bluuebunny/crossref_metadata_2025_split huggingface dataset:
Challenging the Astral™mass analyzer - up to 5300 proteins per single-cell at unseen quantitative accuracy to study cellular heterogeneity
Authors: Bubis Julia A. , Arrey Tabiwang N. , Damoc Eugen , Delanghe Bernard , Slovakova Jana , Sommer Theresa M. , Kagawa Harunobu , Pichler Peter , Rivron Nicolas , Mechtler Karl , Matzinger Manuel 
Published: February 2024

ABSTRACTA detailed proteome map is crucial for understanding molecular pathways and protein functions. Despite significant advancements in sample preparation, instrumentation, and data analysis, single-cell proteomics is currently limited by proteomic depth and quantitative performance. We combine a zero dead-end volume chromatographic column running at high throughput with the Thermo Scientific™ Orbitrap™ Astral™ mass spectrometer running in DIA mode. We demonstrate unprecedented depth of proteome coverage as well as accuracy and precision for quantification of ultra-low input amounts. Using a tailored library, we identify up to 7400 protein groups from as little as 250 pg HeLa at a throughput of 50 samples per day (SPD). We benchmark multiple data analysis strategies, estimate their influence on FDR and show that FDR on protein level can easily be maintained at 1 %. Using a two-proteome mix, we check for optimal parameters of quantification and show that fold change differences of 2 can still be successfully determined at single-cell level inputs. Eventually, we apply our workflow to A549 cells yielding a proteome coverage of up to 5300 protein groups from a single cell, which allows the observation of heterogeneity in a cellular population and studying dependencies between cell size and cell-cycle phase. Additionally, our work-flow enables us to distinguish betweenin vitroanalogs of two human blastocyst lineages: naïve human pluripotent stem cells (epiblast) and trophectoderm (TE)-like cells. Gene Ontology analysis of enriched proteins in TE-like cells harmoniously aligns with transcriptomic data, indicating that single-cell proteomics possesses the capability to identify biologically relevant differences between these two lineages within the blastocyst.
Reduction in neurons immunoreactive for parvalbumin, calretinin and calbindin in the anteroventral thalamic nuclei of individuals with Down syndrome
Authors: Perry James C. , Vann Seralynne D. 
Published: February 2024

AbstractThe anterior thalamic nuclei are important for cognition, and memory in particular. However, little is known about how the anterior thalamic nuclei are affected in many neurological disorders partly due to difficulties in selective segmentation inin vivoscans, due to their size and location. Post-mortem studies, therefore, remain a valuable source of information about the status of the anterior thalamic nuclei. We used post-mortem tissue to assess the status of the anteroventral thalamic nucleus in Down syndrome using samples from males and females ranging from 22-65 years in age and comparing to tissue from age matched controls. As expected, there was increased beta-amyloid plaque expression in the Down syndrome group. While there was a significant increase in neuronal density in the Down syndrome group, the values showed more variation consistent with a heterogeneous population. The surface area of the anteroventral thalamic nucleus was smaller in the Down syndrome group suggesting the increased neuronal density was due to greater neuronal packing but likely fewer overall neurons. There was a marked reduction in the proportion of neurons immunoreactive for the calcium-binding proteins calbindin, calretinin, and parvalbumin in individuals with Down syndrome across all ages. These findings highlight the vulnerability of calcium-binding proteins in the anteroventral nucleus in Down syndrome, which could both be driven by, and exacerbate, Alzheimer-related pathology in this region.
Syntactic Sugars: Crafting a Regular Expression Framework for Glycan Structures
Authors: Bennett Alexander R. , Bojar Daniel 
Published: February 2024

AbstractSummaryStructural analysis of glycans pose significant challenges in glycobiology due to their complex sequences. Research questions such as analyzing the sequence content of the α1-6 branch inN- glycans, are biologically meaningful yet can be hard to automate. Here, we introduce a regular expression system, designed for glycans, feature-complete, and closely aligned with regular expression formatting. We use this to annotate glycan motifs of arbitrary complexity, perform differential expression analysis on designated sequence stretches, or elucidate branch-specific binding specificities of lectins in an automated manner. We are confident that glycan regular expressions will empower computational analyses of these sequences.Availability and implementationOur regular expression framework for glycans is implemented in Python and is incorporated into the open-source glycowork package (version 1.1+). Code and documentation are available athttps://github.com/BojarLab/glycowork/blob/master/glycowork/motif/regex.py.Contactdaniel.bojar@gu.se
A genetic locus in the gut microbeBacteroides thetaiotaomicronencodes activities consistent with mucin-O-glycoprotein processing and plays a critical role inN-acetylgalactosamine metabolism
Authors: Ndeh Didier A. , Nakjang Sirintra , Kwiatkowski Kurt J. , Koropatkin Nicole M. , Hirt Robert P. , Bolam David N. 
Published: February 2024

AbstractIt is increasingly appreciated that members of the gut microbiota are key modulators of human health and the status of major diseases including cancer, diabetes and inflammatory bowel disease. Central to their survival is the ability to metabolise complex dietary and host-derived glycans including intestinal mucins. The latter are critical components of the gut epithelium glycocalyx and mucus barriers, essential for microbiota-gut homeostasis and protection from infections by pathogens. The prominent and model human gut microbeBacteroides thetaiotaomicron (B. theta)is a versatile and highly efficient complex glycan degrader thanks to the expansion of gene clusters termed polysaccharide utilisation loci (PULs) in its genome. While the mechanisms for several singular dietary glycan-induced PULs have been elucidated, studies on the 16-18 mucin-induced PULs inB. thetasignificantly lag behind. A combination of the scale and complexity ofB. thetatranscriptomic response to mucins and complex glycan configurations of mucins represent major hurdles for the functional characterisation of the mucin induced PULs. As a result, there is very limited knowledge on how mucin metabolism is coordinated inB. thetaand what specific PULs, genes and metabolites are critical for mucin-B. theta,and more generally mucin-microbiota interactions and their importance in microbiota-gut homeostasis. Here we show that a mucin inducible PUL BT4240-50, (i) encodes activities consistent with a machinery that couples the processing of mucin-O glycan glycoproteins with the metabolism ofN-acetylgalactosamine (GalNAc), an abundant mucin O-glycan sugar; (ii) is important for competitive growth on mucinsin-vitro; (iii) encodes a key kinase enzyme (BT4240) that is critical for GalNAc metabolism and (iv) has related PULs encoded by a range of prominentBacteroidesspecies in the human gut. Furthermore, BT4240 kinase was also critical for glycosaminoglycan metabolism, thus extending the PULs function beyond mucins. Our work advances our understanding of the vital metabolic processes that govern mucosal glycoprotein metabolism and by implication, a key aspect of host-microbiota interactions at mucosal surfaces and highlight GalNAc as a key metabolite targeted for competitive growth.
Research on the heterogeneity of executives’ nonsalary incentives on corporate green technology innovation
Authors: Xu Ning , Zhang Di , Li Yutong , Bai Yingjie 
Published: February 2024

Purpose
Green technology innovation is the organic combination of green development and innovation driven. It is also a powerful guarantee for shaping sustainable competitive advantages of manufacturing enterprises. To explore what kind of executive incentive contracts can truly stimulate green technology innovation, this study aims to distinguish the equity incentive and reputation incentive, upon their contractual elements characteristics and green governance effects, and then put forward suggestions for green technology innovation accordingly.

Design/methodology/approach
This study establishes an evaluation model and uses empirical methods to test. Concretely, using data from A-share listed manufacturing companies for the period from 2007 to 2020, this study compares and analyzes the impact of equity and reputation incentive on green technology innovation and explores the relationship between internal green business behavior and external green in depth.

Findings
This study finds that reputation incentives focus on long-term and non-utilitarian orientation, which can promote green technology innovation in enterprises. While equity incentives, linked to performance indicators, have a inhibitory effect on green technology innovation. Internal and external institutional factors such as energy conservation measures, the “three wastes” management system, and environmental recognition play the regulatory role in the relationship between incentive contracts and green technology innovation.

Originality/value
Those findings validate and expand the efficient contracting hypothesis and the rent extraction hypothesis from the perspective of green technology innovation and provide useful implications for the design of green governance systems in manufacturing enterprises.
“Respect existence or expect … resilience?” epistemic reflexivity towards liberated disaster studies
Authors: Fuentealba Ricardo 
Published: February 2024

PurposeThis paper proposes a way of reflexing on how we think within critical disaster studies. It focuses on the biases and unthought dimensions of two concepts – resilience and development – and reflects on the relationship between theory and practice in critical disaster studies.Design/methodology/approachPremised on the idea of epistemic reflexivity developed by Pierre Bourdieu, and drawing on previous research, this theoretical article analyses two conceptual biases and shortcomings of disaster studies: how resilience builds on certain agency; and how development assumes certain political imagination.FindingsThe article argues that critical disaster scholars must reflect on their own intellectual practice, including the origin of concepts and what they do. This is exemplified by a description of how the idea of resistance is intimately connected to that of resilience, and by showing that we must go beyond the capitalist realism that typically underlies development and risk creation. The theoretical advancement of our field can provide ways of thinking about the premises of many of our concepts.Originality/valueThe paper offers an invitation for disaster researchers to engage with critical thought and meta-theoretical reflexions. To think profoundly about our concepts is a necessary first step to developing critical scholarship. Epistemic reflexivity in critical disaster studies therefore provides an interesting avenue by which to liberate the field from overly technocratic approaches and develop its own criticality.
Global research mapping in records and archives management: an investigation
Authors: Moid Abdul , Raza M. Masoom , Javed Mohammad , Jahan Keshwar 
Published: February 2024

Purpose
Records are current documents containing crucial personal, legal, financial and medical information, while archives house non-current documents with the same details. This study specifically aims to measure existing research in records and archives management with various scientific indicators.

Design/methodology/approach
Data extraction was conducted using the Web of Science, resulting in a data set of 2003 records for further analysis. Biblioshiny and VOSviewer have been used for mapping and visualization of the extracted data.

Findings
Managing and organizing this essential information is equally vital to maintaining records and archives. The findings encompass various aspects such as publications and citations, influential authors, source impact factors, relevant articles, affiliations, co-authorship trends across the top 10 countries and regions, references, publication year spectroscopy, keyword co-occurrence and historiography. The study concludes that medical records management prominently dominates the selected research area.

Originality/value
The study reflects the advancements in management systems and continues to emerge as research on the management of records and archives has gained significance.
Embracing a rubber rice bowl: women’s transition from paid work to self-employed entrepreneurship in coastal China
Authors: Song Jing 
Published: February 2024

Purpose
This study aims to examine why women transition from wage work to self-employed entrepreneurship, the seemingly insecure and unruly economic sector compared with the stable iron rice bowl and the fancy spring rice jobs.

Design/methodology/approach
Based on in-depth interviews in Zhejiang, the entrepreneurial hotbed in coastal China, this study examines the experiences of self-employed female entrepreneurs who used to work in the iron rice bowl and the spring rice jobs and explores their nonconventional career transition and its gendered implications.

Findings
This study finds that these women quit their previous jobs to escape from gendered suppression in wage work where their femininity was stereotyped, devalued or disciplined. By working for themselves, these women embrace a rubber rice bowl that allows them to improvise different forms of femininity that are better rewarded and recognized.

Originality/value
The study contributes to studies on gender and work by framing femininity as a fluid rather than a fixed set of qualities and fills the research gap by illustrating women’s agency in reacting to gender expectations in certain workplaces. The study develops a new concept of rubber rice bowl to describe how entrepreneurship, a seemingly women-unfriendly sphere, attracts women by allowing them to comply with, resist, or improvise normative gender expectations.
A critical review of personal protective equipments in relation to pandemics
Authors: Sunny Georgy , Lalkrishna S. , James Jerin , Suprasannan Sreejith 
Published: February 2024

PurposePersonal Protective Equipment plays an inevitable part in the current scenario of pandemics in the world. A novel coronavirus, Severe Acute Respiratory Syndrome-Corona Virus-2 (SARS-Cov 2), began as an outbreak of pneumonia in Wuhan, China, in late December 2019, and quickly spread worldwide. It quickly escalated into an international public health crisis. This opened up the high demand for the innovation and research of new materials in the Personal Protective Equipment industry.Design/methodology/approachPubMed, Embase and Google Scholar were searched for relevant literature regarding personal protective equipment and the information was organized in a systematic way.FindingsThere are no adequate number of studies taken up in the field of use of textiles in medical applications especially with PPEs.Research limitations/implicationsThis structured review will generate a sense of the significance of using PPE for controlling pandemics and also awaken need for additional research and innovations in this area.Practical implicationsThe authorities of the management should take timely intervention in choosing the right material for their PPE in their hospitals. Hence health care professionals teams have an inevitable role in preventing the adverse environmental impact due to the inadvertent disposal of PPEs.Social implicationsThere is a lack of systematic way of disposing contaminated single-use face masks in a safe, environmentally acceptable manner. The dumping of single-use PPE in domestic garbage has had an adverse effect on the environment. Mismanaged plastic waste endangers the health of ecosystems by polluting marine and terrestrial environments, posing a significant risk of ingestion or injury to animals and contaminating habitats.Originality/valueThis review article provides an in-depth review of the use of different materials in PPE and challenges regarding its long-term use and implications on the environment.
LCPCWSC: a Web service classification approach based on label confusion and priori correction
Authors: Xue Lin , Zhang Feng 
Published: February 2024

Purpose
With the increasing number of Web services, correct and efficient classification of Web services is crucial to improve the efficiency of service discovery. However, existing Web service classification approaches ignore the class overlap in Web services, resulting in poor accuracy of classification in practice. This paper aims to provide an approach to address this issue.

Design/methodology/approach
This paper proposes a label confusion and priori correction-based Web service classification approach. First, functional semantic representations of Web services descriptions are obtained based on BERT. Then, the ability of the model is enhanced to recognize and classify overlapping instances by using label confusion learning techniques; Finally, the predictive results are corrected based on the label prior distribution to further improve service classification effectiveness.

Findings
Experiments based on the ProgrammableWeb data set show that the proposed model demonstrates 4.3%, 3.2% and 1% improvement in Macro-F1 value compared to the ServeNet-BERT, BERT-DPCNN and CARL-NET, respectively.

Originality/value
This paper proposes a Web service classification approach for the overlapping categories of Web services and improve the accuracy of Web services classification.
Global and domestic drivers of inflation: evidence from select South Asian countries
Authors: Sajid Muhammad , Ali Amanat , Ahmad Sareer , Shil Nikhil Chandra , Arshad Izaz 
Published: February 2024

PurposeThis study empirically examines the impact of some domestic as well as global factors such as trade openness (TO), money supply (MS), exchange rate, global oil prices (GOPs) and interest rate (IR) on inflation.Design/methodology/approachThis study deploys a quantitative method considering 30 years of data (1991–2020) from four South Asian countries, namely, Sri Lanka, Pakistan, Bangladesh and India. To determine the potential impact of different factors on inflation, this study applies the panel analysis of the system generalized method of moments (SGMM).FindingsThis study empirically finds that TO, MS, exchange rate and GOPs have a positive impact on inflation, while IR and the structural adjustment program (SAP) have a negative impact on inflation. Out of the various determinants considered in this study, TO, exchange rate and the SAP are insignificant, while the rest of the variables are significant and consistent with previous studies.Practical implicationsThis study informs policymakers about maintaining price stability and fostering economic growth in South Asian nations. It breaks new ground as the first empirical examination of the International Monetary Fund (IMF)’s SAP impact on inflation in the region.Originality/valueThis study tries to find out whether the SAP of the IMF is responsible for inflation in South Asian countries. It gives renewed attention to the causality of inflation from the perspective of countries receiving loans from donors, especially the IMF.
Labour market insecurity and volunteering in the European Union: policy suggestions for job security
Authors: Nappo Nunzia , Fiorillo Damiano , Lubrano Lavadera Giuseppe 
Published: February 2024

PurposeThere is extensive literature on the determinants of job tenure insecurity. However, very little is known about the individual drivers of labour market insecurity. Additionally, while a piece of literature shows that volunteering improves workers' income, no study considers volunteering as an activity which could help workers to feel more confident about their perception of labour market insecurity if they lost or resigned their jobs. Therefore, purpose of this paper is to study whether workers who volunteer are less likely to perceive labour market insecurity.Design/methodology/approachThe paper employs data from the sixth European working conditions survey which provides a great deal of information on working conditions. For the empirical investigation, probit model as well as robustness analysis have been implemented.FindingsResults show that employees who do voluntary activities have a greater likelihood of declaring perceived labour market insecurity, which is nearly 3 percentage points lower, than employees who do not volunteer. Findings suggest that governments need to improve the relationship between for-profit and non-profit sectors to encourage volunteering.Originality/valueThis is the first study which considers volunteering as an activity which could help workers to feel more confident about their perception of “labour market insecurity”. Most of the studies on “labour market insecurity” do not focus on the workers individual characteristics but mainly on the labour markets institutional characteristics and welfare regimes differences.
Can the Sell in May effect be enhanced by a size tilt?
Authors: Abukari Kobana , Oldford Erin , Jog Vijay 
Published: February 2024

PurposeThe authors evaluate the Sell in May effect in the Canadian context to comprehensively explore the Sell in May effect as well as its interactions with the size effect and risk and with multiple indices.Design/methodology/approachThe authors use ordinary least squares (OLS) regressions to examine the Sell in May effect and Huber M-estimation to handle potential outliers. They also use the generalized autoregressive conditional heteroskedasticity (GARCH) models to explore the role of risk in the Sell in May effect.FindingsThe results demonstrate that the Sell in May effect is present in all three main Canadian stock market indices. More telling, the anomaly is strongest in small cap indices and in indices that give equal weighting to small and large cap stocks. They do not find that the effect is driven by risk.Originality/valueWhile several papers have explored the Sell in May phenomenon in several countries, little scholarly attention has been paid to this effect in Canada and to its interaction with the size effect. The authors contribute to the literature by examining of the interactions between Sell in May and the size effect in Canada. They examine the Sell in May effect using CFMRC value-weighted and equally weighted indices of all Canadian companies. They also incorporate in their analysis the role of risk.
CSR inequality, managerial myopia and hostile takeover threats
Authors: Chatjuthamard Pattanaporn , Chintrakarn Pandej , Jiraporn Pornsit , Kitiwong Weerapong , Chaivisuttangkun Sirithida 
Published: February 2024

PurposeExploiting a novel measure of hostile takeover exposure primarily based on the staggered adoption of state legislations, we explore a crucial, albeit largely overlooked, aspect of corporate social responsibility (CSR). In particular, we investigate CSR inequality, which is the inequality across different CSR categories. Higher inequality suggests a less balanced, more lopsided, CSR policy.Design/methodology/approachIn addition to the standard regression analysis, we perform several robustness checks including propensity score matching, entropy balancing and an instrumental-variable analysis.FindingsOur results show that more takeover exposure exacerbates CSR inequality. Specifically, a rise in takeover vulnerability by one standard deviation results in an increase in CSR inequality by 4.53–5.40%. The findings support the managerial myopia hypothesis, where myopic managers promote some CSR activities that are useful to them in the short run more than others, leading to higher CSR inequality.Originality/valueOur study is the first to exploit a unique measure of takeover vulnerability to investigate the impact of takeover threats on CSR inequality, which is an important aspect of CSR that is largely overlooked in the literature. We aptly fill this void in the literature.