bluuebunny/crossref_metadata_2025_split huggingface dataset:
Pilot of Patient Engagement in Continence Care on Geriatric Rehabilitation Units
Authors: Hunter Kathleen Frances , Dahlke Sherry , Kalogirou Maya R. , Pietrosanu Matthew , Triscott Jean , Savard Winnie , Wagg Adrian 
Published: March 2022

Abstract

Purpose
The aim of this study was to pilot a process of engaging geriatric rehabilitation patients in the assessment and management of their continence concerns.

Design
A descriptive study was conducted.

Methods
The study has four phases: (1) staff education on continence with a pre–post knowledge quiz, (2) design of patient engagement process by a working group, (3) a 6-week pilot of a patient symptom questionnaire and process of engaging patients with audits of disciplinary admission histories and documentation, and (4) patient and staff feedback surveys.

Results
Patients in geriatric rehabilitation identify a range of bladder and bowel symptoms. However, there was little documented evidence from the interprofessional team that corresponded to patients’ reported symptoms.

Conclusion
Further research into symptoms bothersome to patients and engagement of both patients and the interprofessional team in addressing these in the rehabilitation setting is needed.

Clinical Relevance to Rehabilitation Nursing
Patients admitted to geriatric rehabilitation have a range of bladder and bowel symptoms, which need to be addressed.
The Experiences of Robot-Assisted Gait Training in Patients With Neurological Disorders: A Qualitative Study
Authors: Chang Yi-Ya , Chang Shu-Chun , Xiao Xaviera , Chen Carl P. C. 
Published: March 2022

Abstract

Purpose
The aim of this study was to explore the rehabilitation experiences and perceptions of patients with neurological disorders who have used the Lokomat Augmented Feedback module, a robot-assisted gait training device.

Design
A qualitative descriptive study was conducted.

Methods
Purposive sampling was employed to recruit participants with neurological disorders who have used the Lokomat. Semistructured face-to-face interviews were completed in northern Taiwan. Interviews were recorded and transcribed verbatim. Thematic analysis was used.

Results
Thirteen interviews were analyzed. Three themes were identified: learning to walk again, inspiring the fighting spirit, and the joys and worries of technological innovation.

Conclusions
Strong positive emotions and logistical concerns were associated with the use of the Lokomat.

Clinical Relevance
Encouraging patients while also being transparent about the challenges involved in the rehabilitation process and helping set realistic goals is critical. Furthermore, attention directed toward anticipating and mitigating the physical strain associated with the Lokomat is important.
Can Location of Stiffness Measurement Impact Spleen 2-Dimensional Shear Wave Elastography Measurement?
Authors: Song Jinzhen , Li Jiawu , Luo Yan , Lu Qiang 
Published: March 2022

Abstract
Ultrasound-based spleen elastography is a promising surrogate to predict portal hypertension noninvasively. In contrast to defined standards for liver stiffness measurement, the standardized examination procedures for 2-dimensional (2D) shear wave elastography spleen elastography have not been established yet. The aim was to investigate the impact of location of stiffness measurement on 2D shear wave elastography spleen stiffness measurement (SSM). Patients with splenomegaly were enrolled. Both B-mode ultrasound and elastography of spleen were performed. For SSM, 3 regions were chosen for spleen measurement: lower pole region, central region, and the region between lower pole and center. Mean SSM value, success rate, and reliability predicators (standard deviation, standard deviation/mean, size of region of interest) were assessed. A total of 124 patients were included. For mean SSM value, there were no significant differences among 3 regions. Spleen stiffness measurement success rate in lower pole region, central region, and the region between them was 63.7% (79), 91.1% (113), and 78.2% (97), respectively. The success rate in the central region was significantly higher than that in the other 2 regions (P < 0.05). Reliability in the central region was also highest among the 3 regions. Location of stiffness measurement has a limited effect on SSM. Changing location of measurement will not influence mean stiffness value in spleen.
Red Knot Stopover Population Size and Migration Ecology at Delaware Bay, USA, 2021
Authors: Lyons J. E. 
Published: March 2022

AbstractRed Knots (Calidris canutus rufa) stop at Delaware Bay during northward migration to feed on eggs of horseshoe crabs (Limulus polyphemus). In the late 1990s and early 2000s, the number of Red Knots found at Delaware Bay dramatically declined from ~50,000 to ~13,000. Horseshoe crabs have been harvested for use as bait in eel and whelk fisheries since at least 1990, and some avian conservation biologists hypothesized that harvest levels in the 1990s prevented sufficient refueling for successful migration to the breeding grounds, nesting, and survival for the remainder of the annual cycle. Since 2013, the harvest of horseshoe crabs in the Delaware Bay region has been managed using an Adaptive Resource Management (ARM) framework. The objective of the ARM framework is to manage sustainable harvest of Delaware Bay horseshoe crabs while maintaining ecosystem integrity and supporting Red Knot recovery with adequate stopover habitat for Red Knots and other migrating shorebirds. For annual harvest recommendations, the ARM framework requires annual estimates of horseshoe crab population size and the Red Knot stopover population. We conducted a mark-recapture-resight investigation to estimate the passage population of Red Knots at Delaware Bay in 2021. We used a Bayesian analysis of a Jolly-Seber model, which accounts for turnover in the population and the probability of detection during surveys. The 2021 Red Knot mark-resight dataset included a total of 1,591 individual birds that were recorded at least one during mark-resight surveys at Delaware Bay in 2021. The passage population size in 2021 was estimated at 42,271 (95% credible interval: 35,948 – 55,210). Like 2020, the 2021 population estimate is slightly lower than the 2018 and 2019 estimates. The 2021 population size estimate will inform decision making for harvest recommendations in the next management cycle.
Edison: measuring scaffolding accuracy with edit distance
Authors: Sur Aakash , Noble William Stafford , Sullivan Shawn , Myler Peter 
Published: March 2022

AbstractMotivationThe quality of reference genomes critically affects analyses of next generation sequencing experiments. During the construction of the reference genome, contigs are organized into their underlying chromosomes in the scaffolding step. Historically, the quality of scaffolding software has been difficult to evaluate in a systematic and quantitative fashion. To this end, we identified genomic edit distance as a compelling method for evaluating the quality of a scaffold.ResultsWe present Edison, a Python implementation of the Double Cut and Join (DCJ) edit distance algorithm. Edison calculates the overall accuracy of a given scaffold using a reference genome and also provides scores for characterizing different aspects of the scaffolding accuracy, including grouping, ordering, and orientation. All metrics are calculated on a length-weighted basis, which rewards the correct placement of longer contigs over shorter ones. By creating 1000 random assemblies of theS. cerevisiaegenome, we show that our scaffolding accuracy provides a more reliable metric than the commonly used metric, N50. Edison can be used to benchmark new scaffolding algorithms, providing insights into the strengths and weaknesses of each approach.Availability and ImplementationEdison is available under an MIT license athttps://github.com/Noble-Lab/edison.
A SARS-CoV-2 Spike Ferritin Nanoparticle Vaccine is Protective and Promotes a Strong Immunological Response in the Cynomolgus Macaque Coronavirus Disease 2019 (COVID-19) Model
Authors: Johnston Sara C. , Ricks Keersten M. , Lakhal-Naouar Ines , Jay Alexandra , Subra Caroline , Raymond Jo Lynne , King Hannah A. D. , Rossi Franco , Clements Tamara L. , Fetterer David , Tostenson Samantha , Cincotta Camila Macedo , Hack Holly R. , Kuklis Caitlin , Soman Sandrine , King Jocelyn , Peachman Kristina K. , Kim Dohoon , Chen Wei-Hung , Sankhala Rajeshwer S. , Martinez Elizabeth J. , Hajduczki Agnes , Chang William C. , Choe Misook , Thomas Paul V. , Peterson Caroline E. , Anderson Alexander , Swafford Isabella , Currier Jeffrey R. , Paquin-Proulx Dominic , Jagodzinski Linda L. , Matyas Gary R. , Rao Mangala , Gromowski Gregory D. , Peel Sheila A. , White Lauren , Smith Jeffrey M. , Hooper Jay W. , Michael Nelson L. , Modjarrad Kayvon , Joyce M. Gordon , Nalca Aysegul , Bolton Diane L. , Pitt Margaret LM 
Published: March 2022

AbstractThe COVID-19 pandemic has had a staggering impact on social, economic, and public health systems worldwide. Vaccine development and mobilization against SARS-CoV-2 (the etiologic agent of COVID-19) has been rapid. However, novel strategies are still necessary to slow the pandemic, and this includes new approaches to vaccine development and/or delivery, which improve vaccination compliance and demonstrate efficacy against emerging variants. Here we report on the immunogenicity and efficacy of a SARS-CoV-2 vaccine comprised of stabilized, pre-fusion Spike protein trimers displayed on a ferritin nanoparticle (SpFN) adjuvanted with either conventional aluminum hydroxide or the Army Liposomal Formulation QS-21 (ALFQ) in a cynomolgus macaque COVID-19 model. Vaccination resulted in robust cell-mediated and humoral responses and a significant reduction of lung lesions following SARS-CoV-2 infection. The strength of the immune response suggests that dose sparing through reduced or single dosing in primates may be possible with this vaccine. Overall, the data support further evaluation of SpFN as a SARS-CoV-2 protein-based vaccine candidate with attention to fractional dosing and schedule optimization.
Mosaic RBD nanoparticles protect against multiple sarbecovirus challenges in animal models
Authors: Cohen Alexander A. , van Doremalen Neeltje , Greaney Allison J. , Andersen Hanne , Sharma Ankur , Starr Tyler N. , Keeffe Jennifer R. , Fan Chengcheng , Schulz Jonathan E. , Gnanapragasam Priyanthi N.P. , Kakutani Leesa M. , West Anthony P , Saturday Greg , Lee Yu E. , Gao Han , Jette Claudia A. , Lewis Mark G. , Tan Tiong K. , Townsend Alain R. , Bloom Jesse D. , Munster Vincent J. , Bjorkman Pamela J. 
Published: March 2022

AbstractTo combat future SARS-CoV-2 variants and spillovers of SARS-like betacoronaviruses (sarbecoviruses) threatening global health, we designed mosaic nanoparticles presenting randomly-arranged sarbecovirus spike receptor-binding domains (RBDs) to elicit antibodies against conserved/relatively-occluded, rather than variable/immunodominant/exposed, epitopes. We compared immune responses elicited by mosaic-8 (SARS-CoV-2 and seven animal sarbecoviruses) and homotypic (only SARS-CoV-2) RBD-nanoparticles in mice and macaques, observing stronger responses elicited by mosaic-8 to mismatched (not on nanoparticles) strains including SARS-CoV and animal sarbecoviruses. Mosaic-8 immunization showed equivalent neutralization of SARS-CoV-2 variants including Omicron and protected from SARS-CoV-2 and SARS-CoV challenges, whereas homotypic SARS-CoV-2 immunization protected only from SARS-CoV-2 challenge. Epitope mapping demonstrated increased targeting of conserved epitopes after mosaic-8 immunization. Together, these results suggest mosaic-8 RBD-nanoparticles could protect against SARS-CoV-2 variants and future sarbecovirus spillovers.
Distinct regulation ofHoxgenes by Polycomb Group genes in a crustacean
Authors: Sun Dennis A , Takahashi Yuri , Chang Rebecca J , Patel Nipam H 
Published: March 2022

AbstractNon-insect crustaceans exhibit tremendous body plan diversity. The evolution of diverse patterns ofHoxgene expression has been implicated as a primary driver of body plan evolution between crustacean groups, but the mechanisms underlyingHoxregulatory evolution remain unknown. We identify Polycomb and Trithorax Group proteins, crucial for properHoxregulation across bilaterians, in the genome of the amphipod crustaceanParhyale hawaiensis, and demonstrate their essential functions in crustaceanHoxregulation and embryonic development using CRISPR-Cas9 mutagenesis. Examination ofHoxmisexpression patterns between individualHoxgenes with respect to timing, tissue, and PcG mutant gene in mutant embryos reveals that each crustaceanHoxgene follows its own idiosyncratic regulatory mechanism. These results suggest a distinct regulation ofHoxgenes that may have enabled crustacean body plan evolution.Primary Findings- The genome of the amphipod crustaceanParhyale hawaiensiscontains all core Polycomb Group (PcG) and Trithorax Group (TrxG) proteins- CRISPR-Cas9 mutagenesis of PcG proteins induces homeotic transformations and misexpression ofHoxgenes that differ from similar experiments in insects- PcG knockout embryos show proper initiation ofHoxexpression boundaries at early developmental stages- Each of the three posteriorHoxgenes inParhyaledisplays distinct patterns of misexpression in response to PcG knockout-Hoxregulation appears to occur via different mechanisms in the nervous system vs. limbs- PcG phenotypes reveal the potential for distinct layers ofHoxregulation in crustaceans
Genetically engineered MRI-trackable extracellular vesicles as SARS-CoV-2 mimetics for mapping ACE2 bindingin vivo
Authors: Galisova Andrea , Zahradnik Jiri , Allouche-Arnon Hyla , Morandi Mattia I. , Karam Paula Abou , Avinoam Ori , Regev-Rudzki Neta , Schreiber Gideon , Bar-Shir Amnon 
Published: March 2022

AbstractThe elucidation of viral-receptor interactions and an understanding of virus-spreading mechanisms are of great importance, particularly in the era of pandemic. Indeed, advances in computational chemistry, synthetic biology, and protein engineering have allowed precise prediction and characterization of such interactions. Nevertheless, the hazards of the infectiousness of viruses, their rapid mutagenesis, and the need to study viral-receptor interactions in a complexin vivosetup, call for further developments. Here, we show the development of biocompatible genetically engineered extracellular vesicles (EVs) that display the receptor binding domain (RBD) of SARS-CoV-2 on their surface as coronavirus mimetics (EVsRBD). Loading EVsRBDwith iron oxide nanoparticles makes them MRI-visible, and thus, allows mapping of the binding of RBD to ACE2 receptors non-invasively in live subjects. Importantly, the proposed mimetics can be easily modified to display the RBD of SARS-CoV-2mutants, namely Delta and Omicron, allowing rapid screening of newly raised variants of the virus. The proposed platform thus shows relevance and cruciality in the examination of quickly evolving pathogenic viruses in an adjustable, fast, and safe manner.
Changes of Mutations and Copy-number and Enhanced Cell Migration during Breast Tumorigenesis
Authors: Lee Seung Hyuk T. , Kim Joon Yup , Kim Peter , Dong Zhipeng , Su Chia-Yi , Ahn Eun Hyun 
Published: March 2022

AbstractAlthough cancer stem cells (CSCs) play a major role in tumorigenesis and metastasis, the role of genetic alterations in invasiveness of CSCs is still unclear. Tumor microenvironment signals, such as extracellular matrix (ECM) composition, significantly influence cell behaviors. Unfortunately, these signals are often lost inin vitrocell culture. This study determines putative CSC populations, examines genetic changes during tumorigenesis of human breast epithelial stem cells, and investigates single-cell migration properties on ECM-mimetic platforms. Whole exome sequencing data indicate that tumorigenic cells have a higher somatic mutation burden than non-tumorigenic cells, and that mutations exclusive to tumorigenic cells exhibit higher predictive deleterious scores. Tumorigenic cells exhibit distinct somatic copy number variations (CNVs) including gain of duplications in chromosomes 5 and 8. ECM-mimetic topography selectively enhances migration speed of tumorigenic cells, but not of non-tumorigenic cells, and results in a wide distribution of tumorigenic single-cell migration speeds, suggesting heterogeneity in cellular sensing of contact guidance cues. This study identifies mutations and CNVs acquired during breast tumorigenesis, which can be associated with enhanced migration of breast tumorigenic cells, and demonstrates that a nanotopographically-defined platform can be applied to recapitulate an ECM structure for investigating cellular migration in the simulated tumor microenvironment.
Histone marks retained during epigenetic reprogramming and their roles essential for fish early development
Authors: Fukushima Hiroto S. , Takeda Hiroyuki , Nakamura Ryohei 
Published: March 2022

SummaryReprograming of epigenetic modifications after fertilization is required for proper embryonic development and cell differentiation. However, histone modifications that escape reprogramming in non-mammalian vertebrates and their potential functional roles are poorly understood. Here, we quantitatively analyzed histone modification dynamics during reprogramming in Japanese Killifish, medaka (Oryzias latipes) embryos, and revealed that H3K27ac, H3K27me3 and H3K9me3 are retained, while H3K4 methylation is completely erased. Furthermore, we experimentally demonstrated the functional roles of such retained modifications at early stages; H3K27ac at promoters is required for proper patterning of H3K4 and H3K27 methylation at zygotic genome activation (ZGA) and specific retention of H3K9me3 at telomeric regions maintains genomic stability during cleavage stage. These results expand the understanding of diversity and conservation of reprogramming in vertebrates and unveil previously uncharacterized functions of histone modifications retained during epigenetic reprogramming.
A multiplexed in vivo approach to identify driver genes in small cell lung cancer
Authors: Lee Myung Chang , Cai Hongchen , Murray Christopher W. , Li Chuan , Shue Yan Ting , Andrejka Laura , He Andy L. , Holzem Alessandra , Drainas Alexandros P. , Ko Julie H. , Coles Garry L. , Kong Christina , Zhu Shirley , Zhu ChunFang , Wang Jason , van de Rijn Matt , Petrov Dmitri A. , Winslow Monte M. , Sage Julien 
Published: March 2022

ABSTRACTSmall cell lung cancer (SCLC) is a highly lethal form of lung cancer. The high mutation burden in SCLC cells makes it challenging to predict key drivers of SCLC from genome sequencing data, thereby hindering the identification of possible therapeutic targets. Here we develop a quantitative multiplexed approach based on lentiviral barcoding with somatic CRISPR/Cas9-mediated genome editing to functionally investigate candidate regulators of tumor initiation and growth in genetically engineered mouse models of SCLC. Lentiviral vector-mediated SCLC initiation was greatly enhanced by naphthalene pre-treatment, enabling high multiplicity of tumor clones for analysis through high-throughput sequencing methods. Based on a meta-analysis across multiple human SCLC genomic datasets, we quantified the impact of inactivating 39 genes across many candidate pathways and captured both positive and detrimental effects on SCLC initiation and progression upon gene inactivation. This analysis and subsequent validation in human SCLC cells identified TSC1 in the PI3K-AKT-mTOR pathway as a robust tumor suppressor in SCLC. This new approach should illuminate novel drivers of SCLC, facilitate the development of precision therapies for defined SCLC genotypes, and identify new therapeutic targets.
What can 1.8 billion regressions tell us about the pressures shaping high-level visual representation in brains and machines?
Authors: Conwell Colin , Prince Jacob S. , Kay Kendrick N. , Alvarez George A. , Konkle Talia 
Published: March 2022

AbstractThe rapid development and open-source release of highly performant computer vision models offers new potential for examining how different inductive biases impact representation learning and emergent alignment with the high-level human ventral visual system. Here, we assess a diverse set of 224 models, curated to enable controlled comparison of different model properties, testing their brain predictivity using large-scale functional magnetic resonance imaging data. We find that models with qualitatively different architectures (e.g. CNNs versus Transformers) and markedly different task objectives (e.g. purely visual contrastive learning versus vision-language alignment) achieve near equivalent degrees of brain predictivity, when other factors are held constant. Instead, variation across model visual training diets yields the largest, most consistent effect on emergent brain predictivity. Overarching model properties commonly suspected to increase brain predictivity (e.g. greater effective dimensionality; learnable parameter count) were not robust indicators across this more extensive survey. We highlight that standard model-to-brain linear re-weighting methods may be too flexible, as most performant models have very similar brain-predictivity scores, despite significant variation in their underlying representations. Broadly, our findings point to the importance of visual diet, challenge common assumptions about the methods used to link models to brains, and more concretely outline future directions for leveraging the full diversity of existing open-source models as tools to probe the common computational principles underlying biological and artificial visual systems.
STEPS 4.0: Fast and memory-efficient molecular simulations of neurons at the nanoscale
Authors: Chen Weiliang , Carel Tristan , Awile Omar , Cantarutti Nicola , Castiglioni Giacomo , Cattabiani Alessandro , Marmol Baudouin Del , Hepburn Iain , King James G , Kotsalos Christos , Kumbhar Pramod , Lallouette Jules , Melchior Samuel , Schürmann Felix , De Schutter Erik 
Published: March 2022

AbstractRecent advances in computational neuroscience have demonstrated the usefulness and importance of stochastic, spatial reaction-diffusion simulations. However, ever increasing model complexity renders traditional serial solvers, as well as naive parallel implementations, inadequate. This paper introduces a new generation of the STochastic Engine for Pathway Simulation (STEPS) project, denominated STEPS 4.0, and its core components which have been designed for improved scalability, performance, and memory efficiency. STEPS 4.0 aims to enable novel scientific studies of macroscopic systems such as whole cells while capturing their nanoscale details. This class of models is out of reach for serial solvers due to the vast quantity of computation in such detailed models, and also out of reach for naive parallel solvers due to the large memory footprint. Based on a distributed mesh solution, we introduce a new parallel stochastic reaction-diffusion solver and a deterministic membrane potential solver in STEPS 4.0. The distributed mesh, together with improved data layout and algorithm designs, significantly reduces the memory footprint of parallel simulations in STEPS 4.0. This enables massively parallel simulations on modern HPC clusters and overcomes the limitations of the previous parallel STEPS implementation. Current and future improvements to the solver are not sustainable without proper software engineering practices. For this reason, we also give an overview of how the STEPS codebase and the development environment have been updated to follow modern software development practices. We benchmark performance improvement and memory footprint on three published models with different complexities, from a simple spatial stochastic reaction-diffusion model, to a more complex one that is coupled to a deterministic membrane potential solver to simulate the calcium burst activity of a Purkinje neuron. Simulation results of these models suggest that the new solution dramatically reduces the per-core memory consumption by more than a factor of 30, while maintaining similar or better performance and scalability.