bluuebunny/crossref_metadata_2025_split huggingface dataset:
Implication of polymerase recycling for nascent transcript quantification by live cell imaging
Authors: Kindongo Olivia , Lieb Guillaume , Skaggs Benjamin , Dusserre Yves , Vincenzetti Vincent , Pelet Serge 
Published: February 2024

AbstractTranscription enables the production of RNA from a DNA template. Due to the highly dynamic nature of transcription, live‐cell imaging methods play a crucial role in measuring the kinetics of this process. For instance, transcriptional bursts have been visualized using fluorescent phage‐coat proteins that associate tightly with messenger RNA (mRNA) stem loops formed on nascent transcripts. To convert the signal emanating from a transcription site into meaningful estimates of transcription dynamics, the influence of various parameters on the measured signal must be evaluated. Here, the effect of gene length on the intensity of the transcription site focus was analyzed. Intuitively, a longer gene can support a larger number of transcribing polymerases, thus leading to an increase in the measured signal. However, measurements of transcription induced by hyper‐osmotic stress responsive promoters display independence from gene length. A mathematical model of the stress‐induced transcription process suggests that the formation of gene loops that favor the recycling of polymerase from the terminator to the promoter can explain the observed behavior. One experimentally validated prediction from this model is that the amount of mRNA produced from a short gene should be higher than for a long one as the density of active polymerase on the short gene will be increased by polymerase recycling. Our data suggest that this recycling contributes significantly to the expression output from a gene and that polymerase recycling is modulated by the promoter identity and the cellular state.
Class-C Simulations of LEAP-ASIA-2019 via OpenSees Platform by Using a Pressure Dependent Multi-yield Surface Model
Authors: Elbadawy Mohamed A. , Zhou Yan-Guo 
Published: February 2024

AbstractIn this chapter, Class-C numerical simulations were performed for LEAP-ASIA-2019 centrifuge experiments that took place at different universities testing facilities. A comparative study was conducted among the simulated and experimental seismic responses of a mildly sloping ground of medium-dense to dense Ottawa-F65 sand under ramped sinusoidal acceleration input motions. A pressure dependent multi-yield surface model that can simulate the liquefaction potential of sand soils under earthquake loading was chosen for the numerical simulations through the OpenSees finite element modeling software. An initial calibration of the soil constitutive model, namely “Phase I,” was performed against different cyclic torsional shear tests for Ottawa-F65 sand under various Cyclic Stress Ratios (CSRs). Numerical modeling of centrifuge experiments “Phase II” was carried out after a few adjustments to the estimated model parameter values for the sake of providing proper computed output responses. The adopted soil model and simulation technique provide adequate numerical predictions of the liquefaction potential for the mildly sloping ground problem and accurately simulate the time histories of excess pore water pressure, accelerations, and surface deformations, regardless of experiencing a few undesirable responses for simulated Kyoto University centrifuge tests. The capabilities and limitations of the selected constitutive soil model and computational technique are analyzed and discussed through the context.
Population genetic structure of the giant kelp Macrocystis pyrifera in Aotearoa/New Zealand
Authors: Le Duong Minh , Desmond Matthew J. , Knapp Michael , Kardailsky Olga , Nelson Wendy A. , Zuccarello Giuseppe C. , Hepburn Christopher D. 
Published: February 2024

AbstractThe giant kelp Macrocystis pyrifera is in global decline as a result of numerous stressors operating on both local and global scales. It is a species that holds significant value in terms of the ecosystem services that it provides and its application in aquaculture. In order to safeguard, restore and utilize this species, it is essential that a sound understanding of genetic structure and diversity is established at scales relevant to local management. Seven microsatellite markers were used to analyze 389 individuals from sites across eight geographical regions in New Zealand. While samples of M. pyrifera from the west coast of the South Island (Fiordland), were genetically isolated, the biogeographic separation of sites along the east coast of New Zealand, between Wellington and Stewart Island, remained unclear due to low genetic differentiation between regions. The greatest genetic diversity was seen in the southeast sites, whereas the northeast had the lowest diversity. This pattern is likely driven by the effects of stressors such as high sea surface temperature in these areas as well as oceanic circulation patterns. A key finding from this work was the significant genetic isolation, and therefore vulnerability of M. pyrifera in the Fiordland population, an area that is being subjected to more intense and longer lasting heatwave events.
High femoral offset as a risk factor for aseptic femoral component loosening in cementless primary total hip arthroplasty
Authors: Jud Lukas , Rüedi Nico , Dimitriou Dimitris , Hoch Armando , Zingg Patrick O. 
Published: February 2024

Abstract
Purpose
Lateralized stems in primary cementless total hip arthroplasty (THA) showed to be associated with aseptic femoral loosening. However, femoral head length also affects femoral offset but was not considered so far. This study analyzed the impact of high femoral offset (hFO) combinations, formed by lateralized stems or large femoral head lengths, on aseptic femoral component loosening.

Methods
Retrospective cohort study was performed including all patients that underwent primary cementless THA at our institution between July 2004 and December 2016. Patients were screened for aseptic femoral component loosening and grouped in aseptic loosening (AL) and non-aseptic loosening (nAL) group. Medical records were screened; implant details were noted and classified in hFO and standard femoral offset (sFO) combinations. Supposed risk factors for aseptic loosening were analyzed.

Results
Two thousand four hundred fifty-nine THA could be included, containing 14 THA (0.6%) with aseptic femoral component loosening. The AL group contained 11 hFO combinations (78.6%), whereas in the nAL group, 1315 hFO combinations (53.8%) were used. Subgroup analysis showed significant difference between two groups for hFO combinations (p = 0.014), age (p = 0.002), NSAR (p = 0.001), and bilateral THA on same day (p = 0.001). The multiple logistic regression analysis showed that hFO combination was the only variable for increased probability of aseptic loosening (OR, 3.7; p = 0.04).

Conclusion
High femoral offset combinations, formed by lateralized stems or large femoral head lengths in our collective of standard straight stems implanted by an anterior approach, show a 3.7-fold increased probability for aseptic femoral component loosening. Adjustment of the postoperative protocol may be considered in these cases to ensure proper stem ingrowth.
Generalising XTRACT tractography protocols across common macaque brain templates
Authors: Assimopoulos Stephania , Warrington Shaun , Bryant Katherine L. , Pszczolkowski Stefan , Jbabdi Saad , Mars Rogier B. , Sotiropoulos Stamatios N. 
Published: February 2024

AbstractNon-human primates are extensively used in neuroscience research as models of the human brain, with the rhesus macaque being a prominent example. We have previously introduced a set of tractography protocols (XTRACT) for reconstructing 42 corresponding white matter (WM) bundles in the human and the macaque brain and have shown cross-species comparisons using such bundles as WM landmarks. Our original XTRACT protocols were developed using the F99 macaque brain template. However, additional macaque template brains are becoming increasingly common. Here, we generalise the XTRACT tractography protocol definitions across five macaque brain templates, including the F99, D99, INIA, Yerkes and NMT. We demonstrate equivalence of such protocols in two ways: (a) Firstly by comparing the bodies of the tracts derived using protocols defined across the different templates considered, (b) Secondly by comparing the projection patterns of the reconstructed tracts across the different templates in two cross-species (human–macaque) comparison tasks. The results confirm similarity of all predictions regardless of the macaque brain template used, providing direct evidence for the generalisability of these tractography protocols across the five considered templates.
CSMed® wound dressing for prophylaxis and management of radiation dermatitis in breast and head–neck cancer patients: a single hospital prospective clinical trial
Authors: Lee Yueh-Chun , Tseng Hsien-Chun , Yang Huei-Fang , Lee Yi-Hung , Ko Ya-Fang , Chang Shin-Tsung , Chen Hsin-Lin , Chang Bo-Jiun , Chou Ying-Hsiang 
Published: February 2024

AbstractPurposeCSMed®wound dressing, a dressing with various herb extracts, was tested for its therapeutic effect in radiation dermatitis of breast and head-and-neck cancer patients.MethodsThis study included 20 breast cancer patients and 10 head-and-neck cancer patients. Half of the irradiated area was covered with CSMed®and the other half was under routine treatment. The severity of radiation dermatitis was evaluated with radiation therapy oncology group (RTOG) grade throughout the treatment and the follow-up period. The RTOG grade between the dressed and undressed area were compared to illustrate the therapeutic effect of CSMed®dressing.ResultsThe results showed that CSMed®dressed area had significant lower RTOG score at 3–7 weeks and final record during the treatment, and 1–3 weeks during follow-up than undressed area.ConclusionsThis indicated that CSMed®can delay the onset, reduce the severity, and enhance healing of radiation dermatitis. CSMed®can be used for prophylaxis and management of radiation dermatitis.
Novel genotype–phenotype correlations, differential cerebellar allele-specific methylation, and a common origin of the (ATTTC)n insertion in spinocerebellar ataxia type 37
Authors: Sanchez-Flores Marina , Corral-Juan Marc , Gasch-Navalón Esther , Cirillo Davide , Sanchez Ivelisse , Matilla-Dueñas Antoni 
Published: February 2024

AbstractSpinocerebellar ataxia subtype 37 (SCA37) is a rare disease originally identified in ataxia patients from the Iberian Peninsula with a pure cerebellar syndrome. SCA37 patients carry a pathogenic intronic (ATTTC)n repeat insertion flanked by two polymorphic (ATTTT)n repeats in the Disabled-1 (DAB1) gene leading to cerebellar dysregulation. Herein, we determine the precise configuration of the pathogenic 5ʹ(ATTTT)n–(ATTTC)n–3ʹ(ATTTT)n SCA37 alleles by CRISPR–Cas9 and long-read nanopore sequencing, reveal their epigenomic signatures in SCA37 lymphocytes, fibroblasts, and cerebellar samples, and establish new molecular and clinical correlations. The 5ʹ(ATTTT)n–(ATTTC)n–3ʹ(ATTTT)n pathogenic allele configurations revealed repeat instability and differential methylation signatures. Disease age of onset negatively correlated with the (ATTTC)n, and positively correlated with the 3ʹ(ATTTT)n. Geographic origin and gender significantly correlated with age of onset. Furthermore, significant predictive regression models were obtained by machine learning for age of onset and disease evolution by considering gender, the (ATTTC)n, the 3ʹ(ATTTT)n, and seven CpG positions differentially methylated in SCA37 cerebellum. A common 964-kb genomic region spanning the (ATTTC)n insertion was identified in all SCA37 patients analysed from Portugal and Spain, evidencing a common origin of the SCA37 mutation in the Iberian Peninsula originating 859 years ago (95% CI 647–1378). In conclusion, we demonstrate an accurate determination of the size and configuration of the regulatory 5ʹ(ATTTT)n–(ATTTC)n–3ʹ(ATTTT)n repeat tract, avoiding PCR bias amplification using CRISPR/Cas9-enrichment and nanopore long-read sequencing, resulting relevant for accurate genetic diagnosis of SCA37. Moreover, we determine novel significant genotype–phenotype correlations in SCA37 and identify differential cerebellar allele-specific methylation signatures that may underlie DAB1 pathogenic dysregulation.
Surgical and endovascular cerebral revascularization for cerebral vasculitis with inflammatory vessel stenosis: a case series
Authors: Schieferdecker Simon , Caspers Julian , Daniel Weiss , Cornelius Jan Frederick , Muhammad Sajjad 
Published: February 2024

Abstract
Autoimmune vasculitides affect the cerebral vasculature significantly in a considerable number of cases. When immunosuppressive treatments fail to prevent stenosis in cerebral vessels, treatment options for affected patients become limited. In this case series, we present four cases of pharmacoresistant vasculitis with recurrent transient ischemic attacks (TIAs) or stroke successfully treated with either extracranial-intracranial (EC-IC) bypass surgery or endovascular stenting. Both rescue treatments were effective and safe in the selected cases. Our experience suggests that cases of pharmacoresistant cerebral vasculitis with recurrent stroke may benefit from rescue revascularization in combination with maximum medical management.
An efficient starling murmuration-based secure web service model for smart city application using DBN
Authors: Sheeba Adlin , Bushra S. Nikkath , Rajarajeswari S. , Subasini C. A. 
Published: February 2024

AbstractThe advent of IoT devices increased internet usage more than smartphones and personal computers. The manual analysis of the Web Service Description Language (WSDL) document is quite expensive and time-consuming, hence this paper proposes a novel deep learning architecture to overcome the issue associated with web service classification. A structural self-organized deep belief network (SSODBN) is used for real-time web service classification in different fields such as Education, Smart electricity, Intelligent road networks, Health and social care, and Sports, water, and gas distribution. The SSODBN architecture utilizes a dropout strategy to minimize the interrelationship between the feature detectors and a regularized reinforced transfer function to eliminate the irrelevant weights. The main advantage offered by the S-DBN architecture is the improved preprocessing with feature selection. The Starling Murmuration Optimizer (SMO) is utilized in this paper to minimize the reconstruction error of the S-DBN architecture. The security of the smart city architecture is mainly improved via the blockchain defined network (BDN) using user-authenticated blocks. The experimental results revealed that the proposed method managed the scalability, latency, and centralization issues with superior data transmission.
An integrated multi-polar fuzzy N-soft preference ranking organization method for enrichment of evaluations of the digitization of global economy
Authors: Akram Muhammad , Sultan Maheen , Deveci Muhammet 
Published: February 2024

AbstractDigitization represents the ultimate expression of globalization that has revolutionized every facet of global existence, enhancing connectivity, financial terms, trade opportunities, and public services. To further broaden or fortify this digital realm and advance global progress, various strategies for multi-criteria group decision-making (MCGDM) have been developed. This research article extends the literature study on the sensational MCGDM method known as Preference Ranking Organization Method for Enrichment of Evaluations (PROMETHEE), which shares the burden of selecting the best alternative under many terms and conditions. This article aims to make a positive contribution to the development of the digital world. The main principle of the PROMETHEE technique is to calculate positive and negative flows of the selected options according to the divergence of the alternatives’ scores. It provides us with partial and full rankings of options by determining score degrees, suitable preference functions, and a multi-criteria preference index. To deal with the multi-polarity of the modern world and assignN-ordered levels, this paper proposes the multi-polar fuzzyN-soft (mFNS) PROMETHEE technique. Prior to this, an Analytic Hierarchy Process (AHP) technique is applied to guarantee the credibility of the criterion weights for each criterion. After that, the whole strategy ofm-polar fuzzyN-soft PROMETHEE approach to order the selected options is explained, and all the course of action of this remarkable (MCGDM) technique are synchronized in an extensive flowchart, helping us to learn more about the technology keenly. Moreover, the utility of our discussed technology is illustrated by considering two applications of generating electricity through human movement and choosing the best digital currency. The most suitable choice is extracted with the help of the outranked directed graph. The results obtained bymFNS PROMETHEE technique benefits us with the selection of most reliable source to digitized the global economy, in addition, It enables us to rank the alternatives from most preferable to least one, that not only saves time but also produces the better outcomes. Subsequently, the eminence ofmFNS PROMETHEE technology is checked by comparability with the prior art. Lastly, the advantages and disadvantages of our proposed technique are supplemented to demonstrate its productivity and shortcomings.
What can machine vision do for lymphatic histopathology image analysis: a comprehensive review
Authors: Chen Haoyuan , Li Xiaoqi , Li Chen , Rahaman Md. Mamunur , Li Xintong , Wu Jian , Sun Hongzan , Grzegorzek Marcin , Li Xiaoyan 
Published: February 2024

AbstractOver the past 10 years, machine vision (MV) algorithms for image analysis have been developing rapidly with computing power. At the same time, histopathological slices can be stored as digital images. Therefore, MV algorithms can provide diagnostic references to doctors. In particular, the continuous improvement of deep learning algorithms has further improved the accuracy of MV in disease detection and diagnosis. This paper reviews the application of image processing techniques based on MV in lymphoma histopathological images in recent years, including segmentation, classification and detection. Finally, the current methods are analyzed, some potential methods are proposed, and further prospects are made.
Educational and training innovation opportunities in the aquaculture and fisheries sector of Hungarian secondary agricultural education
Authors: Khademi-Vidra Anikó , Urbányi Béla , Bakos Izabella Mária 
Published: February 2024

AbstractAmong the challenges of the aquaculture sector, the present study tries to focus on the necessary modernisation and innovation of the Hungarian sector education by strategically outlining the possibility of a niche secondary-level fisheries PILOT (experimental) training. It is obvious that the “launching” of such a shortage training level is a very complex and long-term task, but in our opinion not unfeasible. To this end, we are considering the development of a multi-stage action plan, the first milestone of which will be a thorough situation survey of the aquaculture education community. The study applies a deductive approach to specific areas of education and training within the general trends in aquaculture, covering the main traces of PILOT training in fisheries as a niche discipline. Our first paper, targeted at educators, focuses on the results of a questionnaire survey of 94 educators. Our main objective was to assess the presence of aquaculture-related knowledge content and associated methodologies in the classroom and the general digital literacy of educators. Our objectives also focus on the general digital readiness of vocational trainers and on the patterns of “professional marketing” opportunities that aquaculture professionals can express.
Occupying Another’s Digital Space: Privacy of Smartphone Users as a Situated Practice
Authors: Avgustis Iuliia , Ibnelkaïd Samira , Iivari Netta 
Published: February 2024

Abstract
A smartphone’s screen is commonly regarded as a private space, and the action of looking at it is usually considered a violation of one’s privacy both by researchers and designers. However, our study demonstrates how participants in the interaction themselves negotiate moment by moment and achieve an understanding of someone’s screen space as public or private. In this paper, we analyze the interactional sequences of uninvited looks at another participant’s phone. Drawing on visual ethnography and ethnomethodologically informed multimodal interaction analysis, we video-recorded and analyzed everyday interactions between friends and acquaintances. Our findings show that looking at someone’s smartphone display is often performed and oriented to as a resource in interaction rather than an invasion of privacy. We therefore characterize the interactional functions of gazes and glances at another’s screen. We also discuss the research and design implications of approaching privacy as a situated practice.
Unveiling salinity-driven shifts in microbial community composition across compartments of naturally saline inland streams
Authors: Ayayee Paul A. , Custer Gordon F. , Tronstad Lusha M. , van Diepen Linda T. A. 
Published: February 2024

AbstractRiverine environments host diverse microbial communities, exhibiting distinctive assemblies at both microscopic and macroscopic levels. Despite the complexity of microbial life in rivers, the underlying factors that shape the community structure across different compartments remain elusive. Herein, we characterized microbial community composition of biofilm and planktonic (water column) compartments in five naturally saline inland streams and a freshwater stream to examine changes in microbial communities following salinization via sequencing of the microbial 16S rRNA gene. Significant differences in specific conductivity, oxidation–reduction potential, dissolved oxygen, and pH among the sampled streams were measured, as were significant differences in the microbial community composition between the planktonic and biofilm. The bacterial families Bacillaceae, Vicinamibacterceae, and Micrococcaceae were significantly more abundant in the biofilm compartment, while Methylophilaceae, Alcaligenaceae, Spirosomaceae, Burkholderiaceae, and Comamonadaceae were more abundant in the planktonic compartment. In addition, salinity (based on specific conductivity) influenced the microbial community composition in both compartments, with higher sensitivity of the planktonic compartment. Increases in the bacterial families Shewanellaceae, Marinomonadaceae, and Saccharospirillaceae or loss of Anaeromyxobacteraceae could be indicative of increased salinity within inland streams. Our results suggest that monitoring of microbial assemblages of freshwater ecosystems could be used as early warning signs of increased salinization levels.