bluuebunny/crossref_metadata_2025_split huggingface dataset:
IS-PRM-based peptide targeting informed by long-read sequencing for alternative proteome detection
Authors: Korchak Jennifer A. , Jeffery Erin D. , Bandyopadhyay Saikat , Jordan Ben T. , Lehe Micah , Watts Emily F. , Fenix Aidan , Wilhelm Mathias , Sheynkman Gloria M. 
Published: April 2024

ABSTRACTAlternative splicing is a major contributor of transcriptomic complexity, but the extent to which transcript isoforms are translated into stable, functional protein isoforms is unclear. Furthermore, detection of relatively scarce isoform-specific peptides is challenging, with many protein isoforms remaining uncharted due to technical limitations. Recently, a family of advanced targeted MS strategies, termed internal standard parallel reaction monitoring (IS-PRM), have demonstrated multiplexed, sensitive detection of pre-defined peptides of interest. Such approaches have not yet been used to confirm existence of novel peptides. Here, we present a targeted proteogenomic approach that leverages sample-matched long-read RNA sequencing (LR RNAseq) data to predict potential protein isoforms with prior transcript evidence. Predicted tryptic isoform-specific peptides, which are specific to individual gene product isoforms, serve as “triggers” and “targets” in the IS-PRM method, Tomahto. Using the model human stem cell line WTC11, LR RNAseq data were generated and used to inform the generation of synthetic standards for 192 isoform-specific peptides (114 isoforms from 55 genes). These synthetic “trigger” peptides were labeled with super heavy tandem mass tags (TMT) and spiked into TMT-labeled WTC11 tryptic digest, predicted to contain corresponding endogenous “target” peptides. Compared to DDA mode, Tomahto increased detectability of isoforms by 3.6-fold, resulting in the identification of five previously unannotated isoforms. Our method detected protein isoform expression for 43 out of 55 genes corresponding to 54 resolved isoforms. This LR RNA seq-informed Tomahto targeted approach, called LRP-IS-PRM, is a new modality for generating protein-level evidence of alternative isoforms – a critical first step in designing functional studies and eventually clinical assays.
Combinatorial expression of neurexin genes regulates glomerular targeting by olfactory sensory neurons
Authors: Park Sung Jin , Wang I-Hao , Lee Namgyu , Jiang Hao-Ching , Uemura Takeshi , Futai Kensuke , Kim Dohoon , Macosko Evan , Greer Paul 
Published: April 2024

AbstractPrecise connectivity between specific neurons is essential for the formation of the complex neural circuitry necessary for executing intricate motor behaviors and higher cognitive functions. Whiletrans-interactions between synaptic membrane proteins have emerged as crucial elements in orchestrating the assembly of these neural circuits, the synaptic surface proteins involved in neuronal wiring remain largely unknown. Here, using unbiased single-cell transcriptomic and mouse genetic approaches, we uncover that the neurexin family of genes enables olfactory sensory neuron (OSNs) axons to form appropriate synaptic connections with their mitral and tufted (M/T) cell synaptic partners, within the mammalian olfactory system. Neurexin isoforms are differentially expressed within distinct populations of OSNs, resulting in unique pattern of neurexin expression that is specific to each OSN type, and synergistically cooperate to regulate axonal innervation, guiding OSN axons to their designated glomeruli. This process is facilitated through the interactions of neurexins with their postsynaptic partners, including neuroligins, which have distinct expression patterns in M/T cells. Our findings suggest a novel mechanism underpinning the precise assembly of olfactory neural circuits, driven by thetrans-interaction between neurexins and their ligands.
TDG orchestrates ATF4-dependent gene transcription during retinoic acid-induced cell fate acquisition
Authors: Turpin Marion , Madigou Thierry , Bizot Maud , Acker Rachael , Avner Stephane , Benoît Gérard , Braud Martin , Fourgeux Cynthia , Palierne Gaëlle , Poschmann Jeremie , Sawvell Katie , Watrin Erwan , Péron Christine Le , Salbert Gilles 
Published: April 2024

ABSTRACTAcquisition of cell identity is associated with a remodeling of the epigenome in part through active DNA demethylation. The T:G mismatch DNA glycosylase (TDG) participates to this process by removing 5-methylcytosines that have been oxidized by Ten-Eleven-Translocation (TET) enzymes. Despite this well-defined molecular function, a comprehensive view of the biological function of TDG is still lacking, especially during cell differentiation. Here, we combined transcriptomic and epigenomic approaches in aTdgknock-out epiblast stem-like cell model to decipher TDG function in pluripotent cells and their retinoic acid-induced progeny. We determined that TDG occupies a majority of active promoters, a large fraction of which are also engaged by the transcription factor ATF4. Consistently, neural fate commitment upon retinoic acid treatment is associated with a TDG-dependent sustained expression of ATF4-dependent genes, in relation with a TDG-associated nucleosome positioning at promoters. We further evidenced that TDG maintains ATF4 pathway activity by positively regulating the mammalian target of rapamycin complex 1 (mTORC1), favoring neural cell fate commitment. These observations highlight the central role of TDG in cell differentiation and support a model linking metabolic reprogramming to cell fate acquisition.
Identification of cell-type-specific response to silicon treatment in soybean leaves through single nucleus RNA-sequencing
Authors: Devkar Vikas , D’Agostino Leonidas , Kshetry Arjun Ojha , Yong Lenin , Nadaf Altafhusain B , Thirumalaikumar VP , Skirycz Aleksandra , Ma Jianxin , Stupar Robert M. , Herrera-Estrella Luis , Deshmukh Rupesh , Patil Gunvant B. 
Published: April 2024

AbstractIn agriculture, mineral nutrients uptake and deposition profoundly influence plant development, stress resilience, and productivity. Despite its classification as a non-essential element, silicon (Si) is crucial in plant physiology, particularly in defense response and stress mitigation. While genetic and molecular mechanisms of Si uptake and transport are well-studied in monocots, particularly rice, its role in dicot species, such as soybean, remains unclear at the cellular and molecular levels. Traditional bulk transcriptomics methods lack the resolution to uncover cellular heterogeneity. Here, we present a study by utilizing single-nucleus RNA sequencing (snRNA-seq) to dissect cellular responses to Si accumulation in soybean leaves. Our analysis revealed distinct cellular populations, including a novel Si-induced cell cluster within vascular cells, suggesting a specific mechanism of Si distribution. Si treatment induced the expression of defense-related genes, particularly enriched in vascular cells, highlighting their specialized role in activating plant defense mechanisms. Moreover, Si modulated the expression of genes involved in RNA silencing, phytoalexin biosynthesis, and immune receptor signaling, suggesting a mechanism of transcriptional priming of genes involved in defense responses. We further investigated putative Si transporters, revealing differential expression patterns in response to Si treatment, suggesting presence of active and gradient-based transport mechanisms. Our findings shed light on the vital biotic stress regulatory networks governed by Si treatment in soybean leaves, paving potential strategies for enhancing stress tolerance and agronomic performance in crops.
Acute and Chronic Neural and Glial Response to Mild Traumatic Brain Injury in the Hippocampus
Authors: Dougan Carey E. , Roberts Brandon L. , Crosby Alfred J. , Karatsoreos Ilia , Peyton Shelly R. 
Published: April 2024

ABSTRACTTraumatic brain injury (TBI) is an established risk factor for developing neurodegenerative disease. However, how TBI leads from acute injury to chronic neurodegeneration is limited to post-mortem models. There is a lack of connections betweenin vitroandin vivoTBI models that can relate injury forces to both macroscale tissue damage and brain function at the cellular level. Needle-induced cavitation (NIC) is a technique that can produce small cavitation bubbles in soft tissues, which allows us to relate small strains and strain rates in living tissue to ensuing acute and chronic cell death, tissue damage, and tissue remodeling. Here, we applied NIC to mouse brain slices to create a new model of TBI with high spatial and temporal resolution. We specifically targeted the hippocampus, which is a brain region critical for learning and memory and an area in which injury causes cognitive pathologies in humans and rodent models. By combining NIC with patch-clamp electrophysiology, we demonstrate that NIC in the Cornu Ammonis (CA)3 region of the hippocampus dynamically alters synaptic release onto CA1 pyramidal neurons in a cannabinoid 1 receptor (CB1R)-dependent manner. Further, we show that NIC induces an increase in extracellular matrix proteins associated with neural repair that is mitigated by CB1R antagonism. Together, these data lay the groundwork for advanced approaches in understanding how TBI impacts neural function at the cellular level, and the development of treatments that promote neural repair in response to brain injury.SIGNIFICANCECurrent models of mild TBI (mTBI) cannot relate injury forces to both macroscale tissue damage and brain function at the cellular level. We combine a microscale injury model inex vivobrain slices while simultaneously recording glutamatergic inputs onto CA1 hippocampal pyramidal neurons. Post-injury examination of chronic tissue regeneration by astrocytes allow us to connect acute neuronal signaling responses to chronic fibrosis after TBI. These studies provide a new tool for understanding the physiological and molecular responses to TBI and lay the groundwork for future experiments unraveling the synaptic mechanisms that mediate these responses seconds, minutes, and days following injury.
Unilateral auditory deprivation reveals brainstem origin of a sensitive period for spatial hearing
Authors: Anbuhl Kelsey L. , Ferber Alexander T. , Brown Andrew D. , Benichoux Victor , Greene Nathaniel T. , Tollin Daniel J. 
Published: April 2024

AbstractEarly sensory experience can exert lasting perceptual consequences. For example, a brief period of auditory deprivation early in life can lead to persistent spatial hearing deficits. Some forms of hearing loss (i.e., conductive; CHL) can distort acoustical cues needed for spatial hearing, which depend on inputs from both ears. We hypothesize that asymmetric acoustic input during development disrupts auditory circuits that integrate binaural information. Here, we identify prolonged maturation of the binaural auditory brainstem in the guinea pig by tracking auditory evoked potentials across development. Using this age range, we induce a reversible unilateral CHL and ask whether behavioral and neural maturation are disrupted. We find that developmental CHL alters a brainstem readout of binaural function which is not observed when the CHL is induced in adulthood. Startle-based behavioral measures reveal poorer spatial resolution of sound sources, but only for high-frequency sound stimuli. Finally, single-unit recordings of auditory midbrain neurons reveal significantly poorer neural acuity to a sound location cue that largely depends on high-frequency sounds. Thus, these findings show that unilateral deprivation can disrupt developing auditory circuits that integrate binaural information and may give rise to lingering spatial hearing deficits.
Single-cell transcriptional landscape of temporal neutrophil response to burn wound in larval zebrafish
Authors: Hou Yiran , Khatri Parth , Rindy Julie , Schultz Zachery , Gao Anqi , Chen Zhili , Gibson Angela LF , Huttenlocher Anna , Dinh Huy Q. 
Published: April 2024

AbstractNeutrophils accumulate early in tissue injury. However, the cellular and functional heterogeneity of neutrophils during homeostasis and in response to tissue damage remains unclear. Here, we use larval zebrafish to understand neutrophil responses to thermal injury. Single-cell transcriptional mapping of myeloid cells during a 3-day time course in burn and control larvae revealed distinct neutrophil subsets and their cell-cell interactions with macrophages across time and conditions. The trajectory formed by three zebrafish neutrophil subsets resembles human neutrophil maturation, with varying transition patterns between conditions. Through ligand-receptor cell-cell interaction analysis, we found neutrophils communicate more in burns in a pathway and temporal manner. Finally, we identified the correlation between zebrafish myeloid signatures and human burn severity, establishing GPR84+ neutrophils as a potential marker of early innate immune response in burns. This work builds the molecular foundation and a comparative single-cell genomic framework to identify neutrophil markers of tissue damage using model organisms.
Identification of Large Japanese field mouseApodemus speciosusfood plant resources in an industrial green space using DNA metabarcoding
Authors: Fujii Taichi , Kawamoto Hirokazu , Shirako Tomoyasu , Nakamura Masatoshi , Minami Motoyasu 
Published: April 2024

AbstractDNA metabarcoding was employed to identify the food plant resources of the Large Japanese field mouse Apodemus speciosus, inhabiting an artificial green space on reclaimed land on the Chita Peninsula in Aichi Prefecture, Central Japan, from 2012 to 2014. DNA metabarcoding was performed using high-throughput sequencing of partial rbcL sequences extracted from feces samples collected in the study area. The obtained sequences, which were analyzed using a constructed local database, revealed that a total of 72 plant taxa were utilized as food plant resources by A. speciosus. Of these plant taxa, 43 could be assigned to species (59.7%), 16 to genus (22.2%), and 13 to family (18.1%). Of the 72 plant taxa identified in this study, the dominant families throughout all collection periods were Lauraceae (81.0% of 100 fecal samples), followed by Fagaceae (70.0%), Rosaceae (68.0%), and Oleaceae (48.0%). Fifty of the 72 plant taxa identified as food plant resources were woody plants. An analysis employing rarefaction techniques for each season in the study site indicated comprehensive coverage of the food plant resources, ranging from 86.4% in winter to 93.6% in spring. Further, 96.5% of the food plant taxa were found throughout the study period. The findings showed that DNA metabarcoding using a local database constructed from the National Center for Biotechnology Information (NCBI) database and field surveys was effective for identifying the dominant food plants in the diet of A. speciosus. The results of this study provided basic information that can be applied to formulation and implementation of management and conservation strategies for local wildlife.
Tuning Collective Behaviour in Zebrafish with Genetic Modification
Authors: Yang Yushi , Kawafi Abdelwahab , Tong Qiao , Hammond Chrissy L. , Kague Erika , Royall C. Patrick 
Published: April 2024

AbstractZebrafish collective behaviour is widely used to assess their physical and mental state, serving as a valuable tool to assess the impact of ageing, disease genetics, and the effect of drugs. The essence of these macroscopic phenomena can be represented by active matter models, where the individuals are abstracted as interactive self-propelling agents. The behaviour of these agents depends on a set of parameters in a manner reminiscent of those between the constituents of physical systems. In a few cases, the system may be controlled at the level of the individual constituents such as the interactions between colloidal particles, or the enzymatic behaviour ofde novoproteins. Usually, however, while the collective behaviour may be influenced by environmental factors, it typically cannot be changed at will. Here, we challenge this scenario in a biological context by genetically modifying zebrafish. We thus demonstrate the potential of genetic modification in the context of controlling the collective behaviour of biological active matter systems at the level of the constituents, rather than externally. In particular, we probe the effect of the lack ofcol11a2gene in zebrafish, which causes the early onset of osteoarthritis. The resultingcol11a2 -/-zebrafish exhibited compromised vertebral column properties, bent their body less while swimming, and took longer to change their orientations. Surprisingly, a group of 25 mutant fish exhibited more orderly collective motion than the wildtype. We show that the collective behaviour of wildtype andcol11a2 -/-zebrafish are captured with a simple active matter model, in which the mutant fish are modelled by self–propelling agents with a higher orientational noise on average. In this way, we demonstrate the possibility of tuning a biological system, changing the state space it occupies when interpreted with a simple active matter model.
The urban transport companies in Spain: analysis of efficiency with data envelopment analysis
Authors: Flores-Ureba Sandra , Simon de Blas Clara , Sánchez Toledano Joaquín Ignacio , Sánchez de Lara Miguel Ángel 
Published: April 2024

PurposeThis paper aims to define the efficiency achieved by urban transport companies in Spain concerning the resources they use, considering the type of management used for implementation, public-private, and size.Design/methodology/approachThis study consisted of an analysis of the efficiency of 229 public-private urban transport operators during the period 2012–2021 using Data Envelopment Analysis, the Malmquist Index and inference estimators to determine productivity, efficiency change into Pure Technical Efficiency Change (PTECH), and scale efficiency change.FindingsBased on the efficiency analysis, the authors concluded that of the 229 companies studied, more than 35 were inefficient in all analysed periods. Considering the sample used, direct management is considered significantly more efficient. It cannot be concluded that the size of these companies influences their efficiency, as the data show unequal development behaviours in the studied years.Originality/valueThis study provides arguments on whether there is a significant difference between the two types of management in the urban transport sector. It also includes firm size as a study variable, which has not been previously considered in other studies related to urban transport efficiency. Efficiency should be a crucial factor in determining funding allocation in this sector, as it encourages operators to optimize and improve their services.
Using the theory of interpersonal behaviour to explain employees’ cybercrime preventative behaviour during the pandemic
Authors: Wright Tim , Ruhwanya Zainab , Ophoff Jacques 
Published: April 2024

Purpose
The COVID-19 pandemic necessitated a significant shift in how employees executed their professional responsibilities. Concurrently, the incidence of cybercrime experienced a noteworthy surge due to the increased utilisation of cyberspace. The abrupt transition to telecommuting altered the interpersonal dynamics inherent in traditional work environments. This paper aims to examine the impact of interpersonal factors on the cybercrime preventative measures adopted by telecommuting employees.

Design/methodology/approach
A conceptual model, grounded in the Theory of Interpersonal Behaviour, is evaluated through an online survey. The data set comprises responses from 209 employees in South Africa, and the analysis uses partial least squares structural equation modelling.

Findings
The results reveal substantial predictive power to explain cybercrime preventative behaviours. Notably, the study underscores the significant influence of habit and affect on intention and subsequent behaviour.

Practical implications
The results suggest that practitioners should give due attention to emotional dimensions (affect) as a catalyst for information security behaviour. The formulation of employees’ information security responsibilities should be pragmatic, fostering subconscious compliance to establish routine behaviour (habit).

Originality/value
This research underscores the pivotal roles played by habit and emotions in shaping behavioural patterns related to information security. Furthermore, it provides researchers with an illustrative model for operationalising these constructs within the realm of security. The results contribute additional perspectives on the repercussions of the COVID-19 pandemic on cybercrime preventative behaviours.
Wellbeing in the age of virtual teams and workplace automation – a systematic review and future research agenda
Authors: Murphy Liam 
Published: April 2024

Purpose
In the wake of the COVID-19 pandemic organisations are adapting to a new environment of global talent shortages, economic uncertainty and geo-political turmoil. As an outcome, the organisational strategies of digital transformation and remote working have been accelerated in the race to boost innovation, competitivity and attract staff. This has led to the rise of two new organisational dynamics: the increase of virtual teams (VTs) and focus on widespread work automation. However, despite the rise of these two related phenomena, literature does not connect them as one research area, and there is a gap in the understanding of the new employee wellbeing needs they form and how to respond to them. This paper aims to bridge this gap through a systematic literature across these areas.

Design/methodology/approach
This paper conducts a systematic literature review across the areas of leadership, VTs and automation over the past three years.

Findings
In this review, a number of newly arising employee wellbeing needs are identified such as fear of job displacement, a lack of self-efficacy and social cohesion, poor relationships with leaders and more. In addition, this paper recommends three fundamental research gaps to be addressed by future studies: 1. How to build and cultivate the new leadership skills needed to support VTs and workplace automation? 2. How to design work in a way that caters for employee wellbeing needs when operating in VTs or hybrid teams and working on or with workplace automation? 3. How to design work in a way that builds and emphasises the new employee skillsets to support augmentation and solves for the new employee wellbeing needs experienced by workplace automation?

Originality/value
This paper provides a novel contribution to literature by centralising current schools of thought across the cross-disciplinary themes and synthesising literature to recommend new wellbeing and leadership skills for organisations to focus on, alongside producing a new research agenda for scholars to focus.