bluuebunny/crossref_metadata_2025_split huggingface dataset:
scplainer: using linear models to understand mass spectrometry-based single-cell proteomics data
Authors: Vanderaa Christophe , Gatto Laurent 
Published: December 2023

AbstractAnalysing mass spectrometry (MS)-based single-cell proteomics (SCP) data is challenging. The data analysis must address numerous problems that are inherent to both MS-based proteomics technologies and single-cell experiments. This has led to the development of complex and divergent data processing workflows within the field. In this work, we present scplainer, a principled and standardised approach for extracting meaningful insights from SCP data. The approach relies on minimal data processing combined with linear modelling. The approach is a simple yet powerful approach for exploring and interpreting various types of SCP data. scplainer performs variance analysis, differential abundance analysis and component analysis while streamlining the visualization of the results. This thorough exploration enhances our capacity to gain a deeper understanding of the biological processes hidden in the data. Finally, we demonstrate that scplainer corrects for technical variability, and even enables the integration of data sets from different SCP experiments. The approach effectively generates high-quality data that are amenable to perform downstream analyses. In conclusion, this work reshapes the analysis of SCP data by moving efforts from dealing with the technical aspects of data analysis to focusing on answering biologically relevant questions.
NMDAR Phosphoproteome Controls Synaptic Growth and Learning
Authors: Funahashi Yasuhiro , Ahammad Rijwan Uddin , Zhang Xinjian , Hossen Emran , Kawatani Masahiro , Nakamuta Shinichi , Yoshimi Akira , Wu Minhua , Wang Huanhuan , Wu Mengya , Li Xu , Faruk Md. Omar , Shohag Md Hasanuzzaman , Lin You-Hsin , Tsuboi Daisuke , Nishioka Tomoki , Kuroda Keisuke , Amano Mutsuki , Noda Yukihiko , Yamada Kiyofumi , Sakimura Kenji , Nagai Taku , Yamashita Takayuki , Uchino Shigeo , Kaibuchi Kozo 
Published: December 2023

AbstractIn the mammalian brain, NMDA receptors (NMDARs) activation triggers a calcium-dependent signal transduction cascade resulting in postsynaptic remodeling and behavioral learning. However, the phosphoprotein signal flow through this transduction network is poorly understood. Here, we show that NMDAR-dependent phosphorylation drives the assembly of protein signaling complexes that regulate synaptic morphology and behavior. We performed large-scale phosphoproteomic analyses of protein kinase target proteins in successive layers of the signaling network in mouse striatal/accumbal slices. NMDARs activation resulted in the phosphorylation of 194 proteins, including Rho GTPase regulators. CaMKII-mediated phosphorylation of ARHGEF2 increased its RhoGEF activity, thereby activating the RhoA-Rho-kinase pathway. Subsequent phosphoproteomics of Rho-kinase revealed 221 protein targets, including SHANK3. Experimental validation revealed a pathway from NMDAR-dependent calcium influx through CaMKII, ARHGEF2, Rho-kinase, and SHANK3 to coordinate assembly of an actin-tethered postsynaptic complex of SHANK3/NMDAR/PSD95/DLGAP3 for spine growth and aversive learning. These findings show that NMDARs initiate metabolic phosphorylation for learning.
MeXpose - A modular imaging pipeline for the quantitative assessment of cellular metal bioaccumulation
Authors: Braun Gabriel , Schaier Martin , Werner Paulina , Theiner Sarah , Zanghellini Jürgen , Wisgrill Lukas , Fyhrquist Nanna , Koellensperger Gunda 
Published: December 2023

AbstractWe introduce MeXpose, an imaging pipeline for single-cell metallomics by laser ablation inductively coupled plasma time-of-flight mass spectrometry (LA-ICP-TOFMS). MeXpose is designed for mechanistic studies on metal exposure unravelling cellular phenotypes and tissue level characteristics of metal bioaccumulation. MeXpose leverages the high-resolution capabilities of low-dispersion laser ablation setups, a standardised approach to quantitative bioimaging, and the toolbox of immunohistochemistry using metal-labelled antibodies for cellular phenotyping. MeXpose further offers the full scope of single-cell metallomics via an extended mass range accessible through ICP-TOFMS instrumentation (covering isotopes from m/z 14-256) and integration of a complete image analysis workflow. This enables studying quantitative metal accumulation in phenotypically characterized tissue at cellular resolution. Metal amounts in the sub-fg range per cell can be absolutely quantified. As a showcase, anex vivohuman skin model exposed to cobalt chloride (CoCl2) was investigated. Metal permeation was studied for the first time at single-cell resolution, showing high bioaccumulation in the epidermal layers and especially in mitotic cells, accumulating cobalt (Co) in the low fg range per cell. In this cellular phenotype, Co accumulation was correlated to DNA damage. While the amount of cobalt was significantly lower in the collagenous matrix of the dermal layer, cells in the vicinity of blood vessels and smooth muscle showed significant Co deposits as well. MeXpose provides unprecedented insights into metal bioaccumulation with the ability to explore novel relationships between metal exposure and cellular responses on a single-cell level, paving the way for advanced toxicological and therapeutic studies.Graphical abstract
Fine tuning of Rpb4 phosphorylation modulates Rpb4/7 stoichiometry within yeast RNA polymerase II and regulates gene expression
Authors: González-Jiménez Araceli , González-Jiménez María del Carmen , Jordán-Pla Antonio , Medina Ithaisa , Alfonso Manuel J. , Richard Stephen , Fernández-Tornero Carlos , Choder Mordechai , Calvo Olga 
Published: December 2023

AbstractRNA polymerase II (RNAPII) consists of 12 subunits, including Rpb4 and Rpb7, which form a heterodimeric stalk domain. In yeast, assembly of Rpb4/7 with the 10-subunit “core” is substoichiometric. Aside from its role in transcription, Rpb4/7 also binds to mRNAs co-transcriptionally (mRNA imprinting), exits the nucleus together with the mRNA, and modulates subsequent cytoplasmic processes like translation and degradation. However, the mechanisms underlying Rpb4/7 functions and its association with RNAPII remain poorly understood. In this study, we identify five phosphorylation sites in Rpb4 that regulate various steps of mRNA and snoRNA biogenesis, including transcription elongation and the polyadenylation step. We also provide evidence that the kinase Hrr25 and the phosphatase Fcp1, known to target the carboxyl-terminal domain (CTD) of Rpb1 and participate in processes at gene 3′-ends, coordinate Rpb4 phosphorylation. Inefficient Rpb4 phosphorylation leads to increased Rpb4 association with RNAPII, particularly at gene 3′-ends, suggesting that Rpb4-P promotes stalk dissociation from RNAPII either before or during transcription termination. Collectively, our findings underscore the pivotal role of dynamic Rpb4 phosphorylation in regulating Rpb4/7 stoichiometry as well as transcription elongation and termination, with an impact on mRNA imprinting.
Learning regular cross-trial shifts of the target location in serial search involves awareness – an eye-tracking study
Authors: Yu Hao , Allenmark Fredrik , Müller Hermann J. , Shi Zhuanghua 
Published: December 2023

AbstractPeople can learn, and utilize, not only static but also dynamic (cross-trial) regularities in the positioning oftargetitems in parallel, ‘pop-out’ visual search. However, while static target-location learning also works in serial search, acquiring dynamic regularities seems prevented by the demands imposed by item-by-item scanning. Also, questions have been raised regarding a role of explicit awareness for utilizing (at least) dynamic regularities to optimize performance. The present study re-investigated whether dynamic regularities may be learned in serial search when regular shifts of the target location occur frequently, and whether such learning would correlate with awareness of the dynamic rule. To this end, we adopted the same regularity used by Yu et al. (2023) to demonstrate dynamic learning in parallel search: a cross-trial shift of the target location in, e.g., clockwise direction within a circular array in 80% of the trials, which was compared to irregular shifts in the opposite (e.g., counterclockwise; 10%) or some other, random direction (10%). The results showed that ⅔ of participants learned the dynamic regularity, with their performance gains correlating with awareness: the more accurately they estimated how likely the target shifted in the frequent direction, the greater their gains. Importantly, part of the gains accrued already early during search: a large proportion of the very first and short-latency eye movements was directed to the predicted location, whether or not the target appeared there. We discuss whether this rule-driven behavior is causally mediated by conscious control. (248 words).
Curvature-induced lipid sorting beyond the critical packing parameter
Authors: König M. , de Vries R. , Grünewald F. , Marrink S.J. , Pezeshkian W. 
Published: December 2023

AbstractOver the last few decades, the spatial organization of biomembranes has received a lot of attention. With the fluid mosaic model, Singer and Nicolson proposed that biomembranes behave as two-dimensional fluids, allowing proteins and lipids to diffuse freely and thus react to external stimuli. Biological functionality and membrane organization are intricately linked to each other, however, how these organizations emerge is yet to be established. Here we use coarse-grained molecular dynamics simulations to explore the relationship between membrane shape and lateral organization at the nanoscale for a broad range of lipid mixtures. Our results illustrate that membrane curvature and lateral organization are intimately linked at the nanoscale and the relationship is much more complicated compared to the traditional views, in particular the lipid shape concept. Furthermore, we show that large membrane curvature can disrupt phase separation, line tension, and interleaflet coupling leading to non-intuitive lipid sorting. Our findings highlight how curvature-driven sorting can alter the phase behavior of lipid mixtures, which could be crucial for cellular functionality.
An RNAi screen to identify proteins required for cohesion rejuvenation during meiotic prophase in Drosophila oocytes
Authors: Haseeb Muhammad A. , Bernys Alana C. , Dickert Erin E. , Bickel Sharon E. 
Published: December 2023

AbstractAccurate chromosome segregation during meiosis requires maintenance of sister chromatid cohesion, initially established during premeiotic S phase. In human oocytes, DNA replication and cohesion establishment occur decades before chromosome segregation and deterioration of meiotic cohesion is one factor that leads to increased segregation errors as women age. Our previous work led us to propose that a cohesion rejuvenation program operates to establish new cohesive linkages during meiotic prophase in Drosophila oocytes and depends on the cohesin loader Nipped-B and the cohesion establishment factor Eco. In support of this model, we recently demonstrated that chromosome-associated cohesin turns over extensively during meiotic prophase and failure to load cohesin onto chromosomes after premeiotic S phase results in arm cohesion defects in Drosophila oocytes. To identify proteins required for prophase cohesion rejuvenation but not S phase establishment, we conducted a Gal4-UAS inducible RNAi screen that utilized two distinct germline drivers. Using this strategy, we identified 29 gene products for which hairpin expression during meiotic prophase, but not premeiotic S phase, significantly increased segregation errors. Prophase knockdown of Brahma or Pumilio, two positives with functional links to the cohesin loader, caused a significant elevation in the missegregation of recombinant homologs, a phenotype consistent with premature loss of arm cohesion. Moreover, fluorescence in situ hybridization confirmed that Brahma, Pumilio and Nipped-B are required during meiotic prophase for maintenance of arm cohesion. Our data support the model that Brahma and Pumilio regulate Nipped-B dependent cohesin loading during rejuvenation. Future analyses will better define the mechanism(s) that govern meiotic cohesion rejuvenation and whether additional prophase-specific positives function in this process.
Use it or lose it: fiscal year-end corporate investment around the world
Authors: Kim Yong H. , Li Bochen , Shin Hyun-Han , Wu Wenfeng 
Published: December 2023

PurposeIt is documented that companies and government agencies in the USA invest more in the fourth fiscal quarter without having higher investment opportunities. While previous studies focus on the agency conflicts and information asymmetry within organizations, this study is motivated by Scharfstein and Stein's (2000) two-tiered agency model and aims to examine how firms' external business environment affects the “fourth quarter effect.”Design/methodology/approachThe authors implement this study in a sample of 41 countries and observe similar seasonality in firm investment as documented in the US market.FindingsMore importantly, using country characteristics, this study finds that firms from countries with better investor rights and protection, and more developed financial markets show less severe over-investment in the fourth fiscal quarter.Originality/valueThis paper contributes to the literature of law and finance, and the internal capital market, by investigating the quarterly investment patterns of firms from 41 countries. The authors find that similar to the results in earlier studies on the US market, firms in the global market increase their capital expenditure in the fourth fiscal quarter, indicating that the internal agency conflicts between the headquarters and divisional managers are widespread across the world. The authors also find that firms that operate in countries with higher investor rights and protection, and more developed financial markets, tend to show less severe “fourth quarter effect”.
Gender-related effects of financial knowledge and confidence on preferences for ethical intermediaries and sustainable investments
Authors: Aristei David , Gallo Manuela 
Published: December 2023

PurposeThis study analyses the role of individuals' objective financial knowledge in shaping preferences for ethical intermediaries and sustainable investments in Italy. Another goal of this study is to assess the impact of individuals' misperceptions about their own financial knowledge and to test for gender-related differences in attitudes towards socially responsible investing (SRI).Design/methodology/approachUsing nationally representative microdata from the Bank of Italy’s “Italian Literacy and Financial Competence Survey” (IACOFI), the authors use probit models, extended to account for potential endogeneity issues, to assess the causal effects of financial knowledge and confidence on stated preferences for SRI. Empirical models also allow to explicitly assess the moderating role of gender on the effects of financial knowledge and confidence on attitudes towards sustainable investing.FindingsResults indicate that individuals' preferences for sustainable finance significantly increase with financial knowledge, suggesting that inadequate financial competencies represent a barrier to participation in SRI. At the same time, lack of confidence in one’s own financial knowledge significantly hampers attitudes towards sustainable investments. Furthermore, the authors show that women have a greater preference for sustainable finance than men and point out that financial knowledge and confidence exert heterogenous effects on attitudes towards SRI.Originality/valueThis study provides several contributions to the literature on SRI. First, the authors give evidence of the causal effect of financial knowledge on preferences for both ethical financial intermediaries and sustainable investments. Moreover, this is the first study to investigate the role of financial underconfidence bias in shaping individuals' SRI attitudes. Finally, extending previous research, the authors assess differences in SRI preferences between women and men and provide novel evidence on gender-related heterogeneity in the effects of financial knowledge and underconfidence.
Intelligent algorithms applied to the prediction of air freight transportation delays
Authors: Mendonça Guilherme Dayrell , Oliveira Stanley Robson de Medeiros , Lima Jr Orlando Fontes , Resende Paulo Tarso Vilela de 
Published: December 2023

PurposeThe objective of this paper is to evaluate whether the data from consignors, logistics service providers (LSPs) and consignees contribute to the prediction of air transport shipment delays in a machine learning application.Design/methodology/approachThe research database contained 2,244 air freight intercontinental shipments to 4 automotive production plants in Latin America. Different algorithm classes were tested in the knowledge discovery in databases (KDD) process: support vector machine (SVM), random forest (RF), artificial neural networks (ANN) and k-nearest neighbors (KNN).FindingsShipper, consignee and LSP data attribute selection achieved 86% accuracy through the RF algorithm in a cross-validation scenario after a combined class balancing procedure.Originality/valueThese findings expand the current literature on machine learning applied to air freight delay management, which has mostly focused on weather, airport structure, flight schedule, ground delay and congestion as explanatory attributes.
Toward a new framework for teaching algorithmic literacy
Authors: Archambault Susan Gardner 
Published: December 2023

PurposeResearch shows that postsecondary students are largely unaware of the impact of algorithms on their everyday lives. Also, most noncomputer science students are not being taught about algorithms as part of the regular curriculum. This exploratory, qualitative study aims to explore subject-matter experts’ insights and perceptions of the knowledge components, coping behaviors and pedagogical considerations to aid faculty in teaching algorithmic literacy to postsecondary students.Design/methodology/approachEleven semistructured interviews and one focus group were conducted with scholars and teachers of critical algorithm studies and related fields. A content analysis was manually performed on the transcripts using a mixture of deductive and inductive coding. Data analysis was aided by the coding software program Dedoose (2021) to determine frequency totals for occurrences of a code across all participants along with how many times specific participants mentioned a code. Then, findings were organized around the three themes of knowledge components, coping behaviors and pedagogy.FindingsThe findings suggested a set of 10 knowledge components that would contribute to students’ algorithmic literacy along with seven behaviors that students could use to help them better cope with algorithmic systems. A set of five teaching strategies also surfaced to help improve students’ algorithmic literacy.Originality/valueThis study contributes to improved pedagogy surrounding algorithmic literacy and validates existing multi-faceted conceptualizations and measurements of algorithmic literacy.
Impact of accrual and real earnings management on the stock liquidity: the month-of-the-year and Ramadan effects
Authors: Salehi Allah Karam , Soleimanizadeh Elham 
Published: December 2023

Purpose
The abnormality of the month-of-the-year and Ramadan effects has extensively existed in the stock and other markets. The commercial strategy pattern and the computation of such predictable patterns in the market allow investors to make money. By using anomalies such as the month-of-the-year and the Ramadan effects on earnings management (EM), it is possible to achieve such a goal. This study aims to investigate the month-of-the-year effect and the Ramadan effect on the relationship between accrual earnings management and real earnings management (AEM and REM, respectively) and liquidity in the Iranian capital market.

Design/methodology/approach
This empirical analysis comprises a panel data set of 80 listed firms (400 observations) on the Tehran Stock Exchange from 2016 to 2020.

Findings
The findings exhibit that when AEM and REM increase, information asymmetry also increases. The simultaneous increase of these variables leads to a decrease in stock liquidity. Furthermore, the results indicate that the month-of-the-year and Ramadan effects intensify the negative relationship between AEM and REM with stock liquidity. Therefore, EM is affected by the investor’s behavior in specific months.

Practical implications
Anomalies caused by the Ramadan effect and the month-of-the-year effect on reducing liquidity in the Iranian stock market were confirmed. Investors can use these anomalies to identify predictable patterns, exchange securities according to those patterns and earn abnormal returns.

Originality/value
To the best of the authors’ knowledge, this is the first study that empirically examined the simultaneous effect of Gregorian and Islamic calendar anomalies on the relationship between EM and liquidity, and while helping managers and other readers, it can be the basis for future research.
The impact of westernisation on the purchase intention of cruelty-free products: a study based on the Sri Lankan cosmetic market
Authors: Dodanwala Kavisha Lashindri , Weerasekera Sandun 
Published: December 2023

PurposeA surge in demand for ethical products, including cruelty-free products, has been well documented in recent years, with direct ramifications for businesses. This trend towards ethical consumption seemed to be swiftly replicated in Eastern countries, especially in South Asian nations, as a result of westernisation. Based on the theory of planned behaviour and the concept of the attitude-behaviour gap, this study aims to investigate the impact of westernisation on the purchase intention of cruelty-free cosmetic products.Design/methodology/approachA positivist research paradigm was utilised in this study. Accordingly, an online self-administered questionnaire was shared among 242 consumers of cosmetic products in Sri Lanka in order to collect responses. The statistical techniques of correlation analysis, the Sobel test and moderator regression analysis have been utilised in this study.FindingsIt was found that there seems to be a positive impact of westernisation and the cruelty-free purchase intention of consumers. Moreover, consumer empowerment appears to mediate this relationship, while the attitude behaviour gap tends to further impact the relationship between consumer empowerment and the purchase intention of cruelty-free products.Originality/valueThis study seems to shed light upon the impact of westernisation on the purchase intention of consumers, especially from an ethical dimension and this study is likely to extend existing studies which have focussed on consumer empowerment, attitude-behaviour gap as well as the theory of planned behaviour, especially in the context of South Asia, where there seems to be a dearth of such investigations. Moreover, this study has attempted to contextualise the construct of “Westernisation” to the South Asian region in line with the tone set by an editorial article Dewasiri et al. (2021).