bluuebunny/crossref_metadata_2025_split huggingface dataset:
ODAMNet: a Python package to identify molecular relationships between chemicals and rare diseases using overlap, active module and random walk approaches
Authors: Térézol Morgane , Baudot Anaïs , Ozisik Ozan 
Published: July 2023

AbstractEnvironmental factors are external conditions that can affect the health of living organisms. For a number of rare genetic diseases, an interplay between genetic and environmental factors is known or suspected. However, the studies are limited by the scarcity of patients and the difficulties in gathering reliable exposure information.In order to aid in fostering research between environmental factors and rare diseases, we propose ODAMNet, a Python package to investigate the possible relationships between chemicals, which are a subset of environmental factors, and rare diseases. ODAMNet offers three different and complementary bioinformatics approaches for the exploration of relationships: overlap analysis, active module identification and random walk with restart. ODAMNet allows systematic analysis of chemical - rare disease relationships and generation of hypotheses for further investigation of effect mechanisms.Metadata
DeepCristae, a CNN for the restoration of mitochondria cristae in live microscopy images
Authors: Papereux Salomé , Leconte Ludovic , Valades-Cruz Cesar Augusto , Liu Tianyan , Dumont Julien , Chen Zhixing , Salamero Jean , Kervrann Charles , Badoual Anaïs 
Published: July 2023

AbstractMitochondria play an essential role in the life cycle of eukaryotic cells. However, we still don’t know how their ultrastructure, like the cristae of the inner membrane, dynamically evolves to regulate these fundamental functions, in response to external conditions or during interaction with other cell components. Although high-resolution fluorescent microscopy coupled with recently developed innovative probes can reveal this structural organization, their long-term, fast and live 3D imaging remains challenging. To address this problem, we have developed a convolutional neural network, called DeepCristae, to restore mitochondria cristae in low spatial resolution microscopy images. Our network is trained from 2D STED images using a novel loss specifically designed for cristae restoration. To efficiently increase the size of the training set, we also developed a random image patch sampling centered on mitochondrial areas. To evaluate DeepCristae, quantitative assessments were carried out using metrics we derived by focusing on the mitochondria and cristae pixels rather than on the whole image as usual. Depending on the conditions of use indicated, DeepCristae works well on broad microscopy modalities (Stimulated Emission Depletion (STED), Live-SR, AiryScan and Lattice Light Sheet Microscopy). It is ultimately applied in the context of mitochondrial network dynamics during interaction with endo/lysosome membranes.
Conversational production and comprehension: fMRI-evidence reminiscent of the classic Broca-Wernicke model
Authors: Arvidsson Caroline , Torubarova Ekaterina , Pereira André , Uddén Julia 
Published: July 2023

AbstractA key question in neurolinguistics is whether language production and comprehension share neural infrastructure, but this question has not been addressed in the context of actual conversation. We utilized a public fMRI dataset where participants (N=24) engaged in unscripted conversations with a confederate outside the scanner via an audio-video link. We provide evidence indicating that production and comprehension, in a conversational setting, diverge with respect to how they modulate the recruitment of regions in the left-lateralized perisylvian language network. Activity in the left inferior frontal gyrus was stronger in production than in comprehension. Compared to production, comprehension showed stronger recruitment of the left anterior middle temporal gyrus and superior temporal sulcus, but this was not the case for the posterior aspect of these loci. Although our results are reminiscent of the classic Broca-Wernicke model, the anterior temporal activation is a notable difference from that model. This is one of the findings which may be a consequence of the conversational setting, another being that conversational production activated what we interpret as higher-level socio-pragmatic processes. In conclusion, we present evidence supporting that the above-mentioned frontal vs temporal regions in the language network are functionally segregated during conversation.
SDF-1 Bound Heparin Nanoparticles Recruit Progenitor Cells for Their Differentiation and Promotion of Angiogenesis After Stroke
Authors: Wilson Katrina L. , Onweller Lauren A. , Joseph Neica I. , David-Bercholz Jennifer , Darling Nicole J. , Segura Tatiana 
Published: July 2023

AbstractAngiogenesis after stroke is correlated with enhanced tissue repair and functional outcomes. The existing body of research in biomaterials for stroke focuses on hydrogels for the delivery of stem cells, growth factors, or small molecules or drugs. Despite the ability of hydrogels to enhance all these delivery methods, no material has significantly regrown vasculature within the translatable timeline of days to weeks after stroke. Here we developed 2 novel biomaterials for tissue regeneration after stroke, a highly porous granular hydrogel termed Cryo microgels, and heparin-norbornene nanoparticles with covalently bound SDF-1α. The combination of these materials resulted in fully revascularized vessels throughout the stroke core in only 10 days, as well as increased neural progenitor cell migration and maintenance and increased neurons.
Cross-species analysis of ARPP19 phosphorylation during oocyte meiotic maturation charts the emergence of a new cAMP-dependent role in vertebrates
Authors: Meneau Ferdinand , Lapébie Pascal , Daldello Enrico Maria , Le Tran , Chevalier Sandra , Houliston Evelyn , Jessus Catherine , Miot Marika 
Published: July 2023

ABSTRACTIn many animal species, elevated cAMP-PKA signaling initiates oocyte meiotic maturation upon hormonal stimulation, whereas in vertebrates, it acts as a negative regulator of this process. To address this “cAMP paradox”, we have focused on ARPP19 proteins. Dephosphorylation ofXenopusARPP19 on a specific PKA site has been identified as a key step in initiating oocyte maturation. We first tracked evolution of the ARPP19 PKA phosphorylation site, revealing that it appeared early during the emergence of metazoans. This contrasts with strong conservation across eukaryotes of a phosphorylation site for the kinase Gwl in ARPP19 proteins, able to transform them into potent PP2A-B55 inhibitors and thus promote M-phase entry. We then compared the phosphorylation and function ofXenopusARPP19 with its orthologue from the jellyfishClytia, a model species showing cAMP-induced oocyte maturation. We confirmed thatClytiaARPP19 is phosphorylated on the conserved Gwl sitein vitroas well as in maturingXenopusandClytiaoocytes, behaving as a PP2A inhibitor and contributing to Cdk1 activation. However, Gwl-phosphorylated ARPP19 was unable to initiate oocyte maturation inClytia, suggesting the presence of additional locks released by hormonal stimulation.ClytiaARPP19 wasin vitrophosphorylated by PKA uniquely on the predicted site, but it was a much poorer substrate of PKA and of its antagonizing phosphatase, PP2A-B55δ, than theXenopusprotein. Correspondingly, PKA-phosphomimeticClytiaARPP19 had a much weaker inhibitory activity on meiosis resumption inXenopusoocytes than itsXenopuscounterpart. Hence, poor recognition ofClytiaARPP19 by PKA and the absence of its targets inClytiaoocytes account for the cAMP paradox. This cross-species study of ARPP19 illustrates how initiation of oocyte maturation has complexified during animal evolution, and provides further insight into its biochemical regulation.
In vitroreconstitution of theM.tbproteasome core particle reveals conserved aspects of bacterial proteasome assembly
Authors: Kante Anupama , Roelofs Jeroen , Deeds Eric J. 
Published: July 2023

ABSTRACTAccording to the WHO, one in three people in the world has a latent tuberculosis infection. Tuberculosis is caused by the bacteriumMycobacterium tuberculosis (M.tb).The development of multi-drug resistant (MDR) tuberculosis indicates a need for novel treatments. Hence, it is important to find a second line of treatment for patients infected with MDR tuberculosis. The proteasome is known to be necessary for survival under stress and pathogenicity inM.tb. However, our ability to use the proteasome as drug target has been limited by our abilities to screen for inhibitor compoundsin vitro.The proteasome is a protease complex that degrades proteins and is crucial for the maintenance of protein homeostasis within cells. Like many protein complexes, the proteasome must assemble into a specific quaternary structure in order to be active. Specifically, the proteolytically-active proteasome Core Particle (CP) consists of 28 subunits (14 α and 14 β) that must assemble into a barrel-like structure in order to become catalytically active. Hence, understanding the assembly process in not only important from a basic cell biological perspective, but may also serve as the basis for the discovery of novel assembly inhibitors. In this study, we have established for the first time a protocol to express and purify theM.tbα and β subunits separatelyin vitro.The subunits are soluble monomers on purification and only assemble into active CPs upon reconstitution. Our assembly experiments revealed thatM.tbCP assembly pathway is almost certainly identical to that seen in previous experiments on the CP from the bacteriumRhodococcus erythropolis(R.e), but assembly inM.tbis much slower. Interestingly, we found that subunits fromM.tbandR.espontaneously self-assembled into active hybrid proteasomes on reconstitution with each other, despite having only 65% sequence similarity. Our work thus strongly suggests that the CP assembly pathway is conserved across bacteria, and the ability to performin vitroassembly experiments on theM.tbproteasome opens up the possibility of performing critical experiments, including screening for potential molecules that could inhibit assembly, directly in this clinically-relevant organism.
pUdOs: concise plasmids for bacterial and mammalian cells
Authors: Manigat France Ourida , Connell Louise B. , Stewart Brittany N. , LePabic Abdel-Rahman , Tessier Christian J.G. , Emlaw Johnathon R. , Calvert Nicholas D. , Rössl Anthony , Shuhendler Adam J. , daCosta Corrie J.B. , Campbell-Valois François-Xavier 
Published: July 2023

AbstractThe pUdOs are 28 plasmids of small size combining four different origins of replication and seven selection markers, which together afford flexible use inEscherichia coliand several related gram- negative bacteria. The promoterless multicloning site is insulated from upstream spurious promoters by strong transcription terminators, and contains type IIP or IIS restriction sites for conventional or Golden-gate cloning. pUdOs can be converted into efficient expression vectors through the insertion of a promoter at the user’s discretion. For example, we demonstrate the utility of pUdOs as the backbone for an improved version of a Type III Secretion System reporter inShigella. In addition, we derive a series of pUdO-based mammalian expression vectors affording distinct levels of expression and transfection efficiencies comparable to commonly used mammalian expression plasmids. Thus, pUdOs could advantageously replace traditional plasmids in a wide variety of cell types and applications.
Defense-related callose synthasePMR4promotes root hair callose deposition and adaptation to phosphate deficiency inArabidopsis thaliana
Authors: Okada Kentaro , Yachi Koei , Nhi Nguyen Tan Anh , Kanno Satomi , Yasuda Shigetaka , Tadai Haruna , Tateda Chika , Lee Tae-Hong , Nguyen Uyen , Inoue Kanako , Tsuchida Natsuki , Ishihara Taiga , Miyashima Shunsuke , Hiruma Kei , Miwa Kyoko , Maekawa Takaki , Notaguchi Michitaka , Saijo Yusuke 
Published: July 2023

SummaryPlants acquire phosphorus (P) primarily as inorganic phosphate (Pi) from the soil. Under Pi deficiency, plants induce an array of physiological and morphological responses, termed phosphate starvation response (PSR), thereby increasing Pi acquisition and use efficiency. However, the mechanisms by which plants adapt to Pi deficiency remain to be elucidated. Here, we report that deposition of a β-1,3-glucan polymer called callose is induced inArabidopsis thalianaroot hairs under Pi deficiency, in a manner independent of PSR-regulatingPHR1/PHL1transcription factors andLPR1/LPR2ferroxidases. Genetic studies revealedPMR4(GSL5) callose synthase being required for the callose deposition in Pi-depleted root hairs. Loss ofPMR4also reduces Pi acquisition in shoots and plant growth under low Pi conditions. The defects are not recovered by simultaneous disruption ofSID2, mediating defense-associated salicylic acid (SA) biosynthesis, excluding SA defense activation from the cause of the observedpmr4phenotypes. Grafting experiments and characterization of plants expressingPMR4specifically in root hair cells suggest that a PMR4 pool in the cell type contributes to shoot growth under Pi deficiency. Our findings thus suggest an important role forPMR4in plant adaptation to Pi deficiency.Significance statementWe reveal that PMR4 callose synthase mediates callose deposition in root hairs under phosphate (Pi) deficiency, without requiring Pi starvation response regulatorsPHR1/PHL1orLPR1/LPR2. The loss of the callose deposition is accompanied by decreases in Pi acquisition and plant growth inpmr4. Root hair cell-specificPMR4expression restores callose deposition in root hairs and shoot growth under Pi deficiency, indicating a critical role for root hair callose in plant adaptation to Pi deficiency.
Giving life to dead: role of WayBack Machine in recovery of dead URLs
Authors: Loan Fayaz Ahmad , Khan Aasif Mohammad , Andrabi Syed Aasif Ahmad , Sozia Sozia Rashid , Parray Umer Yousuf 
Published: July 2023

PurposeThe purpose of the present study is to identify the active and dead links of uniform resource locators (URLs) associated with web references and to compare the effectiveness of Chrome, Google and WayBack Machine in retrieving the dead URLs.Design/methodology/approachThe web references of the Library Hi Tech from 2004 to 2008 were selected for analysis to fulfill the set objectives. The URLs were extracted from the articles to verify their accessibility in terms of persistence and decay. The URLs were then executed directly in the internet browser (Chrome), search engine (Google) and Internet Archive (WayBack Machine). The collected data were recorded in an excel file and presented in tables/diagrams for further analysis.FindingsFrom the total of 1,083 web references, a maximum number was retrieved by the WayBack Machine (786; 72.6 per cent) followed by Google (501; 46.3 per cent) and the lowest by Chrome (402; 37.1 per cent). The study concludes that the WayBack Machine is more efficient, retrieves a maximum number of missing web citations and fulfills the mission of preservation of web sources to a larger extent.Originality/valueA good number of studies have been conducted to analyze the persistence and decay of web-references; however, the present study is unique as it compared the dead URL retrieval effectiveness of internet explorer (Chrome), search engine giant (Google) and WayBack Machine of the Internet Archive.Research limitations/implicationsThe web references of a single journal, namely, Library Hi Tech, were analyzed for 5 years only. A major study across disciplines and sources may yield better results.Practical implicationsURL decay is becoming a major problem in the preservation and citation of web resources. The study has some healthy recommendations for authors, editors, publishers, librarians and web designers to improve the persistence of web references.
Data-driven identification and analysis of passenger riding paths in megacity metro system
Authors: Xie Lianghui , Zhang Zhenji , Qiu Robin , Gong Daqing 
Published: July 2023

Purpose The paper aims to identify and analyze passengers’ riding paths for providing better operational support for digital transformation in megacity metro systems.Design/methodology/approach The authors develop a method to leverage certain passengers’ deterministic riding paths to corroborate other passengers’ uncertain paths. Using Automatic Fare Collection data and train schedules, a witness model is built to recover the actual riding paths for passengers whose paths are unknown otherwise. The identification and analysis of passenger riding paths between three different types of origin–destination) pairs reveal the complexity of passenger path choice.Findings The results show that passenger path choice modeling is usually characterized by complexity, experience and partial blindness. Some passengers choose paths that are not optimal due to their experience and limited access to overall metro system information. These passengers could be the subject of improved path guidance in light of riding efficiency improved through digital transformation.Originality/value This research contributes to the improvement of metro management and operations by leveraging ongoing digital transformation in megacity metro systems. Based on the riding paths and trip chains of a large number of individual passengers identified by the proposed method, metro operation management could prevent risks in areas with concentrated passenger flow in advance, optimally adjust train schedules on a daily basis and deliver real-time riding guidance station by station, which would greatly improve megacity metro systems’ service safety, quality and operational efficacy over time.
How and when temporal leadership facilitates the success of sustainable construction projects
Authors: Siddiquei Ahmad Nabeel , Imam Hassan , Asmi Fahad 
Published: July 2023

PurposeTemporal leadership is a new construct that predicts team outcomes. This study examines the mediating role of shared temporal cognitions and the moderating role of time pressure in the relationship between temporal leadership and project success within sustainable construction projects.Design/methodology/approachThe multi-source and multi-wave data were collected via self-administered questionnaires from teams working on sustainable construction projects. The direct and mediating hypotheses were tested using multi-level structural equation modelling, while moderated mediation hypotheses were examined by applying the bootstrap method using SPSS Process Macro.FindingsThe results showed that temporal leadership enables project success via shared temporal cognitions. Temporal leadership is most beneficial for facilitating project success via shared temporal cognitions when teams experience high time pressure.Originality/valueThis is the first study examining shared temporal cognitions as a mediator of the relationship between temporal leadership and project success. Also, this is the first study that considered time pressure as a boundary condition that influences the relationships between temporal leadership, shared temporal cognitions and project success within sustainable construction projects. The study provides valuable advice to project managers and project-based construction organizations about using and managing time within projects.
Research on the evaluation of academic journals from a multidimensional fusion measurement perspective
Authors: Zhao Rongying , Zhu Weijie 
Published: July 2023

Purpose
This paper aims to conduct a comprehensive analysis to evaluate the current situation of journals, examine the factors that influence their development, and establish an evaluation index system and model. The objective is to enhance the theory and methodologies used for journal evaluation and provide guidance for their positive development.

Design/methodology/approach
This study uses empirical data from economics journals to analyse their evaluation dimensions, methods, index system and evaluation framework. This study then assigns weights to journal data using single and combined evaluations in three dimensions: influence, communication and novelty. It calculates several evaluation metrics, including the explanation rate, information entropy value, difference coefficient and novelty degree. Finally, this study applies the concept of fuzzy mathematics to measure the final results.

Findings
The use of affiliation degree and fuzzy Borda number can synthesize ranking and score differences among evaluation methods. It combines internal objective information and improves model accuracy. The novelty of journal topics positively correlates with both the journal impact factor and social media mentions. In addition, journal communication power indicators compensate for the shortcomings of traditional citation analysis. Finally, the three-dimensional representative evaluation index serves as a reminder to academic journals to avoid the vortex of the Matthew effect.

Originality/value
This paper proposes a journal evaluation model comprising academic influence, communication power and novelty dimensions. It uses fuzzy Borda evaluation to address issues related to the weighing of single evaluation methods. This study also analyses the relationship of the three dimensions and offers insights for journal development in the new media era.
Minimization of exergy destruction with discrete metal foam filling in a pipe under turbulent flow condition
Authors: K Kiran Kumar , Banjara Kotresha , Naik Kishan 
Published: July 2023

Purpose
This study aims to present the numerical analysis of exergy transfer and irreversibility through the discrete filling of high-porosity aluminum metal foams inside the horizontal pipe.

Design/methodology/approach
In this study, the heater is embedded on the pipe’s circumference and is assigned with known heat input. To enhance the heat transfer, metal foam of 10 pores per inch with porosity 0.95 is filled into the pipe. In filling, two kinds of arrangements are made, in the first arrangement, the metal foam is filled adjacent to the inner wall of the pipe [Model (1)–(3)], and in the second arrangement, the foam is located at the center of the pipe [Models (4)–(6)]. So, six different models are examined in this research for a fluid velocity ranging from 0.7 to7 m/s under turbulent flow conditions. Darcy Extended Forchheimer is combined with local thermal non-equilibrium models for forecasting the flow and heat transfer features via metal foams.

Findings
The numerical methodology implemented in this study is confirmed by comparing the outcomes with the experimental outcomes accessible in the literature and found a fairly good agreement between them. The application of the second law of thermodynamics via metal foams is the novelty of current investigation. The evaluation of thermodynamic performance includes the parameters such as mean exergy-based Nusselt number (Nue), rate of irreversibility, irreversibility distribution ratio (IDR), merit function (MF) and non-dimensional exergy destruction (I*). In all the phases, Models (1)–(3) exhibit better performance than Models (4)–(6).

Practical implications
The present study helps to enhance the heat transfer performance with the introduction of metal foams and reveals the importance of available energy (exergy) in the system which helps in arriving at optimum design criteria for the thermal system.

Originality/value
The uniqueness of this study is to analyze the impact of discrete metal foam filling on exergy and irreversibility in a pipe under turbulent flow conditions.