bluuebunny/crossref_metadata_2025_split huggingface dataset:
CAT – A Computational Anatomy Toolbox for the Analysis of Structural MRI Data
Authors: Gaser Christian , Dahnke Robert , Thompson Paul M , Kurth Florian , Luders Eileen ,   Alzheimer’s Disease Neuroimaging Initiative
Published: June 2022

AbstractA large range of sophisticated brain image analysis tools have been developed by the neuroscience community, greatly advancing the field of human brain mapping. Here we introduce theComputational Anatomy Toolbox(CAT) – a powerful suite of tools for brain morphometric analyses with an intuitive graphical user interface, but also usable as a shell script. CAT is suitable for beginners, casual users, experts, and developers alike providing a comprehensive set of analysis options, workflows, and integrated pipelines. The available analysis streams – illustrated on an example dataset – allow for voxel-based, surface-based, as well as region-based morphometric analyses. Notably, CAT incorporates multiple quality control options and covers the entire analysis workflow, including the preprocessing of cross-sectional and longitudinal data, statistical analysis, and the visualization of results. The overarching aim of this article is to provide a complete description and evaluation of CAT, while offering a citable standard for the neuroscience community.
To Smooth or not to Smooth: Enhancing Specificity While Maintaining Sensitivity
Authors: Luders Eileen , Dahnke Robert , Gaser Christian ,   Alzheimer’s Disease Neuroimaging Initiative
Published: June 2022

AbstractTraditionally, when conducting voxel- or vertex-wise analyses in neuroimaging studies, it seemed imperative that brain data are convoluted with a Gaussian kernel, a procedure known as “spatial smoothing”. However, we suggest that – under certain conditions – smoothing may be omitted for the benefit of an improved regional specificity. We demonstrate the suitability of this omission by combining high-dimensional spatial registration and threshold-free cluster enhancement (TFCE) in a sample of 754 brains. Our findings revealed that, without smoothing, it is possible to capture brain atrophy within the hippocampal complex while dissociating neighboring areas (cornu ammonis, dentate gyrys, subiculum, and amygdala). In contrast, the traditional smoothing step would result in a single hippocampal cluster (the larger the smoothing kernel, the lower the specificity). Supplemental analyses not only varying the size of the smoothing kernel, but also the size of the sample, the signal-to-noise ratio, as well as the accuracy of the spatial registration confirm that no smoothing (or less smoothing) leads to increased specificity while maintaining sensitivity, at least for small-scale structures (e.g., hippocampus and amygdala). Nevertheless, classic analyses based on smoothed data will continue to provide important insights, especially for large-scale structures (e.g., cortical regions).
Effects of habitat management on rodent diversity, abundance, and virus infection dynamics
Authors: Mull Nathaniel , Schexnayder Amy , Stolt Abigail , Sironen Tarja , Forbes Kristian M. 
Published: June 2022

AbstractBiodiversity is necessary for healthy ecosystem functioning. As anthropogenic factors continue to degrade natural areas, habitat management is needed to restore and maintain biodiversity. However, the impacts of different habitat management regimes on ecosystems have largely focused on vegetation analyses, with limited evaluation of downstream effects on wildlife.We compared the effects of prairie management regimes (controlled burning, cutting/haying, or no active management) on rodent communities and the viruses they hosted. Rodents were trapped in 13 existing prairie sites in Northwest Arkansas, USA during 2020 and 2021. Rodent blood samples were screened for antibodies against three common rodent-borne virus groups: orthohantaviruses, arenaviruses, and orthopoxviruses.We captured 616 rodents across 5953 trap nights. Burned and unmanaged sites had similarly high abundance and diversity (H), but burned sites had a greater proportion of grassland specialists than control sites; cut sites had the highest proportion of grassland specialist species but the lowest rodent abundance and diversity.A total of 38 rodents were seropositive for one of the three virus groups (34 orthohantavirus, three arenavirus, and one orthopoxvirus). Thirty-six seropositive individuals were found in burned sites, and two orthohantavirus-seropositive individuals were found in cut sites. Cotton rats and prairie voles, two grassland specialists, accounted for 97% of the rodents seropositive for orthohantavirus, and heavier individuals were more likely to be seropositive than lighter individuals.Policy implications: Our study indicates that controlled burns lead to a diverse and abundant community of grassland rodent species when compared to other management regimes; as keystone taxa, these results also have important implications for many other species in food webs. Higher prevalence of antibodies against rodent-borne viruses in burned prairies shows an unexpected consequence likely resulting from these community structures. Ultimately, these results provide empirical evidence that can inform prairie grassland restoration and ongoing management strategies.
Synaptic Spinules are Reliable Indicators of Excitatory Presynaptic Bouton Size and Strength in CA1 Hippocampus
Authors: Gore Ashley , Yurina Amaliya , Yukevich-Mussomeli Anastasia , Nahmani Marc 
Published: June 2022

AbstractSynaptic spinules are thin, finger-like projections from one neuron that become fully embedded within the presynaptic or postsynaptic compartments of another neuron. While spinules are a conserved feature of synapses across the animal kingdom, their specific function(s) remain unknown. Recent focused ion beam scanning electron microscopy (FIB-SEM) image volume analyses have demonstrated that spinules are embedded within ∼ 25% of excitatory boutons in mammalian primary visual cortex, yet the diversity of spinule sizes, origins, and ultrastructural relationship to their boutons remained unclear. To begin to uncover the function of synaptic spinules, we sought to determine the abundance, origins, and 3D ultrastructure of spinules embedded within excitatory presynaptic spinule-bearing boutons (SBBs) in mammalian CA1 hippocampus and compare these boutons with presynaptic boutons bereft of spinules (non-SBBs). Accordingly, we performed a comprehensive 3D analysis of every excitatory presynaptic bouton, their embedded synaptic spinules, and postsynaptic densities, within a 5 nm isotropic FIB-SEM image volume from CA1 hippocampus of an adult male rat. Surprisingly, we found that ∼74% of excitatory presynaptic boutons in this volume contained at least one spinule, suggesting that they are fundamental components of excitatory synapses in CA1. In addition, we found that SBBs are 2.5-times larger and have 60% larger PSDs than non-SBBs. Moreover, synaptic spinules within SBBs are clearly differentiated into two groups: small clathrin-coated spinules, and 29-times larger spinules without clathrin. Together, these findings suggest that the presence of a spinule is a marker for stronger and more stable presynaptic boutons in CA1, and that synaptic spinules serve at least two separable and distinct functions.
Cell types and molecular architecture of the octopus visual system
Authors: Songco-Casey Jeremea O. , Coffing Gabrielle C. , Piscopo Denise M. , Pungor Judit R. , Kern Andrew D. , Miller Adam C. , Niell Cristopher M. 
Published: June 2022

SummaryCephalopods have a remarkable visual system, with a camera-type eye, high acuity vision, and a wide range of sophisticated visual behaviors. However, the cephalopod brain is organized dramatically differently from that of vertebrates, as well as other invertebrates, and little is known regarding the cell types and molecular determinants of their visual system organization beyond neuroanatomical descriptions. Here we present a comprehensive single-cell molecular atlas of the octopus optic lobe, which is the primary visual processing structure in the cephalopod brain. We combined single-cell RNA sequencing with RNA fluorescence in situ hybridization to both identify putative molecular cell types and determine their anatomical and spatial organization within the optic lobe. Our results reveal six major neuronal cell classes identified by neurotransmitter/neuropeptide usage, in addition to non-neuronal and immature neuronal populations. Moreover, we find that additional markers divide these neuronal classes into subtypes with distinct anatomical localizations, revealing cell type diversity and a detailed laminar organization within the optic lobe. We also delineate the immature neurons within this continuously growing tissue into subtypes defined by evolutionarily conserved fate specification genes as well as novel cephalopod- and octopus-specific genes. Together, these findings outline the organizational logic of the octopus visual system, based on functional determinants, laminar identity, and developmental markers/pathways. The resulting atlas presented here delineates the “parts list” of the neural circuits used for vision in octopus, providing a platform for investigations into the development and function of the octopus visual system as well as the evolution of visual processing.HighlightsSingle-cell RNA sequencing coupled with RNA fluorescence in situ hybridization produces a molecular taxonomy of cell types in the octopus visual system.Six major neuronal cell classes are delineated based on neurotransmitters/neuropeptides, and are further subdivided based on laminar organization and additional marker genes.Immature neurons are divided into multiple transcriptional subgroups that correspond to mature cell types, delineated by expression of genes known for their developmental roles in other organisms as well as apparent novel genes.This atlas provides the foundation for future studies of the function, development, and comparative evolution of visual processing in cephalopods.
Plate-Q: A Frugal Microplate-Reader for Bacterial Signal Quantification
Authors: Sendilraj Varun , Gulati Madhav , Standeven Janet , Bhamla Saad 
Published: June 2022

AbstractMicroplate readers are laboratory instruments used to measure biological properties and reactions within a microplate. A microplate consists of small wells in which separated reactions take place. These reactions convert the progression of biochemical processes into optical signals. A microplate reader detects these signals and quantifies a parameter of interest. Most lab-grade microplate readers can cost up to $20,000, making them unaffordable for underfunded labs and developing countries. In light of this, we developed Plate-Q, a $150 frugal microplate reader capable of quantifying green fluorescence protein and optical density of bacterial samples from 96-hole microplates. Rather than using optical sensors found in laboratory microplate readers, Plate-Q takes advantage of a Raspberry-Pi camera to capture images of a microplate and manually extract brightness values using computer vision algorithms. Plate-Q utilizes 440nm excitation lights with a 510nm emission filter to measure GFP expression and 600nm lights for optical density readings. However, camera-based technologies have three main problems: lens distortion, signal interference, and brightness calculations. Plate-Q addresses these problems through camera movement over the well-plate, image optimization, 3D printed well-plate covers and mathematical regression algorithms. In testing with fusarium dual-plasmid biosensors, Plate-Q showed comparable accuracy to commercial microplate readers with an average error of .034 and a root mean squared error of .012 for fluorescence and an average error of .045 and root mean squared error of .023 error for optical density. Users can scan for other fluorescent proteins by changing the light source and filter for different wavelengths. With all aspects of Plate-Q being open source, labs worldwide can quantify samples in an affordable and time-efficient manner.
Complex multiple introductions drive fall armyworm invasions into Asia and Australia
Authors: Rane R , Walsh TK , Lenancker P , Gock A , Dao TH , Nguyen VL , Khin TN , Amalin D , Chittarath K , Faheem M , Annamalai S , Thanarajoo SS , Trisyono YA , Khay S , Kim J , Kuniata L , Powell K , Kalyebi A , Otim MH , Nam K , d’Alençon E , Gordon KHJ , Tay WT 
Published: June 2022

AbstractThe fall armyworm (FAW)Spodoptera frugiperdais thought to have undergone a rapid ‘west-to-east’ spread since 2016 when it was first identified in western Africa. Between 2018 and 2020, it was also recorded from South Asia (SA), Southeast Asia (SEA), East Asia (EA), and Pacific/Australia (PA). Population genomic analyses enabled the understanding of pathways, population sources, and gene flow in this notorious agricultural pest species. Using neutral single nucleotide polymorphic (SNP) DNA markers, we detected genome introgression that suggested most populations were overwhelmingly C- and R-strain hybrids. SNP and mitochondrial DNA markers identified multiple introductions that were most parsimoniously explained by anthropogenic-assisted spread, i.e., associated with international trade of live/fresh plants and plant products, and involved ‘bridgehead populations’ in countries to enable successful pest establishment in neighbouring countries. Distinct population genomic signatures between Myanmar and China do not support the ‘African origin spread’ nor the ‘Myanmar source population to China’ hypotheses. Significant genetic differentiation between populations from different Australian states supported multiple pathways involving distinct SEA populations. Our study identified Asia as a biosecurity hotspot and a FAW genetic melting pot, and demonstrated the use of genome analysis to disentangle preventable human-assisted pest introductions from unpreventable natural pest spread.
Allosteric feedback inhibition of deoxy-D-xylulose-5-phosphate synthase involves monomerization of the active dimer
Authors: Di Xueni , Ortega-Alarcon David , Kakumanu Ramu , Baidoo Edward E.K. , Velazquez-Campoy Adrian , Rodríguez-Concepción Manuel , Perez-Gil Jordi 
Published: June 2022

AbstractIsoprenoids are a very large and diverse family of metabolites required by all living organisms. All isoprenoids derive from the double-bond isomers isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP), which are produced by the methylerythritol 4-phosphate (MEP) pathway in bacteria and plant plastids. Understanding the regulation of the MEP pathway, probably the main metabolic pathway elucidated in this century, is a must for the rational design of biotechnological endeavors aimed at increasing isoprenoid contents in microbial and plant systems. It has been reported that IPP and DMAPP feedback regulate the activity of deoxyxylulose 5-phosphate (DXS), a dimeric enzyme catalyzing the main flux-controlling step of the MEP pathway. Here we provide experimental insights on the underlying mechanism. Our data show that direct allosteric binding of IPP and DMAPP to bacterial and plant DXS promotes monomerization of the enzyme. This allows a fast response to a sudden increase or decrease in IPP/DMAPP supply by rapidly shifting the dimer-monomer equilibrium accordingly. DXS monomers expose hydrophobic domains that are hidden in the dimer, resulting in aggregation and eventual degradation. Removal of monomers that would otherwise be available for dimerization and enzyme reactivation appears as a more drastic response in case of persistent IPP/DMAPP overabundance (e.g., by a blockage in their conversion to downstream isoprenoids). Our model provides a mechanistic explanation of how IPP and DMAPP supply can be adapted to changes in their demand and it also explains the changes in DXS protein levels observed after long-term interference of the MEP pathway flux.Significance StatementIsoprenoids are a vast family of organic compounds with essential roles in respiration, photosynthesis, photoprotection, membrane structure, and signaling. Many of them have great economic and nutritional relevance as pigments, aromas, drugs or phytonutrients. Despite their functional and structural diversity, they all derive from the same five-carbon precursors. We show that these precursors feedback-regulate their own synthesis in bacteria and plant plastids by allosterically shifting the dimer:monomer equilibrium of the enzyme that catalyzes the first step of their biosynthetic pathway towards the inactive monomeric form. This evolutionary conserved mechanism allows for both short-term (immediate) and long-term (sustained) control of the pathway flux, and its manipulation could be critical for the rational engineering of high-value isoprenoid products in bacterial and plant systems.
A Development-Inspired Niche for Homeostatic Human Mini-Intestines
Authors: Childs Charlie J. , Holloway Emily M. , Sweet Caden W. , Tsai Yu-Hwai , Wu Angeline , Wu Joshua H. , Pellón Cardenas Oscar , Capeling Meghan M. , Eiken Madeline , Zwick Rachel , Palikuqi Brisa , Trentesaux Coralie , Zhang Charles , Glass Ian , Loebel Claudia , Yu Qianhui , Camp J. Gray , Sexton Jonathan Z. , Klein Ophir , Verzi Michael P. , Spence Jason R. 
Published: June 2022

SummaryEpithelial organoids derived from intestinal tissue, also referred to as mini-intestines or mini-guts, recapitulate many aspects of the organ in vitro and can be used for biological discovery, personalized medicine, and drug development. Murine intestinal organoids represent a homeostatic system that balances stem cell maintenance within a crypt-like compartment and differentiation within a villus-like compartment1–3. However, this homeostatic balance and spatial organization has not been achieved with human intestinal organoids4. Here, we leverage single cell RNA-seq data (scRNA-seq) and high-resolution imaging to interrogate the developing human intestinal stem cell niche. We identified an EGF-family member, EPIREGULIN (EREG), as uniquely expressed in the developing crypt, and found that EREG can take the place of EGF as an in vitro niche factor. Unlike EGF, which leads to growth of thin-walled cystic organoids, EREG-organoids are spatially resolved into budded and proliferative crypt domains and a differentiated villus-like central lumen. Transcriptomics and epigenomics showed that EREG-organoids are globally similar to the native intestine while EGF-organoids have an altered chromatin landscape, downregulate the master intestinal transcription factor CDX25,6, and ectopically express stomach genes.
Characterization of environmental effects on flowering and plant architecture in an everbearing strawberry F1-hybrid by meristem dissection and gene expression analysis
Authors: Samad Samia , Rivero Rodmar , Kalyandurg Pruthvi Balachandra , Vetukuri Ramesh , Heide Ola M. , Sønsteby Anita , Khalil Sammar 
Published: June 2022

AbstractFloral transition in the cultivated everbearing strawberry is a hot topic because these genotypes flower perpetually and are difficult to maintain in a non-flowering state. However, it has rarely been studied using morphogenetic and molecular analyses simultaneously. We therefore examined morphogenetic effects and the activation of genes involved in floral induction and initiation in seedlings of an everbearing F1-hybrid. Seedlings were grown at 12, 19, and 26°C under 10-h SD and 20-h LD conditions. We observed a strong environmental influence on meristem development and a FLOWERING LOCUS T1 (FaFT1)–SUPPRESSOR OF OVEREXPRESSION OF CONSTANS1 (FaSOC1) pathway similar to that in the everbearing woodland strawberry. The everbearing cultivar showed typical features of a quantitative LD plant, flowering earlier under LD than SD conditions at all temperatures. We also found that floral induction is facilitated by FaFT1 upregulation under LD conditions, while FaSOC1 upregulation in the apex leads to photoperiod-independent floral initiation. Moreover, we confirmed the strawberry meristem identity gene FRUITFULL (FaFUL) can also be used as an early indicator of floral initiation in EB cultivars. This study also highlights the advantages of using seed-propagated F1-hybrids for genetic studies because are genetically identical, and not biased by a previous flowering history.
Online trajectory optimization and guidance algorithm for space interceptors with nonlinear terminal constraints via convex programming
Authors: Li Yuan , Sun Ruisheng , Chen Wei 
Published: June 2022

Purpose
In this paper, an online convex optimization method for the exoatmospheric ascent trajectory of space interceptors is proposed. The purpose of this paper is to transform the original trajectory optimization problem into a sequence of convex optimization subproblems.

Design/methodology/approach
For convenience in calculating accuracy and efficiency, the complex nonlinear terminal orbital elements constraints are converted into several quadratic equality constraints, which can be better computed by a two-step correction method during the iteration. First, the nonconvex thrust magnitude constraint is convexified by the lossless convexification technique. Then, discretization and successive linearization are introduced to transform the original problem into a sequence of one convex optimization subproblem, considering different flight phases. Parameters of trust-region and penalty are also applied to improve the computation performance. To correct the deviation in real time, the iterative guidance method is applied before orbit injection.

Findings
Numerical experiments show that the algorithm proposed in this paper has good convergence and accuracy. The successive progress can converge in a few steps and 3–4 s of CPU time. Even under engine failure or mission change, the algorithm can yield satisfactory results.

Practical implications
The convex optimization method presented in this paper is expected to generate a reliable optimal trajectory rapidly in different situations and has great potential for onboard applications of space interceptors.

Originality/value
The originality of this paper lies in the proposed online trajectory optimization method and guidance algorithm of the space inceptors, especially for onboard applications in emergency situations.
Board characteristics and sustainability reporting: a case of listed firms in East Africa
Authors: Githaiga Peter Nderitu , Kosgei James Kibet 
Published: June 2022

Purpose
This study aims to investigate the influence of board characteristics on sustainability reporting among listed firms in East Africa.

Design/methodology/approach
The study uses a sample of 79 listed firms drawn from East African securities exchanges and data from 2011 to 2020. Sustainability reporting is measured using Global Reporting Initiative, and the data is analyzed by using three-panel data estimation models – fixed effect, random effect and the generalized method of moments.

Findings
The results reveal that board gender diversity, board financial expertise and board independence are positively and significantly associated with sustainability reporting. Conversely, board size has a negative and significant effect on sustainability reporting.

Practical implications
The findings from the study provide valuable insights to firm owners and policymakers. The study highlights the importance of directors with financial knowledge, a high proportion of non-executive directors and women representation in board and smaller boards as a strategy that will help firms improve sustainability practices and reporting in East Africa.

Social implications
Results of this study underscore the effect of corporate governance (CG) dimensions on social responsibility activities, such as philanthropy, emission reduction and waste management initiatives as reported through sustainability responsibility.

Originality/value
This study adds to the growing literature on the relationship between CG attributes and sustainability reporting from a developing economy perspective. Specifically, the study examines how board gender diversity, size, independence and financial expertise affect sustainability reporting adoption.