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A novel method for clustering cellular data to improve classification

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Neural Regeneration Research 2025年第9期20卷 2697-2705页

作者： Diek w.wheeler Giorgio A.Ascoli Center for Neural Informatics Structures&PlasticityKrasnow Institute for Advanced Study Bioengineering Department Volgenau School of Engineering George Mason University FairfaxVAUSA

Many fields,such as neuroscience,are experiencing the vast prolife ration of cellular data,underscoring the need fo r organizing and interpreting large datasets.A popular approach partitions data into manageable subsets via hierarchical clustering,but objective methods to determine the appropriate classification granularity are *** recently introduced a technique to systematically identify when to stop subdividing clusters based on the fundamental principle that cells must differ more between than within *** we present the corresponding protocol to classify cellular datasets by combining datadriven unsupervised hierarchical clustering with statistical *** general-purpose functions are applicable to any cellular dataset that can be organized as two-dimensional matrices of numerical values,including molecula r,physiological,and anatomical *** demonstrate the protocol using cellular data from the Janelia MouseLight project to chara cterize morphological aspects of neurons.

关键词： cellular data clustering dendrogram data classification Levene's one-tailed statistical test unsupervised hierarchical clustering

Genistein:a possible solution for the treatment of Alzheimer’s disease

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Neural Regeneration Research 2025年第10期20卷 2903-2905页

作者： Karolina Pierzynowska Bartosz Karaszewski Grzegorz węgrzyn Department of Molecular Biology University of GdanskGdanskPoland Gdansk Polandand Department of Adult NeurologyFaculty of MedicineMedical University of GdanskGdanskPoland

Neurodegenerative diseases are defined as disorders resulting from the slow and progressive loss of function and eventual death of neural cells that result from the primary pathology of nervous *** can lead to severe nervous system dysfunction,eventually affecting multiple organs and *** hundred neurodegenerative diseases have been described,and owing to their prevalence,severity.

关键词： organs Alzheimer death

Glia-to-neuron reprogramming to the rescue?

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Neural Regeneration Research 2025年第5期20卷 1395-1396页

作者： Jack w.Hickmott Cindi M.Morshead Department of Surgery University of TorontoTorontoONCanada Donnelly Centre for Cellular and Biomolecular Research TorontoONCanada Institute of Biomedical Engineering University of TorontoTorontoONCanada the KItE Research Institute Toronto Rehabilitation InstituteUniversity Health NetworkTorontoONCanada

Over the last two decades,the dogma that cell fate is immutable has been increasingly challenged,with important implications for regenerative *** brea kth rough discovery that induced pluripotent stem cells could be generated from adult mouse fibroblasts is powerful proof that cell fate can be *** exciting extension of the discovery of cell fate impermanence is the direct cellular reprogram ming hypothesis-that terminally differentiated cells can be reprogrammed into other adult cell fates without first passing through a stem cell state.

关键词： programming passing proof

Is the propensity to emit alarm calls associated with health status?

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Current Zoology 2020年第6期66卷 607-614页

作者： Austin L.nash Alexandra H.M.Jebb Daniel t.BLUMStEIN Department of Ecology and Evolutionary Biology University of Colorado265 UCBBoulderCO 80309USA School of Biological Sciences University of AberdeenZoology BuildingTillydrone AvenueAberdeenAB242TZUK the Rocky Mountain Biological Laboratory Box 519 Crested ButteCO 81224USA Department of Ecology and Evolutionary Biology University of California621 Young Drive SouthLos AngelesCA 90095-1606USA

the production and structure of animal signals may depend on an individual's health status and may provide more than one type of information to *** alarm calls are not typically viewed as health condition dependent,recent studies have suggested that their structure,and possibly their propensity to be emitted,depends on an individual,s health condition and *** asked whether the propensity of yellow-bellied marmots(Marmota flaviventer)to emit calls is influen ced by their immuno logical or parasite status,by quantifying both trap-elicited and n atural calling rates as a function of their neutrophil-to-lymphocyte(NL)ratio,the presence of a blood borne trypanosome,and the presenee of several intestinal parasites(Eimeria sp.,Entamoeba sp.,and Ascaris sp.).we fitted mixed effects models to determine if the health measures we collected were associated with the probability of calling in a trap and with annual rates of natural alarm *** infected with a blood-borne trypanosome were marginally more likely to call naturally and when trapped,while those infected with the intestinal parasite Ascaris were less likely to call when *** ratio was not directly associated with in-trap calling probability,but males were more likely to call when they had higher NL ***,health conditions,such as parasite infection and immune system activation,can modulate the production of alarm signals and potentially provide in formation to both predators and prey about the caller's *** experiments are required to confirm if receivers use such information.

关键词： alarm calling animal communication antipredator behavior condition dependenee immune function parasites

High-resolution flood modeling of urban areas using MSN_Flood

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water Science and Engineering 2017年第3期10卷 175-183页

作者： Michael Hartnett Stephen nash Department of Civil Engineering National University of IrelandGalwayIreland

Although existing hydraulic models have been used to simulate and predict urban flooding, most of these models are inadequate due to the high spatial resolution required to simulate flows in urban floodplains. Nesting high-resolution subdomains within coarser-resolution models is an efficient solution for enabling simultaneous calculation of flooding due to tides, surges, and high river flows. MSN_Flood has been developed to incorporate moving boundaries around nested domains, permitting alternate flooding and drying along the boundary and in the interior of the domain. Ghost cells adjacent to open boundary cells convert open boundaries, in effect, into internal boundaries. the moving boundary may be multi-segmented and non-continuous, with recirculating flow across the boundary. when combined with a bespoke adaptive interpolation scheme, this approach facilitates a dynamic internal boundary. Based on an alternating-direction semi-implicit finite difference scheme,MSN_Flood was used to hindcast a major flood event in Cork City resulting from the combined pressures of fluvial, tidal, and storm surge processes. the results show that the model is computationally efficient, as the 2-m high-resolution nest is used only in the urban flooded ***, lower-resolution nests are used. the results also show that the model is highly accurate when compared with measured data. the model is capable of incorporating nested sub-domains when the nested boundary is multi-segmented and highly complex with lateral gradients of elevation and velocities. this is a major benefit when modelling urban floodplains at very high resolution.

关键词： Multi-scale nesting Surge-fluvial flooding Urban flooding Multi-segmented boundary Moving boundary

Dynamic modeling of a three-dimensional braided composite thin plate considering braiding directions

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Applied Mathematics and Mechanics(English Edition) 2025年第1期46卷 123-138页

作者： Chentong GAO Huiyu SUN Jianping GU w.M.HUANG College of Aerospace Engineering Nanjing University of Aeronautics and Astronautics School of Mechanical and Aerospace Engineering Nanyang Technological University Jiangsu Key Laboratory of Advanced Structural Materials and Application technology School of Materials Science and EngineeringNanjing Institute of Technology

Currently, there are a limited number of dynamic models available for braided composite plates with large overall motions, despite the incorporation of three-dimensional(3D) braided composites into rotating blade components. In this paper, a dynamic model of 3D 4-directional braided composite thin plates considering braiding directions is established. Based on Kirchhoff's plate assumptions, the displacement variables of the plate are expressed. By incorporating the braiding directions into the constitutive equation of the braided composites, the dynamic model of the plate considering braiding directions is obtained. the effects of the speeds, braiding directions, and braided angles on the responses of the plate with fixed-axis rotation and translational motion, respectively, are investigated. this paper presents a dynamic theory for calculating the deformation of 3D braided composite structures undergoing both translational and rotational motions. It also provides a simulation method for investigating the dynamic behavior of non-isotropic material plates in various applications.

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An integrated measurement and modeling methodology for estuarine water quality management

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water Science and Engineering 2015年第1期8卷 9-19页

作者： Michael Hartnett Stephen nash Department of Civil Engineering National University of Ireland

this paper describes research undertaken by the authors to develop an integrated measurement and modeling methodology for water quality management of estuaries. the approach developed utilizes modeling and measurement results in a synergistic manner. Modeling results were initially used to inform the field campaign of appropriate sampling locations and times, and field data were used to develop accurate models. Remote sensing techniques were used to capture data for both model development and model validation. Field surveys were undertaken to provide model initial conditions through data assimilation and determine nutrient fluxes into the model domain. From field data, salinity re- lationships were developed with various water quality parameters, and relationships between chlorophyll a concentrations, transparency, and light attenuation were also developed. these relationships proved to be invaluable in model development, particularly in modeling the growth and decay of chlorophyll a. Cork Harbour, an estuary that regularly experiences summer algal blooms due to anthropogenic sources of nutrients, was used as a case study to develop the methodology. the integration of remote sensing, conventional fieldwork, and modeling is one of the novel aspects of this research and the approach developed has widespread applicability.

关键词： Estuarine modeling Hydrodynamics water quality management Nutrients Phytoplankton Field measurements Remote sensing

Controlling the properties of surface acoustic waves using graphene

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Nano Research 2016年第3期9卷 685-691页

作者： Lokeshwar Bandhu Geoffrey R. nash College of Engineering Mathematics and Physical Sciences University of Exeter Exeter EX4 4QF UK

Surface acoustic waves （SAws） are elastic waves that propagate on the surface of a solid, much like waves on the ocean, with SAw devices used widely in communication and sensing. the ability to dynamically control the properties of SAws would allow the creation of devices with improved performance or new functionality. However, so far it has proved extremely difficult to develop a practical way of achieving this control. In this paper we demonstrate voltage control of SAws in a hybrid graphene-lithium niobate device. the velocity shift of the SAws was measured as the conductivity of the graphene was modulated using an ion-gel gate, with a 0.1% velocity shift achieved for a bias of approximately 1 V. this velocity shift is comparable to that previously achieved in much more complicated hybrid semiconductor devices, and optimization of this approach could therefore lead to a practical, cost-effective voltage-controlled velocity shifter. In addition, the piezoelectric fields associated with the SAw can also be used to trap and transport the charge carriers within the graphene. Uniquely to graphene, we show that the acoustoelectric current in the same device can be reversed, and switched off, using the gate voltage.

关键词： graphene sensors surface acoustic wave charge transport

Human induced pluripotent stem cell-derived therapies for regeneration after central nervous system injury

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Neural Regeneration Research 2025年第11期20卷 3063-3075页

作者： Stephen Vidman Yee Hang Ethan Ma Nolan Fullenkamp Giles w.Plant Department of Neuroscience Ohio State UniversityColumbusOHUSA

In recent years,the progression of stem cell therapies has shown great promise in advancing the nascent field of regenerative *** the non-regenerative nature of the mature central nervous system,the concept that“blank”cells could be reprogrammed and functionally integrated into host neural networks remained *** work has also demonstrated the ability of such cells to stimulate intrinsic growth programs in post-mitotic cells,such as *** embryonic stem cells demonstrated great potential in treating central nervous system pathologies,ethical and technical concerns *** barriers,along with the clear necessity for this type of treatment,ultimately prompted the advent of induced pluripotent stem *** advantage of pluripotent cells in central nervous system regeneration is multifaceted,permitting differentiation into neural stem cells,neural progenitor cells,glia,and various neuronal *** precise spatiotemporal application of extrinsic growth factors in vitro,in addition to microenvironmental signaling in vivo,influences the efficiency of this directed *** the pluri-or multipotency of these cells is appealing,it also poses the risk of unregulated differentiation and teratoma *** of the neuroectodermal lineage,such as neuronal subpopulations and glia,have been explored with varying degrees of *** the risk of cancer or teratoma formation is greatly reduced,each subpopulation varies in effectiveness and is influenced by a myriad of factors,such as the timing of the transplant,pathology type,and the ratio of accompanying progenitor ***,successful transplantation requires innovative approaches to develop delivery vectors that can mitigate cell death and support ***,host immune responses to allogeneic grafts must be thoroughly characterized and further developed to reduce the need for *** to a clinical setting wi

关键词： axon regeneration central nervous system regeneration induced pluripotent stem cells neurotrauma regenerative medicine spinal cord injury stem cell therapy