded curvature away from the distractor. This was observed when saccades curved away from distractors contralateral to the recording site and when saccades curved towards distractors ipsilateral to the recording site. These findings indicate that saccadic motor planning involves dynamic push-pull hemispheric interactions producing attraction or repulsion for potential but unselected saccade targets.Significant StatementThis study not only advances our understanding of oculomotor function in dynamic environments but also has potential clinical relevance for diagnosing and understanding disorders characterized by abnormal saccade trajectories. Our research elucidates the neural mechanisms behind saccade trajectories that are not always linear due to the brain’s integration of multiple visual cues and/or motor plans. By analyzing the frontal eye field (FEF) activity in rhesus monkeys, we found that saccade directionality and timing are influenced by the interaction between FEF visual neurons representing target and distractor stimuli. The FEF’s role extends beyond a winner-takes-all approach, incorporating saccade vector averaging computations that produce curved saccades. Furthermore, ipsilateral visual neurons encode distractor suppression that drives curvature away from the distractor.
Retrotransposon expression is upregulated by aging and suppressed during regeneration of the limb in the axolotl (Ambystoma mexicanum)
Authors: Ruiz-Pérez Samuel , Torres-Arciga Karla , Sámano-Salazar Cynthia Gabriela , Ocampo-Cervantes José Antonio , Cervera Alejandra , Castro-Hernández Clementina , Soto-Reyes Ernesto , Alcaraz Nicolas , González-Barrios Rodrigo 
Published: April 2024

AbstractThe axolotl (Ambystoma mexicanum) has a great capacity to regenerate its tissues and whole-body parts; however, the fidelity and success of its regenerative process diminish with age. Retrotransposons make up the largest portion of the axolotl genome, and their expression may be involved in this age-related decline. Through an integrative analysis of repetitive element expression using RNA-seq, we show that Ty3 retrotransposons are highly upregulated in the axolotl as an effect of chronological aging. Other non-LTR transposons, including LINE-1, function as hubs of gene coexpression networks involved in muscle development, N-methyltransferase activity, amyloid proteolysis, and regulation of apoptosis and connective tissue replacement, which are also suppressed by the increase in age. In contrast, we find that during regeneration of the limb these pathways and the expression of Ty3 retrotransposons are distinctly downregulated. Although the blastema is able to readjust most of the transposon dysregulation caused by aging, there are still several elements that remain affected and may have an impact in the metabolic and immune responses during the regenerative process. We also report that numerous C2H2-ZFPs, especially KRAB-ZPFs, are coexpressed with hub retrotransposons, which reveals their potential as important regulators of transposable element expression during aging and regeneration. This integrative analysis provides a comprehensive profile of retrotransposon expression through chronological aging and during limb regeneration in the axolotl and indicates that transposable elements are responsive to physiological changes in a tissue-specific way and participate in the gene co-regulatory networks underlying the regenerative process.Graphical abstract.Transcriptomic analyses of adult and sub-adult axolotls offer an insight into the potential role of retrotransposons during limb regeneration and how they are affected by chronological aging. Retrotransposons of the Ty3 superfamily are usually suppressed during regeneration, but after experiencing a significant upregulation through the aging of the axolotl, their regulation during tissue repair is limited. It has been reported that the success of the axolotl’s regenerative process diminishes with age. Our findings show that Ty3 and other transposon families, such as LINE-1, are involved in the gene regulatory networks that suppress muscle development, apoptosis control, and tissue replacement due to aging. These results suggest that repetitive element expression may indirectly constrain the regenerative capacities of older axolotls.
WENDY: Covariance Dynamics Based Gene Regulatory Network Inference
Authors: Wang Yue , Zheng Peng , Cheng Yu-Chen , Wang Zikun , Aravkin Aleksandr 
Published: April 2024

AbstractDetermining gene regulatory network (GRN) structure is a central problem in biology, with a variety of inference methods available for different types of data. For a widely prevalent and challenging use case, namely single-cell gene expression data measured after intervention at multiple time points with unknown joint distributions, there is only one known specifically developed method, which does not fully utilize the rich information contained in this data type. We develop an inference method for the GRN in this case, netWork infErence by covariaNce DYnamics, dubbed WENDY. The core idea of WENDY is to model the dynamics of the covariance matrix, and solve this dynamics as an optimization problem to determine the regulatory relationships. To evaluate its effectiveness, we compare WENDY with other inference methods using synthetic data and experimental data. Our results demonstrate that WENDY performs well across different data sets.
The Rac1 homolog CED-10 is a component of the MES-1/SRC-1 pathway for asymmetric division of theC. elegansEMS blastomere
Authors: Lamb Helen , Liro Małgorzata , Myles Krista , Fernholz McKenzi , Anderson Holly , Rose Lesilee S. 
Published: April 2024

AbstractAsymmetric cell division is essential for the creation of cell types with different identities and functions. The EMS blastomere of the four-cellCaenorhabditis elegansembryo undergoes an asymmetric division in response to partially redundant signaling pathways. One pathway involves a Wnt signal emanating from the neighboring P2 cell, while the other pathway is defined by the receptor-like MES-1 protein localized at the EMS/P2 cell contact, and the cytoplasmic kinase SRC-1. In response to these pathways, the EMS nuclear-centrosome complex rotates so that the spindle forms on the anterior-posterior axis; after division, the daughter cell contacting P2 becomes the endodermal precursor cell. Here we identify the Rac1 homolog, CED-10, as a new component of the MES-1/SRC-1 pathway. Loss of CED-10 affects both spindle positioning and endoderm specification. Although MES-1 is still present at the EMS/P2 contact inced-10embryos, SRC-1 dependent phosphorylation is reduced. These and other results suggest that CED-10 acts downstream of MES-1 and upstream of, or at the level of, SRC-1 activity. In addition, we find that the branched actin regulator ARX-2 is enriched at the EMS/P2 cell contact site, in a CED-10 dependent manner. Loss of ARX-2 results in spindle positioning defects, suggesting that CED-10 acts through branched actin to promote the asymmetric division of the EMS cell.
STARDUST: a pipeline for the unbiased analysis of astrocyte regional calcium dynamics
Authors: Wu Yifan , Dai Yanchao , Lefton Katheryn B. , Holy Timothy E. , Papouin Thomas 
Published: April 2024

SummaryCalcium imaging has become a popular way to probe astrocyte activity, but few analysis methods holistically capture discrete calcium signals that occur across the astrocyte domain. Here, we introduce STARDUST, a pipeline for the Spatio-Temporal Analysis of Regional Dynamics & Unbiased Sorting of Transients from fluorescence recordings of astrocytes, and provide step-by-step guidelines. STARDUST yields fluorescence time- series from data-defined regions of activity and performs systematic signal detection and feature extraction, enabling the in-depth and unbiased study of astrocyte calcium signals.Graphical abstract