bluuebunny/crossref_metadata_2025_split huggingface dataset:
Greater working memory and speech perception scores in cochlear implant users predict better subjective quality of life and hearing
Authors: Prince Priyanka , Chen Joseph , Le Trung , Lin Vincent , Dimitrijevic Andrew 
Published: September 2022

AbstractA common concern in individuals with cochlear implants (CIs) is difficulty following conversations in noisy environments and social settings. The ability to accomplish these listening tasks relies on the individual’s working memory abilities and draws upon limited cognitive resources to accomplish successful listening. For some individuals, allocating too much, can result deficits in speech perception and in long term detriments of quality of life. For this study, 31 CI users and NH controls completed a series of online behavioural tests and quality of life surveys, in order to investigate the relationship between visual and auditory working memory, clinical and behavioural measures of speech perception and quality of life and hearing. Results showed NH individuals were superior on auditory working memory and survey outcomes. In CI users, recall performance on the three working memory span tests declined from visual reading span to auditory listening in quiet and then listening in noise and speech perception was predictably worse when presented with noise maskers. Bilateral users performed better on each task compared to unilateral/HA and unilateral only users and reported better survey outcomes. Correlation analysis revealed that memory recall and speech perception ability were significantly correlated with sections of CIQOL and SSQ surveys along with clinical speech perception scores in CI users. These results confirm that hearing condition can predict working memory and speech perception and that working memory ability and speech perception, in turn, predict quality of life. Importantly, we demonstrate that online testing can be used as a tool to assess hearing, cognition, and quality of life in CI users.
Huntingtin Interacting Protein 1 (HIP1) autoantibodies as a novel potential surrogate marker for Rheumatoid Arthritis: Pilot Study
Authors: Surbhi  , Goel Ayushi , Chaturvedi Ved , Verma Sneha , Rawat Sonia , Ganguly Nirmal Kumar , Mittal Shivani Arora 
Published: September 2022

ABSTRACTRheumatoid Arthritis (RA), an autoimmune disease, primarily affects synovial joints but has systemic manifestations upon progression. Considering limited specific diagnostic and prognostic biomarkers, identifying the disease early and monitoring its progression is important. Previous reports have shown that Huntingtin Interacting Protein 1 (HIP1) is over-expressed in rat synoviocytes, and its autoantibodies in sera of some cancers has diagnostic relevance. Here, we explored HIP1 and its autoantibody levels along with Th1/Th2/Th17 cytokines in sera of RA patients for their potential as surrogate markers. Relative level of autoantibodies to HIP1 was detected using an in-house developed ELISA. HIP1 expression was found comparable in RA patients and controls. HIP1 autoantibodies were found significantly raised in RA patients (p=0.002) and were higher in patients with active disease, thereby correlating with disease progression (p=0.042). Elevated Th1 and IL-6 cytokines (p=0.024) were found in a subset of patients with active disease, coinciding with their pro-inflammatory profile. This is the first report demonstrating a humoral immune response against HIP1 in RA patients, correlating with an active disease status. Further studies in a larger cohort are required to validate this as a surrogate marker.Key Points⍰HIP1 autoantibodies are significantly increased in sera of RA patients.⍰HIP1 autoantibodies correlate with active disease in RA patients.
Power and sample sizes estimation in clinical trials with treatment switching in intention-to-treat analysis: a simulation study
Authors: Deng Lejun , Hsu Chih-Yuan , Shyr Yu 
Published: September 2022

AbstractBackgroundTreatment switching, also called crossover, is common in clinical trials because of ethical concerns or other reasons. When it occurs and the primary objective is to identify treatment effects, the most widely used intention-to-treat analysis may lead to underpowered trials. Therefore, we plan to propose an approach to preview power reductions and to estimate sample sizes required for the desired power when treatment switching occurs in the intention-to-treat analysis.MethodsWe proposed a simulation-based approach and developed an R package to attain the purpose.ResultsWe simulated a number of randomized trials incorporating treatment switching and investigated the impact of the relative effectiveness of the experimental treatment to the control, the switching probability, the allocation ratio, and the switching time on power reductions and sample sizes estimation. The switching probability and the switching time are key determinants for significant power decreasing and thus sample sizes surging to maintain the desired power. The sample sizes required in randomized trials absence of treatment switching varied from around three-fourths to one-twelfths of the sample sizes required in randomized trials allowing treatment switching as the probability of switched patients increased. The power reductions and sample sizes increase with the decrease of switching time.ConclusionsThe simulation-based approach not only provides a preview for power declining but also calculates the required sample size to achieve an expected power in the intention-to-treat analysis when treatment switching occurs. It will provide researchers and clinicians with useful information before randomized controlled trials are conducted.
Adverse childhood experiences and their impacts on subsequent depression and cognitive impairment in Chinese adults
Authors: Zhang Tiantian , Kan Lena , Jin Changbo , Shi Wenming 
Published: September 2022

AbstractBackgroundAdverse childhood experiences (ACEs) are prevalent and have long lasting effects. This study aimed to explore the associations between ACEs exposure with subsequent depression and cognitive impairment and to assess whether sociodemographic characteristics modify these associations.MethodA total of 14,484 participants from the China Health and Retirement Longitudinal Study (CHARLS) 2015 and life history survey in 2014 were enrolled. Depression was assessed by the 10-item Center for Epidemiologic Studies Depression scale. Cognitive performance was evaluated by three composite measures: episodic memory, mental intactness and global cognition. A wide range of 12 ACE indicators were measured by a validated questionnaire. Multiple regression models and stratified analysis explore the relationship between accumulated ACEs with subsequent depression and cognitive impairment and potential modifiers.ResultsCompared with individuals without ACEs, those who experienced four or more ACEs have a higher risk of subsequent depression (adjusted odds ratio, aOR=2.65, 95% confidence intervals [CIs]: 2.21-3.16), poorer mental intactness (β= -0.317 [-0.508 to -0.125]) and worse global cognition (β= -0.437 [-0.693 to -0.181]). Trend analyses showed a dose-response association between accumulated ACEs with subsequent depression and cognitive impairment. The modifications of the association by age, sex, educational level and family’s financial status during childhood were not observed.ConclusionOur study suggests that higher ACEs exposure increases the risk of subsequent depression and cognitive impairment in Chinese adults regardless of sociodemographic characteristics. The findings provide important implications for mitigating the adverse effects of early-life stress and promoting health in adulthood.
A scenario-guided strategy for the future management of biological invasions
Authors: Roura-Pascual Núria , Saul Wolf-Christian , Pérez-Granados Cristian , Rutting Lucas , Peterson Garry D. , Latombe Guillaume , Essl Franz , Adriaens Tim , Aldridge David C. , Bacher Sven , Bernardo-Madrid Rubén , Brotons Lluís , Diaz François , Gallardo Belinda , Genovesi Piero , Golivets Marina , González-Moreno Pablo , Hall Marcus , Kutlesa Petra , Lenzner Bernd , Liu Chunlong , Pagitz Konrad , Pastor Teresa , Rabitsch Wolfgang , Robertson Peter , Roy Helen E. , Seebens Hanno , Solarz Wojciech , Starfinger Uwe , Tanner Rob , Vilà Montserrat , Leung Brian , Garcia-Lozano Carla , Jeschke Jonathan M. 
Published: September 2022

AbstractFuture dynamics of biological invasions are highly uncertain because they depend on multiple environmental, societal and socio-economic drivers. We adopted a qualitative scenario approach to explore the future of invasive alien species (IAS) in Europe and created an overall strategy for their management that considers different plausible future developments. The scenarios and strategy were developed during two online workshops with a multidisciplinary team of experts. First, we downscaled four global scenarios of biological invasions to the European level. Second, we developed a management strategy structured into 19 goals that cover a broad array of IAS-related topics (i.e. policy, research, public awareness and biosecurity), and provided solutions for achieving these goals considering the European scenarios. Third, we identified four interrelated recommendations around which any long-term strategy for managing IAS in Europe can be structured: (i) a European biosecurity regime, (ii) a dedicated communication strategy, (iii) data standardization and management tools, and (iv) a monitoring and assessment system. Finally, we identified the feasibility of the IAS management strategy, finding strong differences among the four scenarios. High levels of technological development, public environmental awareness, and effectiveness of IAS policies facilitated the implementation of the overall management strategy. Together, our results indicate that it is time for a new management of biological invasions in Europe based on a more integrative perspective across sectors and countries to be better prepared for future challenges.
Environmental determinants of round goby invasion refuges at a river scale: implications for conservation of native biodiversity
Authors: Morissette Olivier , Charette Cristina , Windle Matthew J.S. , Francis Abraham , Drouin Annick , Goldsmit Jesica , Derry Alison M. 
Published: September 2022

AbstractIntroductions of exotic invasive species are a global disturbance for natural habitats. The severity of invasions can greatly vary from local to global scales, as observed in invasion refuges, exhibiting lower-than-expected invasion intensity. In this study, we analyzed the effects of water conductivity and wetland presence on the density of the round goby (Neogobius melanostomus) in a large-scale study (> 1300 sites), spanning a 400 km stretch of the St. Lawrence River (Canada). Our results showed that round goby density was null in sites with water conductivity under 100 µS/cm and increased toward a probable biological optimum at 300 µS/cm. The presence of wetlands appeared to also decrease round goby density along the conductivity continuum. Similarly, fish community diversity was maximal outside of the round goby water conductivity optimum. Hence, low water conductivity (<100 µS/cm), in interaction with the presence of wetlands, can provide a refuge for native aquatic species, establishing a simple risk assessment tool for managers. Our results also highlighted the high value of wetland conservation for conservation of native species biodiversity.
The topological shape of gene expression across the evolution of flowering plants
Authors: Palande Sourabh , Kaste Joshua A.M. , Roberts Miles D. , Abá Kenia Segura , Claucherty Carly , Dacon Jamell , Doko Rei , Jayakody Thilani B. , Jeffery Hannah R. , Kelly Nathan , Manousidaki Andriana , Parks Hannah M , Roggenkamp Emily M , Schumacher Ally M , Yang Jiaxin , Percival Sarah , Pardo Jeremy , Husbands Aman Y , Krishnan Arjun , Montgomery Beronda L , Munch Elizabeth , Thompson Addie M , Rougon-Cardoso Alejandra , Chitwood Daniel H , VanBuren Robert 
Published: September 2022

AbstractSince they emerged ~125 million years ago, flowering plants have evolved to dominate the terrestrial landscape and survive in the most inhospitable environments on earth. At their core, these adaptations have been shaped by changes in numerous, interconnected pathways and genes that collectively give rise to emergent biological phenomena. Linking gene expression to morphological outcomes remains a grand challenge in biology, and new approaches are needed to begin to address this gap. Here, we implemented topological data analysis (TDA) to summarize the high dimensionality and noisiness of gene expression data using lens functions that delineate plant tissue and stress responses. Using this framework, we created a topological representation of the shape of gene expression across plant evolution, development, and environment for the phylogenetically diverse flowering plants. The TDA-based Mapper graphs form a well-defined gradient of tissues from leaves to seeds, or from healthy to stressed samples, depending on the lens function. This suggests there are distinct and conserved expression patterns across angiosperms that delineate different tissue types or responses to biotic and abiotic stresses. Genes that correlate with the tissue lens function are enriched in central processes such as photosynthetic, growth and development, housekeeping, or stress responses. Together, our results highlight the power of TDA for analyzing complex biological data and reveal a core expression backbone that defines plant form and function.Significance statementA grand challenge in biology is to link gene expression to phenotypes across evolution, development, and the environment, but efforts have been hindered by biological complexity and dataset heterogeneity. Here, we implemented topological data analysis across thousands of gene expression datasets in phylogenetically diverse flowering plants. We created a topological representation of gene expression across plants and observed well-defined gradients of tissues from leaves to seeds, or from healthy to environmentally stressed. Using this framework, we identified a core and deeply conserved expression backbone that defines plant form and function, with key patterns that delineate plant tissues, abiotic, and biotic stresses. Our results highlight the power of topological approaches for analyzing complex biological datasets.
Neurostimulation Artifact Removal for Implantable Sensors Improves Signal Clarity and Decoding of Motor Volition
Authors: Earley Eric J. , Berneving Anton , Zbinden Jan , Ortiz-Catalan Max 
Published: September 2022

AbstractAs the demand for prosthetic limbs with reliable and multi-functional control increases, recent advances in myoelectric pattern recognition and implanted sensors have proven considerably advantageous. Additionally, sensory feedback from the prosthesis can be achieved via stimulation of the residual nerves, enabling closed-loop control over the prosthesis. However, this stimulation can cause interfering artifacts in the electromyographic (EMG) signals which deteriorate the reliability and function of the prosthesis. Here, we implement two real-time stimulation artifact removal algorithms, Template Subtraction and ε-Normalized Least Mean Squares, and investigate their performance in offline and real-time myoelectric pattern recognition in two transhumeral amputees implanted with nerve cuff and EMG electrodes. We show that both algorithms are capable of significantly improving signal-to-noise ratio and offline pattern recognition accuracy of artifact-corrupted EMG signals. Furthermore, both algorithms improved real-time decoding of motor intention during active neurostimulation. Although these outcomes are dependent on the user-specific sensor locations and neurostimulation settings, they nonetheless represent progress towards bi-directional neuromusculoskeletal prostheses capable of multifunction control and simultaneous sensory feedback.
A cocktail of rapamycin, acarbose and phenylbutyrate prevents age-related cognitive decline in mice by altering aging pathways
Authors: Jiang Zhou , He Qianpei , Ladiges Warren 
Published: September 2022

AbstractAging is a primary risk factor for cognitive dysfunction and exacerbates multiple biological processes in the brain, including but not limited to nutrient sensing dysregulation, insulin sensing dysfunction and histone deacetylation. Therefore, pharmaceutical intervention of aging targeting several distinct but overlapping pathways provides a basis for testing combinations of drugs as a cocktail. A recent study showed that middle-aged mice treated with a drug cocktail of rapamycin, acarbose, and phenylbutyrate for three months had increased resilience to age related cognitive decline. This finding provided the rationale to investigate the comprehensive transcriptomic and molecular changes within the brain of mice that received this cocktail treatment or control substance. Transcriptome profiles were generated through RNA sequencing and pathway analysis was performed by gene set enrichment analysis to evaluate the overall RNA message effect of the drug cocktail. Molecular endpoints representing aging pathways were measured through immunohistochemistry to further validate the attenuation of brain aging in the hippocampus of mice that received the cocktail treatment, each individual drug or controls. Results indicated that biological processes that enhance aging were suppressed, while autophagy was increased in the brains of mice given the drug cocktail. The molecular endpoint assessments indicated that treatment with the drug cocktail was overall more effective than any of the individual drugs for relieving cognitive impairment by targeting multiple aging pathways.
Accelerated ensemble generation for cyclic peptides using a Reservoir-REMD implementation in GROMACS
Authors: Hsueh Shawn C.C. , Aina Adekunle , Plotkin Steven S. 
Published: September 2022

AbstractCyclic peptides naturally occur as antibiotics, fungicides, and immunosuppressants, and have been adapted for use as potential therapeutics. Scaffolded cyclic peptide antigens have many protein characteristics such as reduced toxicity, increased stability over linear peptides, and conformational selectivity, but with fewer amino acids than whole proteins. The profile of shapes presented by a cyclic peptide modulates its therapeutic efficacy, and is represented by the ensemble of its sampled conformations. Although some algorithms excel in creating a diverse ensemble of cyclic peptide conformations, they seldom address the entropic contribution of flexible conformations, and they often have significant practical difficulty producing an ensemble with converged and reliable thermodynamic properties. In this study, an accelerated molecular dynamics (MD) method, reservoir replica exchange MD (R-REMD or Res-REMD), was implemented in GROMACS-4.6.7, and benchmarked on three small cyclic peptide model systems: a cyclized segment of Aβ(cyclo-(CGHHQKLVG)), a cyclized furin cleavage site of SARS-CoV-2 spike (cyclo-(CGPRRARSG)), and oxytocin (disulfide bonded CY-IQNCPLG). Additionally, we also benchmarked Res-REMD on Alanine dipeptide and Trpzip2 to demonstrate its validity and efficiency over REMD. Compared to REMD, Res-REMD significantly accelerated the ensemble generation of cyclo-(CGHHQKLVG), but not cyclo-(CGPRRARSG) or oxytocin. This difference is due to the longer auto-correlation time of torsional angles in cyclo-(CGHHQKLVG)vs. the latter two cyclic peptide systems; The randomly seeded reservoir in Res-REMD thus accelerates sampling and convergence. The auto-correlation time of the torsional angles can thus be used to determine whether Res-REMD is preferable to REMD for cyclic peptides. We provide a github page with modified GROMACS source code for running Res-REMD athttps://github.com/PlotkinLab/Reservoir-REMD.
Comparison of Evaluation Metrics of Deep Learning for Imbalanced Imaging Data in Osteoarthritis Studies
Authors: Liu Shen , Roemer Frank , Ge Yong , Bedrick Edward J. , Li Zong-Ming , Guermazi Ali , Kwoh C. Kent , Sun Xiaoxiao 
Published: September 2022

AbstractObjectiveTo compare the evaluation metrics for deep learning methods in the imbalanced imaging data in osteoarthritis (OA) studies.MethodWe first divided MOAKS (MRI Osteoarthritis Knee Score) grades into the presence (MOAKS > 0) and absence (MOAKS = 0) categories. Second, a deep-learning model was trained to the sagittal intermediate-weighted (IW) fat-suppressed (FS) knee MRI images with MOAKS readings from the Osteoarthritis Initiative (OAI) study to predict the presence of bone marrow lesions (BMLs). After the deep learning models were trained, we obtained probabilities of the presence of BMLs from MRI images at the sub-region (15 sub-regions), compartment, and whole-knee levels. We compared different evaluation metrics (e.g., receiver operating characteristic (ROC) and precision-recall (PR) curves) of the deep learning model in the testing data with various class ratios (presence of BMLs vs. absence of BMLs) at these three data levels to assess the model’s performance.ResultsWe have demonstrated that the commonly used ROC curve is not sufficiently informative when evaluating the performance of deep learning models in the imbalanced data in OA studies.ConclusionThe class ratios coupled with results of ROC, PR, and Matthews correlation coefficient (MCC) should be reported in OA studies.
Assessment of the performance of Lyoplant® Onlay for duraplasty. An observational, multi-center Post Market Clinical Follow-up study
Authors: Greifzu Franziska , Breuskin David , Prajsnar Anna , Geletneky Karsten , Bode Frank , Tuettenberg Jochen , Oertel Joachim , Stadie Axel 
Published: September 2022

AbstractObjectiveDuraplasty with a dura mater substitute can become necessary after cranial or spinal surgery. Several dura grafts from different materials are available. The goal of this study was to assess the clinical performance of a suturable onlay dura substitute composed of bovine collagen.MethodsA prospective, observational, multicenter, single-arm clinical study with the dura substitute Lyoplant® Onlay was performed. Different performance parameters for safety and performance were assessed. Additionally, postoperative MRI / CT images were evaluated.ResultsData of 61 patients recruited by three study centers were included. Lyoplant® Onlay was used by a variety of surgeons with different levels of experience. Cranial and spinal cases with a wide range of dura defect sizes were included. No reoperation due to a cerebrospinal fluid leakage occurred until discharge (primary endpoint), as well as to the follow-up (about four months postoperatively). The incidence rate of cerebrospinal fluid leakages was 6.6%. All of these adverse events were reported as non-serious complications without the need of a surgical intervention and were resolved without sequelae. The handling properties of Lyoplant® Onlay were positively rated. In external radiologic analysis of postoperative MRI / CT images at discharge and follow-up, additional fluid collection, edema, and swelling were observed. However, they were clinically inapparent and considered normal postsurgical findings.ConclusionsThe incidence rate of cerebrospinal fluid leakages was 6.6% and ranged in the values reported in the literature.These results show that Lyoplant® Onlay is a safe and efficient dura substitute.HighlightsLyoplant® Onlay is a safe and effective bovine dura substituteUniversal product for onlay or suturable application, cranial and spinal surgeriesNo re-operations because of CSF leakageVery good handling characteristicsProspective study with 61 patients, 3 study centers and 4 months follow-up