bluuebunny/crossref_metadata_2025_split huggingface dataset:
Feedforward amplification in recurrent networks underlies paradoxical neural coding
Authors: Daie Kayvon , Fontolan Lorenzo , Druckmann Shaul , Svoboda Karel 
Published: August 2023

AbstractThe activity of single neurons encodes behavioral variables, such as sensory stimuli (Hubel & Wiesel 1959) and behavioral choice (Britten et al. 1992; Guo et al. 2014), but their influence on behavior is often mysterious. We estimated the influence of a unit of neural activity on behavioral choice from recordings in anterior lateral motor cortex (ALM) in mice performing a memory-guided movement task (H. K. Inagaki et al. 2018). Choice selectivity grew as it flowed through a sequence of directions in activity space. Early directions carried little selectivity but were predicted to have a large behavioral influence, while late directions carried large selectivity and little behavioral influence. Consequently, estimated behavioral influence was only weakly correlated with choice selectivity; a large proportion of neurons selective for one choice were predicted to influence choice in the opposite direction. These results were consistent with models in which recurrent circuits produce feedforward amplification (Goldman 2009; Ganguli et al. 2008; Murphy & Miller 2009) so that small amplitude signals along early directions are amplified to produce low-dimensional choice selectivity along the late directions, and behavior. Targeted photostimulation experiments (Daie et al. 2021b) revealed that activity along the early directions triggered sequential activity along the later directions and caused predictable behavioral biases. These results demonstrate the existence of an amplifying feedforward dynamical motif in the motor cortex, explain paradoxical responses to perturbation experiments (Chettih & Harvey 2019; Daie et al. 2021b; Russell et al. 2019), and reveal behavioral relevance of small amplitude neural dynamics.
A molecular atlas of adultC. elegansmotor neurons reveals ancient diversity delineated by conserved transcription factor codes
Authors: Smith Jayson J. , Taylor Seth R. , Blum Jacob A. , Gitler Aaron D. , Miller David M. , Kratsios Paschalis 
Published: August 2023

ABSTRACTMotor neurons (MNs) constitute an ancient cell type targeted by multiple adult-onset diseases. It is therefore important to define the molecular makeup of adult MNs in animal models and extract organizing principles. Here, we generated a comprehensive molecular atlas of adultCaenorhabditis elegansMNs and a searchable database (http://celegans.spinalcordatlas.org). Single-cell RNA-sequencing of 13,200 cells revealed that ventral nerve cord MNs cluster into 29 molecularly distinct subclasses. All subclasses are delineated by unique expression codes of either neuropeptide or transcription factor gene families. Strikingly, we found that combinatorial codes of homeodomain transcription factor genes define adult MN diversity both inC. elegansand mice. Further, molecularly defined MN subclasses inC. elegansdisplay distinct patterns of connectivity. Hence, our study couples the connectivity map of theC. elegansmotor circuit with a molecular atlas of its constituent MNs, and uncovers organizing principles and conserved molecular codes of adult MN diversity.
Primed and ready: Nanopore metabarcoding can now recover highly accurate consensus barcodes that are generally indel-free
Authors: Chang Jia Jin Marc , Ip Yin Cheong Aden , Neo Wan Lin , Mowe Maxine A. D. , Jaafar Zeehan , Huang Danwei 
Published: August 2023

AbstractBackgroundDNA metabarcoding applies high-throughput sequencing approaches to generate numerous DNA barcodes from mixed sample pools for mass species identification and community characterisation. To date, however, most metabarcoding studies employ second-generation sequencing platforms like Illumina, which are limited by short read lengths and longer turnaround times. While third-generation platforms such as the MinION (Oxford Nanopore Technologies) can sequence longer reads and even in real-time, application of these platforms for metabarcoding has remained scarce due to the relatively high read error rate as well as the paucity of specialised software for processing such reads.FindingsWe show that this is no longer the case by performing nanopore-based metabarcoding on 34 zooplankton bulk samples with amplicon_sorter, benchmarking the results against conventional Illumina MiSeq sequencing. The R10.3 sequencing chemistry and super accurate (SUP) basecalling model reduced raw read error rates to ∼4%, and consensus calling with amplicon_sorter (without further error correction) generated metabarcodes that were ≤1% erroneous. Although Illumina recovered a higher number of molecular operational taxonomic units (MOTUs) than nanopore sequencing (589 vs. 471), we found no significant differences in the zooplankton communities inferred between the sequencing platforms. Indeed, the same ecological conclusions were obtained regardless of the sequencing platform used. Moreover, 406 of 444 (91.4%) shared MOTUs between Illumina and nanopore were found to be indel-free.ConclusionsCollectively, our results illustrate the viability of nanopore metabarcoding for characterising communities, and paves the way for greater utilisation of nanopore sequencing in various metabarcoding applications.
The cell adhesion molecule Echinoid promotes tissue survival and separately restricts tissue overgrowth inDrosophilaimaginal discs
Authors: Spitzer Danielle C. , Sun William Y. , Rodríguez-Vargas Anthony , Hariharan Iswar K. 
Published: August 2023

AbstractThe interactions that cells inDrosophilaimaginal discs have with their neighbors are known to regulate their ability to survive. In a screen of genes encoding cell surface proteins for gene knockdowns that affect the size or shape of mutant clones, we found that clones of cells with reduced levels ofechinoid(ed) are fewer, smaller, and can be eliminated during development. In contrast, discs composed mostly ofedmutant tissue are overgrown. We find thatedmutant tissue has lower levels of the anti-apoptotic protein Diap1 and has increased levels of apoptosis which is consistent with the observed underrepresentation ofedmutant clones and the slow growth ofedmutant tissue. The eventual overgrowth ofedmutant tissue results not from accelerated growth, but from prolonged growth resulting from a failure to arrest growth at the appropriate final size. Ed has previously been shown to physically interact with multiple Hippo-pathway components and it has been proposed to promote Hippo pathway signaling, to exclude Yorkie (Yki) from the nucleus, and restrain the expression of Yki-target genes. We did not observe changes in Yki localization inedmutant tissue and found decreased levels of expression of several Yorkie-target genes, findings inconsistent with the proposed effect of Ed on Yki. We did, however, observe increased expression of several Yki-target genes in wild-type cells neighboringedmutant cells, which may contribute to elimination ofedmutant clones. Thus,edhas two distinct functions: an anti-apoptotic function by maintaining Diap1 levels, and a function to arrest growth at the appropriate final size. Both of these are unlikely to be explained by a simple effect on the Hippo pathway.
Ultrafast Power Doppler Ultrasound Enables Longitudinal Tracking of Vascular Changes that Correlate with Immune Response After Radiotherapy
Authors: Martello Shannon E. , Xia Jixin , Kusunose Jiro , Hacker Benjamin C. , Mayeaux McKenzie A. , Lin Erica J. , Hawkes Adrienne , Singh Aparna , Caskey Charles F. , Rafat Marjan 
Published: August 2023

AbstractBackgroundWhile immunotherapy shows great promise in patients with triple negative breast cancer, many will not respond to treatment. Radiotherapy has the potential to prime the tumor-immune microenvironment for immunotherapy. However, predicting response is difficult due to tumor heterogeneity across patients, which necessitates personalized medicine strategies that incorporate tumor tracking into the therapeutic approach. Here, we investigated the use of ultrasound (US) imaging of the tumor vasculature to monitor the tumor response to treatment.MethodsWe utilized ultrafast power doppler US to track the vascular response to radiotherapy over time. We used 4T1 (metastatic) and 67NR (non-metastatic) breast cancer models to determine if US measurements corroborate conventional immunostaining analysis of the tumor vasculature. To evaluate the effects of radiation, tumor volume and vascular index were calculated using US, and the correlation between vascular changes and immune cell infiltration was determined.ResultsUS tumor measurements and the quantified vascular response to radiation were confirmed with caliper measurements and immunostaining, respectively, demonstrating a proof-of-principle method for non-invasive vascular monitoring. Additionally, we found significant infiltration of CD8+T cells into irradiated tumors 10 days after radiation, which followed a sustained decline in vascular index and an increase in splenic CD8+T cells that was first observed 1 day post-radiation.ConclusionsOur findings reveal that ultrafast power doppler US can evaluate changes in tumor vasculature that are indicative of shifts in the tumor-immune microenvironment. This work may lead to improved patient outcomes through observing and predicting response to therapy.
Molecular insights into the activation of Mre11-Rad50 endonuclease activity by Sae2/CtIP
Authors: Nicolas Yoann , Bret Hélène , Cannavo Elda , Cejka Petr , Borde Valerie , Guerois Raphael 
Published: August 2023

SummaryInS. cerevisiae, the Mre11-Rad50-Xrs2 (MRX)-Sae2 nuclease activity is required for the resection of DNA breaks with secondary structures or protein blocks, while in humans, the MRE11-RAD50-NBS1 (MRN) homologue with CtIP is needed to initiate DNA end resection of all breaks. Phosphorylated Sae2/CtIP stimulates the endonuclease activity of MRX/N. Structural insights into the activation of the Mre11 nuclease are available only for organisms lacking Sae2/CtIP, so little is known how Sae2/CtIP activates the nuclease ensemble. Here, we uncover the mechanism of Mre11 activation by Sae2 using a combination of AlphaFold2 structural modeling, biochemical and genetic assays. We show that Sae2 stabilizes the Mre11 nuclease in a conformation poised to cleave substrate DNA. Several designs of compensatory mutations establish how Sae2 activates MRXin vitroandin vivo,validating the structural model. Last, our study uncovers how human CtIP, despite considerable sequence divergence, employs a similar mechanism to activate MRN.
Extracellular filaments revealed by affinity capture cryo-electron tomography
Authors: Engel Leeya , Zaoralová Magda , Zhou Momei , Dunn Alexander R. , Oliver Stefan L. 
Published: August 2023

ABSTRACTCryogenic-electron tomography (cryo-ET) has provided an unprecedented glimpse into the nanoscale architecture of cells by combining cryogenic preservation of biological structures with electron tomography. Micropatterning of extracellular matrix proteins is increasingly used as a method to prepare adherent cell types for cryo-ET as it promotes optimal positioning of cells and subcellular regions of interest for vitrification, cryo-focused ion beam (cryo-FIB) milling, and data acquisition. Here we demonstrate a micropatterning workflow for capturing minimally adherent cell types, human T-cells and Jurkat cells, for cryo-FIB and cryo-ET. Our affinity capture system facilitated the nanoscale imaging of Jurkat cells, revealing extracellular filamentous structures. It improved workflow efficiency by consistently producing grids with a sufficient number of well positioned cells for an entire cryo-FIB session. Affinity capture can be extended to facilitate high resolution imaging of other adherent and non-adherent cell types with cryo-ET.
What claims best convey the quality of retailers' standard private label products?
Authors: Louis Didier , Lombart Cindy , Grappe Cindy G. , Durif Fabien , Florence Charton-Vachet , Untilov Olga 
Published: August 2023

PurposeConsumers consider retailers' standard private labels (PLs) as relevant choices, compared to national brands (NBs), and their demand for private label products has increased significantly over the past decade. At the same time, PLs have undergone a profound transformation as retailers have enhanced their quality. The goal of this research is to investigate the impact of claims used to highlight the enhanced quality of standard PL products on consumers' perceptions and behaviours.Design/methodology/approachA between-subjects experiment, set in a store laboratory, was used to study consumers' perceptions and behaviours. The impact of six non-nutrition claims – linked, according to the self-other trade-off, either to concern for consumers' health (internal to the self) or for the environment (external to the self) – on consumers' reactions has been studied. Then, the data collected were analysed with partial least squares structural equation modelling (PLS-SEM).FindingsThis research indicates that health claims retailers make to echo consumers' own concerns have positive impacts at three basic levels: the brand, the retail chain and the store. It also highlights the central role of trust in standard PLs, which, once activated by the non-nutrition claims made by retailers and the increase in the quality of standard PLs thus inferred by consumers, can improve consumers' attitude toward the food retailers' stores and reinforce their intentions to visit again and recommend them.Research limitations/implicationsFrom a theoretical perspective, this research supplements cue utilisation theory as it applies this framework to standard PLs and establishes that consumers use extrinsic cues (i.e. communications on non-nutrition claims) to infer the quality of standard PL brand products. It also complements scant studies on retailers' corporate social responsibility (CSR) with quality aspects of their own labels as it specifies the levers (i.e. the claims) to use to improve retailers' CSR image and consumers' behaviours.Practical implicationsFrom a managerial perspective, this research highlights the superiority of retailers' claims related to consumer health and, more specifically, of claims highlighting the natural origin of ingredients. For this specific assertion, trust in the standard PL and the CSR image of the brand have direct and indirect impacts, via attitude toward the stores, on consumers' intentions to return to and to recommend these stores.Originality/valueDespite the increasing importance of products as effective tools for communicating companies' CSR policies, scant research has been conducted on consumers' reactions to non-nutrition claims, which are increasingly prominent in the marketplace.
Leader's work engagement in relation to team performance is a contagion event explained through the lens of affective process theory
Authors: Yun Mansik 
Published: August 2023

PurposeThe purpose of the current research is (1) to test affective mechanisms by which a leader's work engagement predicts team performance via a follower's work engagement in a trickle-down fashion and (2) to examine the moderating role of relational identification with the leader on the trickle-down effect.Design/methodology/approachMultisource and three-wave data was collected from 404 followers working in 76 teams from a construction company in South Korea. By aggregating all study variables, a 2-2-2 level approach by using the PROCESS macro with bootstrapping (10,000 samples) in SPSS was used to test the proposed model.FindingsThe current research uses a team-level analysis to examine (1) the effect of a leader's work engagement on team performance via a follower's work engagement and (2) moderating role of relational identification via the lens of the affective processing theory (APT) and the conservation of resource (COR) theory.Originality/valueBased the lens of APT and COR theory, the current research found that the contagious effect of a leader's work engagement on followers is conditional. Specifically a leader's work engagement has a positive effect on followers' work engagement only when followers have a high sense of relational identification with their leader. However, a leader's work engagement has an adverse effect on followers when followers have a low sense of relational identification.
Neighbourhood cooperatives for the integrated urban regeneration of mass housing areas: speculations on a proposed model
Authors: Rosa-Jiménez Carlos , Márquez-Ballesteros María José , García-Moreno Alberto E. , Navas-Carrillo Daniel 
Published: August 2023

Purpose
This paper seeks to define a theoretical model for the urban regeneration of mass housing areas based on citizen initiative, self-management and self-financing in the form of the neighbourhood cooperative. This paper aims to identify mechanisms for economic resource generation that enable the improvement of the urban surroundings and its buildings without assuming disproportionate economic burdens by the local residents based on two principles, the economies of scale and service provision.

Design/methodology/approach
The research is structured in three phases: a literature review of the different trends in self-financing for urban regeneration and the conceptual framework for the definition of a cooperative model; the definition of theoretical model by analysing community ecosystem, neighbourhood-based services and the requirements for its economic equilibrium; and the discussion of the results and the conclusions.

Findings
The results show the potential of the cooperative model to generate a social economy capable of reducing costs and producing additional resources to finance the rehabilitation process. The findings show not only the extent of economic advantages but also multiple social, physical and environmental benefits. Its implementation involves the participation of multiple actors, which is one of its significant advantages.

Originality/value
The main contribution is to approach comprehensive urban rehabilitation from a collaborative understanding, overcoming the main financing difficulties of the current practices based on public subsidy policies. The model also allows an ethical relationship to be built with supplier companies by means of corporate social responsibility.
The secretome atlas of two mouse models of progeria
Authors: Quintana‐Torres Diego , Valle‐Cao Alejandra , Bousquets‐Muñoz Pablo , Freitas‐Rodríguez Sandra , Rodríguez Francisco , Lucia Alejandro , López‐Otín Carlos , López‐Soto Alejandro , Folgueras Alicia R. 
Published: August 2023

AbstractHutchinson‐Gilford progeria syndrome (HGPS) is a rare genetic disease caused by nuclear envelope alterations that lead to accelerated aging and premature death. Several studies have linked health and longevity to cell‐extrinsic mechanisms, highlighting the relevance of circulating factors in the aging process as well as in age‐related diseases. We performed a global plasma proteomic analysis in two preclinical progeroid models (LmnaG609G/G609G and Zmpste24−/− mice) using aptamer‐based proteomic technology. Pathways related to the extracellular matrix, growth factor response and calcium ion binding were among the most enriched in the proteomic signature of progeroid samples compared to controls. Despite the global downregulation trend found in the plasma proteome of progeroid mice, several proteins associated with cardiovascular disease, the main cause of death in HGPS, were upregulated. We also developed a chronological age predictor using plasma proteome data from a cohort of healthy mice (aged 1–30 months), that reported an age acceleration when applied to progeroid mice, indicating that these mice exhibit an “old” plasma proteomic signature. Furthermore, when compared to naturally‐aged mice, a great proportion of differentially expressed circulating proteins in progeroid mice were specific to premature aging, highlighting secretome‐associated differences between physiological and accelerated aging. This is the first large‐scale profiling of the plasma proteome in progeroid mice, which provides an extensive list of candidate circulating plasma proteins as potential biomarkers and/or therapeutic targets for further exploration and hypothesis generation in the context of both physiological and premature aging.
Pricing cloud stocks: Evidence from China
Authors: Lin Lichao , Cheung Adrian (Wai Kong) 
Published: August 2023

AbstractUsing factor models, we examine two pricing issues of cloud stocks in China's stock market. In particular, we test whether the Fama and French factor models are useful to explain the stock prices of cloud stocks and whether there are abnormal returns unexplained by these models. Using the daily stock prices of 1670 cloud stocks from 2012 to 2022, we find that the factor models explain up to nearly 97% of the stock return variations of the cloud stocks, and mispricing. The results are robust to alternative measure of factors, outliers, sampling period and different approaches of factor modelling.
Years of life lost to drug overdose in the Latinx community during the most recent wave of overdose deaths
Authors: Harris Rebecca A. , Mandell David S. 
Published: August 2023

AbstractBackground and ObjectivesThis study estimated years of life lost (YLL) among US Latinx individuals during the most recent wave of drug overdose deaths.MethodsA serial cross‐sectional study of YLL (life expectancy minus age at death) from death certificate records of Latinx individuals who died from drug overdoses from 2015 to mid‐2022.ResultsOver the study period, 58,209 Latinx individuals aged 15–64 years died from drug overdoses resulting in 2,266,784 YLL. Age‐group YLL differences remained stable, but gender YLL trajectories diverged.Conclusions and Scientific SignificanceThis study extends our understanding of the immense loss to Latinx communities from preventable drug deaths.
Unfilled prescriptions: Surveying patients' experiences with buprenorphine treatment in Massachusetts before and during the COVID‐19 pandemic
Authors: Rosansky Joseph A. , Albanese Mark , Phillips Joshua , Schuman‐Olivier Zev 
Published: August 2023

AbstractBackground and ObjectivesWe explored potential challenges to accessing office‐based opioid treatment (OBOT) with buprenorphine during the COVID‐19 pandemic.MethodsUsing Facebook advertisements, we recruited a sample of N = 72 participants and conducted four repeated‐measures analysis of variance comparing ratings of participants' abilities to access aspects of OBOT treatment.ResultsParticipants reported increased difficulty filling buprenorphine prescriptions during the pandemic than before, p = .011, partial η2 = 0.092, and this was correlated with past month opioid use, r = .236, p = .042.Discussion, Conclusions, and Scientific SignificanceThis is the first investigation to report unfilled prescriptions during the pandemic and an association with opioid use. Unfilled prescriptions may contribute to relapse and partially explain increased overdose deaths during COVID‐19.