bluuebunny/crossref_metadata_2025_split huggingface dataset:
Early transcriptional similarities between two distinct neural lineages during ascidian embryogenesis
Authors: Copley Richard R , Buttin Julia , Arguel Marie-Jeanne , Williaume Géraldine , Lebrigand Kevin , Barbry Pascal , Hudson Clare , Yasuo Hitoyoshi 
Published: December 2023

AbstractIn chordates, the central nervous system arises from precursors that have distinct developmental and transcriptional trajectories. Anterior nervous systems are ontogenically associated with ectodermal lineages while posterior nervous systems are associated with mesoderm. Taking advantage of the well-documented cell lineage of ascidian embryos, we asked how the transcriptional states of the different neural lineages become similar during the course of progressive lineage restriction. We performed single-cell RNA sequencing (scRNA-seq) analyses on hand-dissected neural precursor cells of the two distinct lineages, together with those of their sister cell lineages, with a high temporal resolution covering five successive cell cycles from the 16-cell to neural plate stages. A transcription factor binding site enrichment analysis of neural specific genes at the neural plate stage revealed limited evidence for shared transcriptional control between the two neural lineages, consistent with their different ontogenies. Nevertheless, PCA analysis and hierarchical clustering showed that, by neural plate stages, the two neural lineages cluster together. Consistent with this, we identified a set of genes enriched in both neural lineages at the neural plate stage, includingmiR-124, CELF3/5/6, Zic.r-b,andEts1/2.
Model-Based Closed-Loop Control of Thalamic Deep Brain Stimulation
Authors: Tian Yupeng , Saradhi Srikar , Bello Edward , Johnson Matthew , D’Eleuterio Gabriele , Popovic Milos R. , Lankarany Milad 
Published: December 2023

AbstractClosed-loop control of deep brain stimulation (DBS) is crucial for effective and automatic treatments of various neurological disorders like Parkinson’s disease (PD) and essential tremor (ET). Manual (open-loop) DBS programming solely based on clinical observations relies on neurologists’ expertise and patients’ experience. The continuous stimulation in open-loop DBS may decrease battery life and cause side effects. On the contrary, a closed-loop DBS system utilizes a feedback biomarker/signal to track worsening (or improving) patient’s symptoms and offers several advantages compared to open-loop DBS. Existing closed-loop DBS control systems do not incorporate physiological mechanisms underlying the DBS or symptoms, for example how DBS modulates dynamics of synaptic plasticity. In this work, we proposed a computational framework for development of a model-based DBS controller where a biophysically-reasonable model can describe the relationship between DBS and neural activity, and a polynomial-based approximation can estimate the relationship between the neural and behavioral activity. A controller is utilized in our model in a quasi-real-time manner to find DBS patterns that significantly reduce the worsening of symptoms. These DBS patterns can be tested clinically by predicting the effect of DBS before delivering it to the patient. We applied this framework to the problem of finding optimal DBS frequencies for essential tremor given EMG recordings solely. Building on our recent network model of ventral intermediate nuclei (Vim), the main surgical target of the tremor, in response to DBS, we developed a biophysically-reasonable simulation in which physiological mechanisms underlying Vim-DBS are linked to symptomatic changes in EMG signals. By utilizing a PID controller, we showed that a closed-loop system can track EMG signals and adjusts the stimulation frequency of Vim-DBS so that the power of EMG in [2, 200] Hz reaches a desired target. We demonstrated that our model-based closed-loop control system of Vim-DBS finds an appropriate DBS frequency that aligns well with clinical studies. Our model-based closed-loop system is adaptable to different control targets, highlighting its potential usability for different diseases and personalized systems.
DNA barcoding reveals an increased diversity within the genusCulex(Diptera: Culicidae) in Ireland
Authors: Curran Thomas G. , O’Hanlon Aidan , Gallagher Finán , Pedersen Rasmus S. , Zintl Annetta , Isiye Elsie , Olmeda Angela Valcarcel , O’Neill David , McDevitt Allan D. , O’Reilly Catherine , O’Meara Denise B. 
Published: December 2023

AbstractArthropod populations are changing globally due to the combined impacts of climate change, land-use transformation, globalisation and trade. Changes in arthropod populations can potentially result in the decline and extinction of some native and/or endemic species, while other species that potentially pose threats may increase. Such dynamics lead to weakened ecosystem resilience, which can facilitate the establishment and spread of species with vector capabilities, such as mosquitoes. While many of the mosquito species present in Ireland possess vector capabilities, populations have not been nationally surveyed since 1991. At that time, species identification relied on morphological examination, a method that was even then recognised as inadequate for differentiating certain species within complexes. In this study, we present the first DNA barcoding investigation of Irish mosquito populations and reveal species and hidden diversity not previously recognised in Ireland. These include two potential new species/ecotypes,Culex torrentiumandCulex pipiensformpipiens, which were recorded for the first time in Ireland. We demonstrate that barcoding with Cytochrome C Oxidase Subunit 1 (COI) based primers is suitable for the majority of species-level identifications. However, additional primer sets targeting the Internal Transcribed Spacer regions 1 and 2 (ITS1 and ITS2) were necessary to differentiate species within theCulex pipienscomplex. The multi-locus approach employed in this study can enhance national surveillance efforts, especially in monitoring mosquitoes that may transmit vector-borne diseases, and in recognising increased species diversity from a biodiversity perspective.
Estimating Genome-wide Phylogenies Using Probabilistic Topic Modeling
Authors: Khodaei Marzieh , Edwards Scott V. , Beerli Peter 
Published: December 2023

AbstractMethods for rapidly inferring the evolutionary history of species or populations with genome-wide data are progressing, but computational constraints still limit our abilities in this area. We developed an alignment-free method to infer genome-wide phylogenies and implemented it in the Python package TopicContml. The method uses probabilistic topic modeling (specifically, Latent Dirichlet Allocation or LDA) to extract ‘topic’ frequencies fromk-mers, which are derived from multilocus DNA sequences. These extracted frequencies then serve as an input for the program Contmlin the PHYLIP package, which is used to generate a species tree. We evaluated the performance of TopicContmlon simulated datasets with gaps and three biological datasets: (1) 14 DNA sequence loci from two Australian bird species distributed across nine populations, (2) 5162 loci from 80 mammal species, and (3) raw, unaligned, non-orthologous PacBiosequences from 12 bird species. Our empirical results and simulated data suggest that our method is efficient and statistically robust. We also assessed the uncertainty of the estimated relationships among clades using a bootstrap procedure.
Assembly and analysis of the genome ofNotholithocarpus densiflorus
Authors: Cai Ying , Anderson Ellis , Xue Wen , Wong Sylvia , Cui Luman , Cheng Xiaofang , Wang Ou , Mao Qing , Liu Sophie Jia , Davis John T. , Magalang Paulo R. , Schmidt Douglas , Kasuga Takao , Garbelotto Matteo , Drmanac Radoje , Kua Chai-Shian , Cannon Charles , Maloof Julin N. , Peters Brock A. 
Published: December 2023

AbstractTanoak (Notholithocarpus densiflorus) is an evergreen tree in the Fagaceae family found in California and southern Oregon. Historically, tanoak acorns were an important food source for Native American tribes and the bark was used extensively in the leather tanning process. Long considered a disjunct relictual element of the Asian stone oaks (Lithocarpus spp.), phylogenetic analysis has determined that the tanoak is an example of convergent evolution. Tanoaks are deeply divergent from oaks (Quercus) of the Pacific Northwest and comprise a new genus with a single species. These trees are highly susceptible to ‘sudden oak death’ (SOD), a plant pathogen (Phytophthora ramorum) that has caused widespread mortality of tanoaks. Here, we set out to assemble the genome and perform comparative studies among a number of individuals that demonstrated varying levels of susceptibility to SOD. First, we sequenced andde novoassembled a draft reference genome ofN. densiflorususing co-barcoded library processing methods and an MGI DNBSEQ-G400 sequencer. To increase the contiguity of the final assembly, we also sequenced Oxford Nanopore (ONT) long reads to 30X coverage. To our knowledge, the draft genome reported here is one of the more contiguous and complete genomes of a tree species published until now, with a contig N50 of ∼1.2 Mb and a scaffold N50 of ∼2.1 Mb. In addition, we sequenced 11 genetically distinct individuals and mapped these onto the draft reference genome enabling the discovery of almost 25 million single nucleotide polymorphisms and ∼4.4 million small insertions and deletions. Finally, using co-barcoded data we were able to generate complete haplotype coverage of all 11 genomes.
Systematic cross-species comparison of prefrontal cortex functional networks targeted via Transcranial Magnetic Stimulation
Authors: Berger Taylor , Xu Ting , Opitz Alexander 
Published: December 2023

AbstractTranscranial Magnetic Stimulation (TMS) is a non-invasive brain stimulation method that safely modulates neural activity in vivo. Its precision in targeting specific brain networks makes TMS invaluable in diverse clinical applications. For example, TMS is used to treat depression by targeting prefrontal brain networks and their connection to other brain regions. However, despite its widespread use, the underlying neural mechanisms of TMS are not completely understood. Non-human primates (NHPs) offer an ideal model to study TMS mechanisms through invasive electrophysiological recordings. As such, bridging the gap between NHP experiments and human applications is imperative to ensure translational relevance. Here, we systematically compare the TMS-targeted functional networks in the prefrontal cortex in humans and NHPs. To conduct this comparison, we combine TMS electric field modeling in humans and macaques with resting-state functional magnetic resonance imaging (fMRI) data to compare the functional networks targeted via TMS across species. We identified distinct stimulation zones in macaque and human models, each exhibiting variations in the impacted networks (macaque: Frontoparietal Network, Somatomotor Network; human: Frontoparietal Network, Default Network). We identified differences in brain gyrification and functional organization across species as the underlying cause of found network differences. The TMS-network profiles we identified will allow researchers to establish consistency in network activation across species, aiding in the translational efforts to develop improved TMS functional network targeting approaches.
Synaptic mechanisms modulate the spatiotemporal dynamics of striatal direct pathway neurons and motor output
Authors: Marshall John J , Xu Jian , Yeh Nai-Hsing , Yun Seongsik , Nomura Toshihiro , Armstrong John N , Parker Jones G , Contractor Anis 
Published: December 2023

AbstractStriatal spiny-projection neurons (SPNs) integrate glutamatergic inputs from the motor cortex and thalamus with neuromodulatory signals to regulate motor output.In vivoCa2+imaging has demonstrated that ensembles of direct and indirect pathway SPNs (dSPNs, iSPNs) are coactive during spontaneous movement. Co-activity is statistically greater among nearby neurons, correlates with behavioral state, and undergoes plasticity in an SPN-type-specific manner under pathological conditions. This spatially clustered co-activity could reflect shared excitatory inputs. However, whether and how synaptic mechanisms generate this distinctive spatiotemporal activity is unknown. Here, we show that the Group I metabotropic glutamate receptor 5 (mGluR5), which regulates synaptic strength at corticostriatal synapses, is a key mediator of spatially clustered SPN co-activity. Pharmacological modulation of mGluR5 signaling bidirectionally altered movement and spatially clustered dynamics, but not the absolute level of activity of dSPNs. Targeted deletion of mGluR5 in dSPNs recapitulated the effects on spatiotemporal neural dynamics and movement demonstrating a striatum-specific effect of mGluR5. Targeted deletion of mGluR5 also produced changes in the synaptic properties of dSPNs. These results show that properties of excitatory synapses influence motor function by shaping the characteristic spatially clustered patterns of co-activity that typify dSPN activationin vivo.
Does CEO power moderate the link between labor productivity and financial performance: agency theory or stewardship theory
Authors: Aliahmadi Saeid 
Published: December 2023

PurposeThis study investigates the moderating effect of CEO power on the relationship between labor productivity and financial performance in the Tehran Stock Exchange (TSE).Design/methodology/approachIn this study, the power of the CEO variable was measured using the power index method and its effect on the relationship between labor productivity and financial performance was tested using a multivariate regression. The study sample consisted of 1,040 observations and 130 firms listed on the TSE over an eight-year period between 2012 and 2019. Panel data and appropriate statistical techniques were applied to estimate models. In this study, Tobin’s Q and return on assets (ROA) are the two variables used to measure financial performance.FindingsThe results of the hypotheses show that the link between labor productivity and financial performance based on Tobin’s Q and ROA strengthens with increasing CEO power. Thus, the stewardship theory is approved on the TSE. In addition, CEO power and labor productivity have a positive impact on firm performance.Research limitations/implicationsTo the best of the author’s knowledge, this is the first study to examine the moderating impact of CEO power on the relationship between labor productivity and firms' financial performance in emerging capital markets. Therefore, the results of this study can be used by investors, board of directors, policymakers and regulations.Practical implicationsTaking into consideration the sanctions on Iran's economy during the study period and to increase the productivity and financial performance of the company, the results of this study can provide a practical guide for the board of directors to consider the characteristics of CEO power and how to choose it in the emerging capital market. Additionally, the study results show that investors should choose companies with strong CEO to invest in the Iranian capital market.Originality/valueThe current study is the first study conducted in an emerging economy to examine the moderating impact of CEO power on the link between labor productivity and financial performance.
How and when domestic and international collaboration networks influence innovation performance of SMEs: evidence from China
Authors: Lu Chang , Qi Yong , Hao Shibo , Yu Bo 
Published: December 2023

PurposeThis study aims to explore the effect of collaboration networks (domestic and international collaboration networks) on the innovation performance of small and medium-sized enterprises (SMEs). It also investigates the mediating role of business model innovation, the moderating role of entrepreneurial orientation and government institutional support between them.Design/methodology/approachHierarchical regression analysis is adopted to test the hypotheses based on survey data provided by 223 manufacturing SMEs in China.FindingsThe results reveal that domestic and international collaboration networks positively affect SMEs' innovation performance. Business model innovation mediates domestic and international collaboration networks-SMEs’ innovation performance relationships. Entrepreneurial orientation positively moderates international collaboration networks–SMEs’ innovation performance relationship, and government institutional support positively moderates domestic and international collaboration networks–SMEs’ innovation performance relationships.Practical implicationsThe findings indicate that managers of SMEs should invest in domestic and international collaboration networks and business model innovation to enhance SMEs' innovation performance. Moreover, entrepreneurial orientation and government institutional support should be valued when SMEs try to enhance their innovation performance by embedding in domestic and international collaboration networks.Originality/valueThis study broadens the authors' understanding of the relationship between collaboration networks and firms' innovation performance by classifying collaboration networks into domestic and international dimensions and investigating their direct impacts on SMEs' innovation performance. Besides, this study reveals how and when domestic and international collaboration networks influence the innovation performance of SMEs.
Gender diversity on corporate boards: perceptions on quotas
Authors: Lefley Frank , Vychová Helena , Trnková Gabriela 
Published: December 2023

PurposeThis paper aims to seek the perceptions of potential future corporate managers and directors on the issues raised in the literature, especially recent articles in the corporate communications literature, concerning corporate board gender quotas. It focusses on the Czech Republic, where research on board gender diversity is sparse.Design/methodology/approachThe study is part of much more comprehensive research into board gender diversity. It adopts a questionnaire approach, with this paper focussing on 13 research statements. A Likert Scale of 1–4 (Strongly Agree; Agree; Disagree; Strongly Disagree) was applied to the perceived views expressed. The questionnaires were completed by university students at a public university in the Czech Republic during March–April 2023. A pilot questionnaire was conducted in February 2023, resulting in minor changes being made. The data is analysed using SPSS and MedCalc® statistical software.FindingsThere is overwhelming opposition to quotas, even from women. The opinions expressed by the respondents to this research, in many respects, support the literature, but there is unmistakable evidence of gender bias. Regarding the positive female benefits of quotas, male respondents disagreed; regarding the negative issues of quotas, male respondents agreed more than their female counterparts.Practical implicationsThe research findings have important implications for how women recruited through quotas may be received onto corporate boards – what challenges will they likely face? Some current female candidates for directorship, who would have been selected on merit and perceived as such by their male counterparts, may now be hesitant to apply for such positions if they are seen as being appointed due to quotas. Therefore, the selection procedure must continue to be based on merit and seen as such.Originality/valueOne of the important aspects of the paper is that it focusses on a country that has, until recently, resisted pressures to implement mandatory corporate board gender quotas; in this respect, it has a corpus of originality and value. The Czech Republic and other European countries will also be affected by the recent EU law on gender balance or corporate boards. The paper also highlights the perceptions of potential future directors on various issues of board gender quotas.
Influence of corporate governance on exit time: evidence from French zombie firms
Authors: Veganzones David , Severin Eric 
Published: December 2023

Purpose
This study investigates the connection between corporate governance and zombie firm’s exit time.

Design/methodology/approach
With a sample of 2,794 French zombie firms, the analysis focuses on four aspects of corporate governance: board size (BS), managerial ownership (MO), director turnover (DT) and ownership concentration, using tobit regression.

Findings
Dimensions of corporate governance have an important role in determining zombie firms’ exit time. MO and ownership concentration increase zombie firm exit time, whereas larger BSs and DT reduce it.

Originality/value
To the best of the authors’ knowledge, this study is the first to include corporate governance as a characteristic relevant to zombie firms’ exit time. It provides new insights on why some zombie firms remain in the market longer than expected.
Using the conservation of resources theory to understand volunteer adaptability: a personal resource for reducing burnout
Authors: Allen Joseph A. 
Published: December 2023

Purpose
Burnout has been known to negatively affect volunteers. However, information involving various factors that influence their burnout is severely lacking. This study aims to examine how volunteers displayed adaptability, the ability to change their thoughts, actions and/or behaviors in uncertain situations, to offset the negative relationship with burnout. This study also examined the amount of training a volunteer reported as one factor that may act to moderate this negative relationship between adaptability and burnout.

Design/methodology/approach
Using the conservation of resources (COR) theory, the author investigated how volunteers try to maintain their current level of resources, which aids in coping with stress and lowering their risk of burnout.

Findings
Using regression, the author discovered that adaptability was negatively related to burnout and this relationship was stronger for volunteers who reported less training. Training was confirmed as a moderator in this relationship. In sum, training acted as a buffer in the negative relationship involving adaptability and burnout.

Originality/value
The current study is one of the few to adopt theories often used to understand employee experiences, and apply them to volunteers. Interestingly, across a variety of volunteer environments, these employment theories and relationships, including adaptability, appear to matter.