bluuebunny/crossref_metadata_2025_split huggingface dataset:
Single-cell Total RNA Miniaturized sequencing (STORM-seq) reveals differentiation trajectories of primary human fallopian tube epithelium
Authors: Johnson Benjamin K. , Rhodes Mary , Wegener Marc , Himadewi Pamela , Foy Kelly , Schipper Joshua L. , Siwicki Rebecca A. , Rossell Larissa L. , Siegwald Emily J. , Chesla Dave W. , Teixeira Jose M. , Sheridan Rachael T. C. , Adams Marie , Triche Timothy J. , Shen Hui 
Published: March 2022

AbstractWe present Single-cell TOtal RNA Miniaturized sequencing (STORM-seq), a full-length single-cell ribo-reduced RNA sequencing protocol, optimized to profile thousands of cells per run. Using off-the-shelf reagents and random hexamer priming, STORM-seq recovers comprehensive RNA profiles from single cells with library complexity approaching that of bulk RNA-seq. Importantly, STORM-seq does not require specialized equipment and can be performed using standard lab equipment. STORM-seq identifies thousands of additional coding and non-coding transcripts not detected by existing methods, and recovers clinically relevant structural variants at the single-cell level. We apply STORM-seq to primary human fallopian tube epithelium (FTE), a complex solid tissue key to both human reproductive biology and ovarian carcinogenesis. In differentiation trajectory analyses, the improved resolution from STORM-seq reveals intermediate/transitional cell states, and a putative progenitor cell population. The results support a trajectory from a bipotent progenitor population to ciliated and secretory cell types in normal FTE. These findings are consistent across human subjects, sequencing depths, and platforms. Long intergenic non-coding RNAs (lincRNAs) appear as key driver genes in both ciliated and secretory lineage trajectories, underscoring the importance of both coding and non-coding RNA in this tissue. By capturing essentially complete individual cellular transcriptomes, STORM-seq sheds new light on the transcriptional programs that establish cellular state and fate in complex tissues.
Mitochondrial Redox Adaptations Enable Aspartate Synthesis in SDH-deficient Cells
Authors: Hart Madeleine L. , Quon Evan , Vigil Anna-Lena B. G. , Engstrom Ian A. , Newsom Oliver J. , Davidsen Kristian , Hoellerbauer Pia , Carlisle Samantha M. , Sullivan Lucas B. 
Published: March 2022

AbstractThe oxidative tricarboxylic acid (TCA) cycle is a central mitochondrial pathway integrating catabolic conversions of NAD+ to NADH and anabolic production of aspartate, a key amino acid for cell proliferation. Several TCA cycle components are implicated in tumorigenesis, including loss of function mutations in subunits of succinate dehydrogenase (SDH), also known as complex II of the electron transport chain (ETC). Mechanistic understanding of how proliferating cells tolerate the metabolic defects of SDH loss is still lacking. Here, we identify that SDH supports cell proliferation through aspartate synthesis but, unlike other ETC impairments, is not restored by electron acceptor supplementation. Interestingly, we find aspartate production and cell proliferation are restored to SDH impaired cells by concomitant inhibition of ETC complex I (CI). We determine that the benefits of CI inhibition in this context are dependent on decreasing mitochondrial NAD+/NADH, which drives SDH-independent aspartate production. We also find that genetic loss or restoration of SDH selects for cells with concordant CI activity, establishing distinct modalities of mitochondrial metabolism for maintaining aspartate synthesis. Collectively, these data identify a metabolically beneficial mechanism for CI loss in proliferating cells and reveal that compartmentalized redox changes can impact cellular fitness.
Structural basis of Omicron immune evasion: A comparative computational study of Spike protein-Antibody interaction
Authors: Contractor Darshan , Globisch Christoph , Swaroop Shiv , Jain Alok 
Published: March 2022

AbstractThe COVID-19 pandemic has caused more than 424 million infections and 5.9 million deaths so far. The vaccines used against SARS-COV-2 by now have been able to develop some neutralising antibodies in the vaccinated human population and slow down the infection rate. The effectiveness of the vaccines has been challenged by the emergence of the new strains with numerous mutations in the spike (S) protein of SARS-CoV-2. Since S protein is the major immunogenic protein of the virus and also contains Receptor Binding Domain (RBD) that interacts with the human Angiotensin-Converting Enzyme 2 (ACE2) receptors, any mutations in this region should affect the neutralisation potential of the antibodies leading to the immune evasion. Several variants of concern (VOC) of the virus have emerged so far. Among them, the most critical are Delta (B.1.617.2), and recently reported Omicron (B. 1.1.529) which have acquired a lot of mutations in the spike protein. We have mapped those mutations on the modelled RBD and evaluated the binding affinities of various human antibodies with it. Docking and molecular dynamics simulation studies have been used to explore the effect of the mutations on the structure of the RBD and the RBD-antibody interaction. The analysis shows that the mutations mostly at the interface of a nearby region lower the binding affinity of the antibody by ten to forty per cent, with a downfall in the number of interactions formed as a whole and therefore, it implies the generation of immune escape variants. Notable mutations and their effect was characterised by performing various analyses that explain the structural basis of antibody efficacy in Delta and a compromised neutralisation effect for the Omicron variant. Our results pave the way for robust vaccine design that can be effective for many variants.Graphical AbstractSynopsisThe research study utilises comparative docking and MD simulations analyses to illustrate how mutations in delta and omicron variants affect the binding of antibodies to the spike receptor binding domain (RBD) of SARS CoV-2.
Application of machine learning in predicting pitting corrosion – electrochemical data around the open circuit potential
Authors: Boucherit Mohamed Nadir , Amzert Sid Ahmed , Arbaoui Fahd 
Published: March 2022

Purpose
The purpose of this study is to confirm the idea that observing the electrochemical data of a steel polarized around its open circuit potential can provide insight into its performance against pitting corrosion. To confirm this idea a two-step work was carried out. The authors collected electrochemical data through experiments and exploited them through machine learning by building neural networks capable of predicting the behaviour of the steel against the pitting corrosion.

Design/methodology/approach
The electrochemical experiments consist in plotting voltammograms of the steel in chemical solutions of various degrees of corrosiveness. For each experiment, the authors observe how the open-circuit potential evolves over a period of 1 min, and following this, the authors observe the current evolution when they impose a potential scan that starts from the open-circuit potential. For each of these situations, the pitting potential Epit is noted. The authors then build different artificial neural networks, which after learning, can, by receiving electrochemical data, calculate a pitting potential Epit′. The performance of the neural networks is evaluated by the correlation of Epit and Epit′.

Findings
Through this work, different types of networks were compared. The results show that recurrent or convolutional networks can better capture the temporal nature of the input data.

Originality/value
The results of this work support the idea that the measurable electrochemical data around the free potential of a material can be correlated with its behaviour at more anodic potentials, particularly the initiation of pits.
Horizontal collaboration in the last mile distribution: gauging managerial response to disruption and abnormal demand
Authors: Argyropoulou Maria , Zissis Dimitris , Korfiatis Nikolaos , Zampou Eleni 
Published: March 2022

PurposeLast mile distribution is a crucial element of any supply chain network, and its complexity has challenged established practices and frameworks in the management literature. This is particularly evident when demand surges, as with recent lockdowns due to the COVID-19 pandemic and subsequent demand for home delivery services. Given the importance of this critical component, this study recommends horizontal collaboration as a possible solution for retailers seeking to improve the quality of their services.Design/methodology/approachThis study investigates whether horizontal collaboration should be considered as an option for faster and greener distribution of groceries ordered online. Using the United Kingdom and Greek grocery markets that differ in terms of online grocery penetration, distribution network structure and delivery times, the study discusses how the effectiveness of pooling resources can create positive spillover effects for consumers, businesses and society.FindingsDespite their differences, both markets indicate the need for horizontal collaboration in the highly topical issue of last mile delivery.Originality/valueTaking a theoretical and practical view in cases of disruption and constant pressure in last mile distribution, horizontal collaboration supports retailers to coordinate routes, increase fleet and vehicle utilisation, reduce traffic and carbon emissions while improving customer satisfaction.
The impact of supply chain specific investments on firms’ market performance: the mediating role of innovation
Authors: Huo Baofeng , Guo Mengqiu , Tian Min 
Published: March 2022

Purpose
Manufacturers’ specific investments (SIs) in a specific partner that are of lower value when used in an alternative relationship, such as training employees and tailoring systems to achieve better cooperation, can help improve market performance. However, previous studies lack a simultaneous focus on a manufacturer’s SIs in its upstream and downstream partners. The purpose of this study is to address the effects of manufacturers’ SIs in their suppliers and customers on the two types of innovation and market performance individually and jointly and the mediating effects of radical and incremental innovation on relationships between SIs and market performance.

Design/methodology/approach
This study tests proposed relationships based on data collected from 206 manufacturers in China using regression methods.

Findings
Results show that SIs in customers directly and indirectly affect market performance through radical and incremental innovation. However, SIs in suppliers cannot directly improve market performance but indirectly enhance market performance through radical innovation. Furthermore, results also show the interaction of SIs in suppliers and customers is positively related to market performance and radical innovation.

Originality/value
This study contributes to the literature on SIs by identifying supply chain SIs (SCSIs) through simultaneously focusing on SIs in suppliers and customers and exploring the direct and indirect effects of SCSIs on market performance. This study also contributes to the innovation literature by empirically verifying incremental and radical innovation as effective intermediaries that help convert SIs into the actual performance improvement.
Get to know me, homey: exploring critical, relational and racial literacy possibilities in co-excavative letter writing
Authors: Bell Jordan , Zaino Karen 
Published: March 2022

Purpose
There is currently a dearth of research on the implications of the epistolary as a site for knowledge production. This paper aims to demystify the process of academic theorizing through the co-authors’ co-excavative epistolary method.

Design/methodology/approach
Through co-excavative epistolary practices, the co-authors’ relationship was deepened, the collective sense was made of Covid-19, and racial literacy-centered academic theorizing commenced. In the co-authors making meaning of their letter-writing data, they provide examples of and analyze their co-excavative letter-writing process.

Findings
The co-excavative epistolary method deepened the co-authors’ relationship to one another and improved their ability to produce useful and complicated knowledge.

Research limitations/implications
The co-excavative epistolary exchanges mark a new site for academic theorizing and incite creative approaches to academic co-writing, as well as more transparency about the academic writing process in general.

Social implications
Co-excavative methods disrupt traditional academic sites of knowledge production and engender space for relational intimacy.

Originality/value
The work introduces both a new method, co-excavative epistolary writing and a new rational framework, the critical dignity relational framework.
Luxury fashion consumption: a review, synthesis and research agenda
Authors: Aleem Aihoor , Loureiro Sandra Maria Correia , Bilro Ricardo Godinho 
Published: March 2022

Purpose
This paper aims to review the topic of “luxury fashion consumption”, a field of recent interest for academics and practitioners. However, a literature review that can map the existing knowledge and aggregate it into relevant topics and offers a research agenda for future research is still lacking.

Methodology
This paper uses a systematic review and a text mining approach to analyse 73 articles on luxury fashion consumption aiming to clarify, rationalise and critically interpret the literature on luxury fashion consumption; identify the core topic, create an integrative framework of core constructs; and offer research gaps and suggest a research agenda for future studies.

Findings
From this analysis, eight major research topics are found and analysed (brand desire, authenticity, luxury markets, value perceptions, luxury retail experience, luxury brands communication, responsible consumption and sustainability and status signalling). Based on these topics and following the TCM framework, this review offers directions for future research.

Value
This research offers a text-mining review of luxury fashion consumption to help scholars and managers further develop this field, as there is no comprehensive review on the topic exploring the themes, theories, constructs and methods used in prior studies.
Structural behavior of small-scale reinforced concrete secant pile wall
Authors: El-Nimr Maher Taha , Basha Ali Mohamed , Abo-Raya Mohamed Mohamed , Zakaria Mohamed Hamed 
Published: March 2022

Purpose
To predict the real behavior of the full-scale model using a scale model, optimized simulation should be achieved. In reinforced concrete (RC) models, scaling can be substantially more critical than in single-material models because of multiple reasons such as insufficient bonding strength between small-diameter steel bars and concrete, and excessive aggregate size. Overall, there is a shortfall of laboratory and field-testing studies on the behavior of secant pile walls under lateral and axial loads. Accordingly, the purpose of this study is to investigate the validity and the performance of the 1/10th scaled RC secant pile wall under the influence of different types of loading.

Design/methodology/approach
The structural performance of the examined models was evaluated using two types of tests: bending and axial compression. A self-compacting concrete mix was suggested, which provided the best concrete mix workability and appropriate compressive strength.

Findings
Under axial and bending loads, the failure modes were typical. Where the plain and reinforced concrete piles worked in tandem to support the load throughout the loading process, even when they failed. The experimental results were relatively consistent with some empirical equations for calculating the modulus of elasticity and critical buckling load. This confirmed the validity of the proposed model.

Originality/value
According to the analysis and verification of experimental tests, the proposed 1/10th scaled RC secant pile model can be used for future laboratory purposes, especially in the field of geotechnical engineering.
Measuring the Trustworthiness of Health Care Organizations and Systems
Authors: ANDERSON ANDREW , GRIFFITH DEREK M. 
Published: March 2022

Policy Points
Current efforts to measure and improve trust in health care focus on changing patients’ attitudes rather than measuring and improving the trustworthiness of health care organizations and systems.
We present a conceptual model to understand and explain the constructs of trust and trustworthiness in the context of health care through the application of existing theories of human behavior.
Developing and publicly reporting measures that can enable patients, particularly from historically marginalized groups, to better assess the trustworthiness of providers is necessary to promote health care equity.
Cross‐species conservation of a transposase‐linked element enables genetic sexing of commercial populations of Russian sturgeon (Acipenser gueldenstaedtii)
Authors: Curzon Arie Y. , Shirak Andrey , Meerson Ari , Degani Gad , Hurvitz Avshalom , Ben‐Naim Naama , Domovitz Roee , Ron Micha , Seroussi Eyal 
Published: March 2022

SummaryAll‐female culture of sturgeon is essential for efficient caviar production. However, Russian sturgeon (Acipenser gueldenstaedtii) does not exhibit external sexual dimorphism, and therefore, commercial farms apply gonadal endoscopy or ultrasound at the earliest age of 4–5 years to separate the sexes, with ~90% accuracy. Recently, a dominant genomic marker (AllWSEX2) has been found with association to femaleness in sturgeons. We developed a duplex PCR (dAllWSEX2) with the adjacent bmp7 gene as an internal control, to validate an effective PCR. Robust amplification of control fragments was observed for all samples of our commercial A. gueldenstaedtii stock (n = 337). The dAllWSEX2 assay was significantly associated with sex (n = 43, p < 1.6 × 10−8), yet four (18%) of the endoscopy‐determined females were genetic males. To examine whether some females display a male genetic profile, we tested 96 egg‐producing females, which were all verified as genetic females, indicating that the observed mismatches may be attributed to wrong sexing by endoscopy. Application of dAllWSEX2 on 100 7‐month‐old fish showed no sex‐dependent differences in body weight, indicating that weighing is not an applicable tool for sorting females at a young age. Sanger sequencing of the bmp7 fragment revealed octaploidy and sex‐independent variation, suggesting that the critical sex‐determining region harboring AllWSEX2 is small. In keeping with a model of a single‐ploidy encoding female determination, AllWSEX2 showed no variation despite being a transposase‐linked repetitive element. Cross‐species conservation of AllWSEX2, and absence of annotated sex‐determination genes in this region suggests that, in sturgeons, the sex‐determining mechanism is different from mechanisms identified in other fish.
Broad maternal geographic origin of domestic sheep in Anatolia and the Zagros
Authors: Her Charlotte , Rezaei Hamid‐Reza , Hughes Sandrine , Naderi Saeid , Duffraisse Marilyne , Mashkour Marjan , Naghash Hamid‐Reza , Bălășescu Adrian , Luikart Gordon , Jordan Steve , Özüt Deniz , Kence Aykut , Bruford Michael W. , Tresset Anne , Vigne Jean‐Denis , Taberlet Pierre , Hänni Catherine , Pompanon François 
Published: March 2022

AbstractWe investigated the controversial origin of domestic sheep (Ovis aries) using large samples of contemporary and ancient domestic individuals and their closest wild relatives: the Asiatic mouflon (Ovis gmelini), the urial (Ovis vignei) and the argali (Ovis ammon). A phylogeny based on mitochondrial DNA, including 213 new cytochrome‐b sequences of wild Ovism confirmed that O. gmelini is the maternal ancestor of sheep and precluded mtDNA contributions from O. vignei (and O. gmelini × O. vignei hybrids) to domestic lineages. We also produced 54 new control region sequences showing shared haplogroups (A, B, C and E) between domestic sheep and wild O. gmelini which localized the domestication center in eastern Anatolia and central Zagros, excluding regions further east where exclusively wild haplogroups were found. This overlaps with the geographic distribution of O. gmelini gmelini, further suggesting that the maternal origin of domestic sheep derives from this subspecies. Additionally, we produced 57 new CR sequences of Neolithic sheep remains from a large area covering Anatolia to Europe, showing the early presence of at least three mitochondrial haplogroups (A, B and D) in Western colonization routes. This confirmed that sheep domestication was a large‐scale process that captured diverse maternal lineages (haplogroups).
Fully independent validation and updating of a clinical pharmacy prioritizing risk score in an infectious disease hospital ward
Authors: dos Santos Barreto Paula Gabriela , Barbosa Rezende Renato , dos Santos André Luiz , de Oliveira Silva Fernando , Rodrigues Bezerra Góis Vanessa , Corsino Freire Eduardo , Alvarenga Americano do Brasil Pedro Emmanuel 
Published: March 2022

AimsThe aim of this study was to validate and update the risk score originally developed at Hospital de Clínicas de Porto Alegre, verifying its performance in an infectious disease population.MethodsThis is an observational study with consecutive selection of admission in a ward of participants with infectious diseases. Predictors were age, number of medications, intravenous drugs, potentially dangerous drugs, renal dysfunction, liver dysfunction, use of nasoenteral tube, nasogastric tube, gastrostomy feeding, jejunostomy feeding, oral enteral tube, total parenteral nutrition, cardiac or pulmonary dysfunction and immunosuppression. Outcome was defined as preventable prescription incidents by a clinical pharmacist. A GEE model was fit to make predictions each week.ResultsA total of 219 patients participated in the study, 79.25% of whom had prescription incidents in the first week of admission. Predictors of the updated model were number of drugs prescribed, number of intravenous drugs, use of tubes, truncated age at 36 years and week of hospitalization. The performance of the original model was poor. The updated model's discrimination and calibration were moderate (overall AUC 0.74). A calculator to apply the model is available at https://pedrobrasil.shinyapps.io/INDWELL/.ConclusionThe updated risk score enabled the user to make predictions at admission and throughout the weeks, allowing for a prioritized weekly update for clinical pharmacy intervention. The updated model has a moderate and satisfactory performance for infectious disease patients.