bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Comprehensive Benchmark of Tools for Efficient Genomic Interval Querying
Authors: Schäfer Richard A. , Yang Rendong 
Published: February 2025

ABSTRACTEfficiently querying genomic intervals is fundamental to modern bioinformatics, enabling researchers to extract and analyze specific regions from large genomic datasets. While various tools have been developed for this purpose, there lacks a comprehensive comparison of their performance, memory usage, and practical utility. We present a systematic evaluation of genomic interval query tools using simulated datasets of varying sizes. Our benchmarking framework,segmeter, assesses both basic and complex interval queries, examining runtime performance, memory efficiency, and query precision across different tools and data structures. This comprehensive analysis provides insights into the strengths and limitations of different approaches to genomic interval querying, offering guidance for tool selection based on specific use cases and data requirements. Thesegmeterframework and all benchmark data are freely available, facilitating reproducibility and enabling researchers to conduct their own comparative analyses.
Literature-scaled immunological gene set annotation using AI-powered immune cell knowledge graph (ICKG)
Authors: He Shan , Tan Yukun , Ye Qing , Gubin Matthew , Rafei Hind , Peng Weiyi , Rezvani Katayoun , Mohanty Vakul , Chen Ken 
Published: February 2025

AbstractLarge scale application of single-cell and spatial omics in models and patient samples has led to the discovery of many novel gene sets, particularly those from an immunotherapeutic context. However, the biological meaning of those gene sets has been interpreted anecdotally through over-representation analysis against canonical annotation databases of limited complexity, granularity, and accuracy. Rich functional descriptions of individual genes in an immunological context exist in the literature but are not semantically summarized to perform gene set analysis. To overcome this limitation, we constructed immune cell knowledge graphs (ICKGs) by integrating over 24,000 published abstracts from recent literature using large language models (LLMs). ICKGs effectively integrate knowledge across individual, peer-reviewed studies, enabling accurate, verifiable graph-based reasoning. We validated the quality of ICKGs using functional omics data obtained independently from cytokine stimulation, CRISPR gene knock-out, and protein-protein interaction experiments. Using ICKGs, we achieved rich, holistic, and accurate annotation of immunological gene sets, including those that were unannotated by existing approaches and those that are in use for clinical applications. We created an interactive website (https://kchen-lab.github.io/immune-knowledgegraph.github.io/) to perform ICKG-based gene set annotations and visualize the supporting rationale.
Enhancing tandem MS sensitivity and peptide identification via ion pre-accumulation in an Orbitrap mass spectrometer
Authors: Harking Florian , Guzman Ulises H. , Kraegenbring Julia , Stewart Hamish , Aizikov Konstantin , Koch Heiner , Fort Kyle L. , Harder Alexander , Olsen Jesper V. 
Published: February 2025

AbstractHigh-throughput mass spectrometry-based proteomics has gained increasing interest for both academic and industrial applications. As implementation of faster gradients has facilitated higher sample throughput, mass spectrometers must adapt to shorter analysis times by enhancing scanning speed and sensitivity. For Orbitrap™ mass spectrometers, faster scan rates are constrained by the need for sufficient ion accumulation time, particularly given limitations on duty cycle at high repetition rate, and transient length, which determines analyzer sensitivity and resolving power. In this context, implementing alternative ion scheduling and better ion signal-processing strategies are needed to unleash the speed of these instruments. Here, we introduce a new scanning strategy termed pre-accumulation, which enables the storage of ions in the bent flatapole in parallel to the operation of the C-trap/IRM, leading to a significant improvement in ion beam utilization and enabling for the first time scanning speeds of >70 Hz on hybrid Orbitrap instruments. The combination of pre-accumulation and increased scan speeds notably enhances peptide and protein group identifications for short LC gradients and improves sensitivity for high-throughput applications. These benefits were further amplified when coupled with the full mass range phase-constrained spectrum deconvolution method (ΦSDM), especially for fast, lower-resolving Orbitrap measurements used with short LC gradients. Overall, we demonstrate that pre-accumulation of ions in the bent flatapole offers distinct advantages, particularly for conditions with reduced signal input. Since no hardware changes are required, this approach is highly attractive for Orbitrap mass spectrometers operated with fast MS/MS acquisition methods.
Most ventral pallidal cholinergic neurons are cortically projecting bursting basal forebrain cholinergic neurons
Authors: Schlingloff Dániel , Szabó Írisz , Gulyás Éva , Király Bálint , Kispál Réka , Stephenson-Jones Marcus , Hangya Balázs 
Published: February 2025

SummaryThe ventral pallidum (VP) lies at the intersection of basal ganglia and basal forebrain circuitry, possessing attributes of both major subcortical systems. Basal forebrain cholinergic neurons are rapidly recruited by reinforcement feedback and project to cortical and subcortical forebrain targets; in contrast, striatal cholinergic cells are local interneurons exhibiting classical ‘pause-burst’ responses to rewards. However, VP cholinergic neurons (VPCNs) are less characterized, and it is unclear whether basal forebrain and striatal type cholinergic neurons mix in the VP. Therefore, we performed anterograde and mono-transsynaptic retrograde labeling, in vitro acute slice recordings and bulk calcium recordings of VPCNs. We found that VPCNs broadly interact with the affective circuitry that processes rewards and punishments, targeting the basolateral amygdala, the nucleus accumbens, the medial prefrontal cortex and the lateral habenula, while receiving inputs from the nucleus accumbens, hypothalamus, central amygdala, bed nucleus of stria terminalis and the ventral tegmental area. Bulk calcium recordings revealed VPCN responses to rewards, punishments and reward-predicting cues, like those of the horizontal diagonal band of Broca of the basal forebrain. Acute slice recordings showed that most VPCNs resembled the bursting type of basal forebrain cholinergic neurons (BFCNs), while a few of them were of the regular rhythmic type, which sharply differentiated most VPCNs from striatal cholinergic interneurons. These results were confirmed by in vivo electrophysiological recordings of putative VPCNs largely resembling bursting BFCNs. We conclude that most VPCNs are BFCNs with specialized connectivity to relay aversive and appetitive stimuli to the reinforcement circuitry, possibly implicated in mood disorders and addiction.
Changes in pneumococcal deaths in the United States following the COVID-19 pandemic
Authors: Shang Lianhan , Perniciaro Stephanie , Weinberger Daniel M 
Published: February 2025

AbstractBackgroundAlthough changes in the rates of pneumococcal cases during the COVID-19 pandemic have been extensively described, changes in rates of death due to pneumococcus during this period are not well understood.MethodsWe obtained vital statistics data for the United States (National Center for Health Statistics), including age, sex, race/ethnicity, cause of death (ICD-10), 2014-2022. Generalized linear models were fit to the period from January 2014-February 2020 and extrapolated to March 2020-December 2022 to generate an expected number of pneumococcal deaths and a 95% prediction interval. We used a lasso regression model to identify clinical and demographic factors most strongly associated with pneumococcal deaths during the pandemic period as compared with a pre-pandemic baseline.ResultsFor most of 2020, pneumococcal deaths were not notably different from the pre-pandemic period and largely followed the typical seasonal pattern. However, at the end of 2020 and early 2021, when pneumococcal deaths would typically peak, the rates of death remained lower than normal and stayed lower than expected in the spring of 2021. Starting around mid-2021, there was a notable spike above baseline that coincided with the Delta wave of COVID-19. The 2021 winter – 2022 spring peak followed the pre-pandemic trend. Some of the changes could be attributed to changes in the seasonality of respiratory viruses that interact with pneumococcus. The prevalence of certain risk factors among pneumococcal deaths elevated following the pandemic, including obesity (OR = 1.40), diabetes mellitus without complication (OR = 1.39) and heart failure (OR = 1.31).ConclusionsThe COVID-19 pandemic significantly disrupted pneumococcal mortality patterns in ways that were distinct from the changes described in clinical cases of invasive pneumococcal disease.Key pointsCOVID-19 pandemic significantly disrupted pneumococcal mortality patterns. Respiratory viruses are important trigger for pneumococcal diseases.
Macrophages promote collagen deposition through circadian regulation of fibroblasts
Authors: Lowles Katherine , Cutiongco Marie F.A. , Hughes Joshua J. , Li Shiyang , Knox John , Coy Madeleine , Lin Wei-Hsiang , MacDonald Andrew S. , Kadler Karl E. , Meng Qing Jun , Hussell Tracy , Chang Joan 
Published: February 2025

AbstractCollagen deposition in fibroblasts, the primary collagen-producing cells, is regulated by both macrophages and the circadian rhythm, although how these regulatory processes interact with one another is unknown. Here, we reveal that macrophage-fibroblast interaction enhances collagen deposition which requires a functional circadian rhythm. This response is also dependent on macrophage polarisation status, where M0 (naïve) and M1 (pro-inflammatory) macrophages require direct cell-cell contact; whereas M2 (anti-inflammatory) macrophages utilise an additional mechanism through secreted soluble factors that strengthen circadian rhythms and significantly increase collagen deposition in fibroblasts, independent of cell-cell contact. Using mass spectrometry proteomics analysis, we identified PDGFA as a key factor in induction of circadian amplitude in fibroblasts. Crucially, macrophages lacking PDGFA showed diminished ability to modulate fibroblast circadian rhythms and collagen production. Further, in fibroblasts with impaired circadian rhythms, neither macrophages nor macrophage-secreted factors are capable of inducing collagen deposition. These results confirmed that the collagen secretory pathway is also under circadian clock control in lung fibroblasts, and demonstrated that macrophages influence collagen deposition via circadian clock mediated mechanisms. In conclusion, our findings highlight M2-derived PDGFA as a key macrophage-derived factor in extracellular matrix remodelling.
Endogenous structure of antimalarial targetPfATP4 reveals new class of apicomplexan P-type ATPase modulators
Authors: Haile Meseret T. , Shukla Anurag , Zhen James , Mather Michael W. , Bhatnagar Suyash , Zhang Zhening , Vaidya Akhil B. , Ho Chi-Min 
Published: February 2025

AbstractThePlasmodium falciparumsodium efflux pumpPfATP4 is a leading antimalarial target, but suffers from a lack of high-resolution structural information needed to identify functionally important features in conserved regions and guide rational design of next generation inhibitors. Here, we determine a 3.7Å cryoEM structure ofPfATP4 purified from CRISPR-engineeredP. falciparumparasites, revealing a previously unknown, apicomplexan-specific binding partner,PfABP, which forms a conserved, likely modulatory interaction withPfATP4. The discovery ofPfABP presents a new avenue for designing novelPfATP4 inhibitors.
First Measurement of Missing Energy due to Nuclear Effects in Monoenergetic Neutrino Charged-Current Interactions
Authors: Marzec E. , Ajimura S. , Antonakis A. , Botran M. , Cheoun M. K. , Choi J. H. , Choi J. W. , Choi J. Y. , Dodo T. , Furuta H. , Goh J. H. , Haga K. , Harada M. , Hasegawa S. , Hino Y. , Hiraiwa T. , Hwang W. , Iida T. , Iwai E. , Iwata S. , Jang H. I. , Jang J. S. , Jang M. C. , Jeon H. K. , Jeon S. H. , Joo K. K. , Jung D. E. , Kang S. K. , Kasugai Y. , Kawasaki T. , Kim E. J. , Kim J. Y. , Kim E. M. , Kim S. Y. , Kim W. , Kim S. B. , Kinoshita H. , Konno T. , Kuwata K. , Lee D. H. , Lee S. , Lim I. T. , Little C. , Maruyama T. , Masuda S. , Meigo S. , Monjushiro S. , Moon D. H. , Nakano T. , Niiyama M. , Nishikawa K. , Noumachi M. , Pac M. Y. , Park B. J. , Park H. W. , Park J. B. , Park J. S. , Park J. S. , Park R. G. , Peeters S. J. M. , Roellinghoff G. , Rott C. , Ryu J. W. , Sakai K. , Sakamoto S. , Shima T. , Shin C. D. , Spitz J. , Stancu I. , Suekane F. , Sugaya Y. , Suzuya K. , Taira M. , Takeuchi Y. , Wang W. , Waterfield J. , Wei W. , White R. , Yamaguchi Y. , Yeh M. , Yeo I. S. , Yoo C. , Yu I. , Zohaib A. ,   <math xmlns="http://www.w3.org/1998/Math/MathML" display="inline"><mrow><msup><mrow><mi>JSNS</mi></mrow><mn>2</mn></msup></mrow></math> Collaboration
Published: February 2025

We present the first measurement of the missing energy due to nuclear effects in monoenergetic, muon neutrino charged-current interactions on carbon, originating from K+→μ+νμ decay at rest (Eνμ=235.5  MeV), performed with the J-PARC Sterile Neutrino Search at the J-PARC Spallation Neutron Source liquid scintillator based experiment. Toward characterizing the neutrino interaction, ostensibly νμn→μ−p or νμC12→μ−N12, we define the energy as the energy transferred to the nucleus (ω) minus the kinetic energy of the outgoing proton(s), Em≡ω−∑Tp, and relate this to visible energy in the detector, Em=Eνμ(235.5  MeV)−mμ(105.7  MeV)+[mn−mp(1.3  MeV)]−Evis. The missing energy, which is naively expected to be zero in the absence of nuclear effects (e.g., nucleon separation energy, Fermi momenta, and final-state interactions), is uniquely sensitive to many aspects of the interaction, and has previously been inaccessible with neutrinos. The shape-only, differential cross section measurement reported, based on a (77±3)% pure double-coincidence kaon decay-at-rest signal (621 total events), provides detailed insight into neutrino-nucleus interactions, allowing even the nuclear orbital shell of the struck nucleon to be inferred. The measurement provides an important benchmark for models and event generators at hundreds of MeV neutrino energies, characterized by the difficult-to-model transition region between neutrino-nucleus and neutrino-nucleon scattering, and relevant for applications in nuclear physics, neutrino oscillation measurements, and Type-II supernova studies.

Published by the American Physical Society
2025
Causes, effects and solutions of delay and cost overruns in Iranian deep excavation projects
Authors: Bayandor Sara , Kalatehjari Roohollah , Akherati Reza , Kasebzadeh Jalal 
Published: February 2025

PurposeThrough a case study for Iran, this research seeks to pinpoint the dominant causes of delay and cost overruns in two standard Support of Excavation methods (Bracing strut and top-down construction) in deep excavation projects from various points of view involving contractors, consultants and owners. This investigation identifies the root causes, compares them with existing literature to find similarities and differences with tunnelling and construction projects and proposes practical solutions.Design/methodology/approachThe primary factors were identified after an extensive literature review and expert interview. Subsequently, a questionnaire was designed to classify related factors, considering impact indices, occurrence likelihood and overall significance. Eventually, the findings of the analysis were visually represented through cause-and-effect diagrams.FindingsThe results indicate that “inflation and exchange rate fluctuation” is the top-rated cause, followed by designers’ limited overall perspective of implementation issues. Also, comparing the roles of related teams shows that the contractor sector is the most responsible for delay and overruns in both methods. Finally, practical solutions are presented regarding the main affecting factors.Originality/valuePrior research often addresses delay and costs in construction, but insufficient focus is given to deep excavation projects, particularly in Iran. This study not only fills the identified knowledge gap but also delves into the causes of delay, pursued until the fourth bone in some cases and proposes a solution framework derived from previous research, case studies and expert insights to mitigate construction delay.
Co-creating inclusive work-integrated learning opportunities: insights for stakeholders
Authors: Wilkinson Helene , Nagar Swati 
Published: February 2025

Purpose
This study aims to position work-integrated learning (WIL) as a transformative pedagogy for international business (IB) education. By embedding diversity, equity and inclusion (DEI) into WIL, the authors demonstrate how universities can better prepare IB students to navigate global challenges and thrive in multicultural, dynamic business environments. WIL brings together students, industry and higher education providers to meet the needs of the labour market, where DEI increasingly matter from both a business case and social justice perspective. Building on over 30 years of cumulative experience in industry engagement and WIL, the authors discuss key forces, trends, challenges and opportunities in co-creating inclusive WIL opportunities for an increasingly diverse group of learners.

Design/methodology/approach
Drawing on illustrative examples and institutional best practices the authors discuss the experiences in WIL and posit that a practically driven pedagogical approach to IB education can co-create an inclusive WIL environment.

Findings
Embedding DEI within WIL not only enhances inclusivity but also equips IB students with critical skills such as cultural intelligence adaptability and emotional resilience. These capabilities enable learners to effectively navigate the complexities contexts and connections unique to IB as a field. The authors argue for a systematic DEI-driven WIL approach to foster better integration of academic knowledge with real-world IB practices.

Originality/value
Existing literature discusses WIL as a practice-based learning approach but limited research examines its intersection with DEI in the context of IB education. The viewpoint bridges this gap showcasing specific strategies and best practices that enhance IB students’ readiness for global industries. The authors propose a framework for embedding DEI into WIL informed by both institutional initiatives and theoretical insights to improve employability and global competence diversity co-creation equity and inclusion.
Effects of surface texture on tribological performance and bonding strength of phosphate coatings in cylindrical thrust roller bearings
Authors: Xu Xiao , Zhang Yimin , Gao Shuzhi 
Published: February 2025

Purpose
This study aims to enhance the bonding strength and wear performance of manganese phosphate conversion coatings on cylindrical thrust roller bearings (CTRBs) through laser surface texturing.

Design/methodology/approach
This study uses laser surface texturing to enhance the bonding strength and wear performance of manganese phosphate conversion coatings on GCr15 bearing steel. A laser marking machine is used to create micro-groove textures, and a micro-scratch test evaluates the effects of texturing parameters on coating adhesion. Friction and wear tests analyze the impact of textured coatings on CTRBs.

Findings
The results indicate that the textured coatings exhibit a 16.7% increase in scratch hardness and a 20.1% improvement in scratch shear strength compared to the untextured coatings. Friction and wear testing machines are used to analyze the effects of different texturing parameters and positions on the wear performance of the coated bearings. The results show that, compared to untextured coated bearings, the textured coated bearings can achieve a maximum reduction of 20.3% in friction temperature during testing, a 32.9% decrease in average friction force and a 20.8% reduction in wear losses.

Originality/value
This study introduces laser surface texturing as a novel approach to enhance the bonding strength and tribological performance of manganese phosphate conversion coatings.

Peer review
The peer review history for this article is available at: https://publons.com/publon/10.1108/ILT-12-2024-0484/
Impact of non-tariff measures on India’s exports to ASEAN
Authors: Takkar Ittika , Bhattacharjee Mahua , Tandon Anjali 
Published: February 2025

Purpose
This study aims to assess the impact of non-tariff measures (NTMs) imposed by the Association of South East Nations (ASEAN) on India’s exports and examine whether India’s free trade agreements (FTAs) with the ASEAN have played any role in reducing any trade-impeding impact of NTMs.

Design/methodology/approach
An augmented gravity model has been used. Poisson pseudo maximum likelihood regression and random effect generalized least squares model with time, sector and importer specific effects have been used along with clustered standard errors.

Findings
Sanitary and phytosanitary measures, technical barriers to trade, quality control measures, measures affecting competition and trade-investment measures have positively impacted India’s exports to ASEAN. Finance measures negatively impact India’s exports. Pre-shipment inspection measures and price control measures negatively impact India’s exports at HS2-digit and positively impact ASEAN’s imports from India at HS6-digit. Export-related measures positively impact India’s exports at HS2-digit and negatively impact the mirror data at HS6-digit. India’s FTAs with ASEAN countries have helped in reducing the trade-impeding impact of NTMs.

Originality/value
Studies assessing the impact of NTMs on India’s trade have concentrated largely on establishing only the imposition of NTMs. Those studies that have quantified the impact of NTMs on India’s trade have focused only on select sectors. Thus, this paper is novel in assessing the impact of NTMs on India’s overall exports to ASEAN and examining the role of FTAs in reducing any trade-impeding impact of NTMs for India.
Strategic innovation: exploring governance drivers of FinTech investments
Authors: Ferri Luca , Spagnuolo Flavio , Troise Ciro , Zampella Annamaria 
Published: February 2025

PurposeThe innovation brought by FinTech is strategically transforming the business models of banking entities, their operational efficiency and their relationship with customers and stakeholders. Although the financial drivers behind FinTech investments have been extensively explored, there remains a gap in the extant research regarding the influence of governance factors on these kinds of investments. This study seeks to address this gap by investigating whether and how governance composition and characteristics are associated with investments in FinTech projects, exploring a sample of Cooperative Credit Banks (CCBs) operating in Italy, a unique context where these small institutions represent more than half of the banking sector and that often face difficulties in adopting innovative and digital tools.Design/methodology/approachThis study adopted a quantitative approach. Specifically, multiple regressions analyses were performed on a sample of 230 Italian CCBs during the period 2017–2022.FindingsWe find that the presence of a corporate social responsibility committee, managers with high IT skills, Board’s gender diversity, younger generation of managers and their educational level can significantly stimulate FinTech investments.Originality/valueThe study contributes to enriching the literature on FinTech and digital transformation in the banking sector, offering particular insights for regulators and managers of CCBs, who are particularly sensitive to innovation matters and increasingly inclined to strategically satisfy the needs of a 4.0 clientele.