bluuebunny/crossref_metadata_2025_split huggingface dataset:
Full-Dimensional Proportional-Derivative Control Technique for Turing Pattern and Bifurcation of Delayed Reaction-Diffusion Bidirectional Ring Neural Networks
Authors: Du Xiangyu , Xiao Min , Luan Yifeng , Ding Jie , Rutkowski Leszek 
Published: July 2024

Abstract
In neural networks, the states of neural networks often exhibit significant spatio-temporal heterogeneity due to the diffusion effect of electrons and differences in the concentration of neurotransmitters. One of the macroscopic reflections of this time-spatial inhomogeneity is Turing pattern. However, most current research in reaction-diffusion neural networks has focused only on one-dimensional location information, and the remaining results considering two-dimensional location information are still limited to the case of two neurons. In this paper, we conduct the dynamic analysis and optimal control of a delayed reaction-diffusion neural network model with bidirectional loop structure. First, several mathematical descriptions are given for the proposed neural network model and the full-dimensional partial differential proportional-derivative (PD) controller is introduced. Second, by analyzing the characteristic equation, the conditions for Hopf bifurcation and Turing instability of the controlled network model are obtained. Furthermore, the amplitude equation of the controlled neural network is obtained based on the multiscale analysis method. Subsequently, we determine the key parameters affecting the formation of Turing pattern depending on the amplitude equation. Finally, multiple sets of computer simulations are carried out to support our theoretical results. It is found that the diffusion coefficients and time delays have significant effects on spatio-temporal dynamics of neural networks. Moreover, after reasonable parameter proportioning, the full-dimensional PD control method can alleviate the spatial heterogeneity caused by diffusion projects and time delays.
The Genome Explorer genome browser
Authors: Herson James , Krummenacker Markus , Spaulding Aaron , O'Maille Paul , Karp Peter D. 
Published: July 2024

ABSTRACT

Are two adjacent genes in the same operon? What are the order and spacing between several transcription factor binding sites? Genome browsers are software data visualization and exploration tools that enable biologists to answer questions such as these. In this paper, we report on a major update to our browser, Genome Explorer, that provides nearly instantaneous scaling and traversing of a genome, enabling users to quickly and easily zoom into an area of interest. The user can rapidly move between scales that depict the entire genome, individual genes, and the sequence; Genome Explorer presents the most relevant detail and context for each scale. By downloading the data for the entire genome to the user’s web browser and dynamically generating visualizations locally, we enable ﬁne control of zoom and pan functions and real-time redrawing of the visualization, resulting in smoother and more intuitive exploration of a genome than is possible with other browsers. Further, genome features are presented together, in-line, using familiar graphical depictions. In contrast, many other browsers depict genome features using data tracks, which have low information density and can visually obscure the relative positions of features. Genome Explorer diagrams have a high information density that provides larger amounts of genome context and sequence information to be presented in a given-sized monitor than for tracks-based browsers. Genome Explorer provides optional data tracks for the analysis of large-scale data sets and a unique comparative mode that aligns genomes at orthologous genes with synchronized zooming.

IMPORTANCE
Genome browsers provide graphical depictions of genome information to speed the uptake of complex genome data by scientists. They provide search operations to help scientists find information and zoom operations to enable scientists to view genome features at different resolutions. We introduce the Genome Explorer browser, which provides extremely fast zooming and panning of genome visualizations and displays with high information density.
Changes in sick notes associated with COVID-19 from 2020 to 2022: a cohort study in 24 million primary care patients in OpenSAFELY-TPP
Authors: Schaffer Andrea L , Park Robin Y , Tazare John , Bhaskaran Krishnan , MacKenna Brian , Denaxas Spiros , Dillingham Iain , Bacon Sebastian C J , Mehrkar Amir , Bates Christopher , Goldacre Ben , Greaves Felix , Macleod John ,   The OpenSAFELY Collaborative,   National Core Studies Collaborative, Tomlinson Laurie A , Walker Alex 
Published: July 2024

ObjectivesLong-term sickness absence from employment has negative consequences for the economy and can lead to widened health inequalities. Sick notes (also called ‘fit notes’) are issued by general practitioners when a person cannot work for health reasons for more than 7 days. We quantified the sick note rate in people with evidence of COVID-19 in 2020, 2021 and 2022, as an indication of the burden for people recovering from COVID-19.DesignCohort study.SettingWith National Health Service (NHS) England approval, we used routine clinical data (primary care, hospital and COVID-19 testing records) within the OpenSAFELY-TPP database.ParticipantsPeople 18–64 years with a recorded positive test or diagnosis of COVID-19 in 2020 (n=365 421), 2021 (n=1 206 555) or 2022 (n=1 321 313); general population matched in age, sex and region in 2019 (n=3 140 326), 2020 (n=3 439 534), 2021 (n=4 571 469) and 2022 (n=4 818 870); people hospitalised with pneumonia in 2019 (n=29 673).Primary outcome measureReceipt of a sick note in primary care.ResultsAmong people with a positive SARS-CoV-2 test or COVID-19 diagnosis, the sick note rate was 4.88 per 100 person-months (95% CI 4.83 to 4.93) in 2020, 2.66 (95% CI 2.64 to 2.67) in 2021 and 1.73 (95% CI 1.72 to 1.73) in 2022. Compared with the age, sex and region-matched general population, the adjusted HR for receipt of a sick note over the entire follow-up period (up to 10 months) was 4.07 (95% CI 4.02 to 4.12) in 2020 decreasing to 1.57 (95% CI 1.56 to 1.58) in 2022. The HR was highest in the first 30 days postdiagnosis in all years. Among people hospitalised with COVID-19, after adjustment, the sick note rate was lower than in people hospitalised with pneumonia.ConclusionsGiven the under-recording of postacute COVID-19-related symptoms, these findings contribute a valuable perspective on the long-term effects of COVID-19. Despite likely underestimation of the sick note rate, sick notes were issued more frequently to people with COVID-19 compared with those without, even in an era when most people are vaccinated. Most sick notes occurred in the first 30 days postdiagnosis, but the increased risk several months postdiagnosis may provide further evidence of the long-term impact.
Menstrual Practice Needs Scale short form (MPNS-SF) and rapid (MPNS-R):
development in Khulna, Bangladesh, and validation in cross-sectional surveys
from Bangladesh and Uganda
Authors: Hennegan Julie , Hasan Md Tanvir , Jalil Tasfiyah , Hunter Erin C , Head Alexandra , Jabbar Abdul , Mohosin Arifa Bente , Zoha Nigar Sultana , Alam Muhammad Khairul , Dunstan Laura , Akter Sabina , Zaman Afreen , Kaiser Adrita , Smith Calum , Bagala Lillian , Azzopardi Peter S 
Published: July 2024

Objectives
Develop and validate short and rapid forms of the 36-item Menstrual
Practice Needs Scale (MPNS-36).

Design
Item reduction prioritised content validity and was informed by
cognitive interviews with schoolgirls in Bangladesh, performance of
scale items in past research and stakeholder feedback. The original
MPNS-36 was revalidated, and short and rapid forms tested in a
cross-sectional survey. This was followed by further tests of
dimensionality, internal consistency and validity in multiple
cross-sectional surveys.

Setting and participants
Short form (MPNS-SF) and rapid form (MPNS-R) measures were developed
in a survey of 313 menstruating girls (mean age=13.51) in Khulna,
Bangladesh. They were further tested in the baseline survey of the
Adolescent Menstrual Experiences and Health Cohort, in Khulna,
Bangladesh (891 menstruating girls, mean age=12.40); and the dataset
from the MPNS-36 development in Soroti, Uganda (538 menstruating girls,
mean age=14.49).

Results
The 18-item short form reflects the six original subscales, with the
four core subscales demonstrating good fit in all three samples (Khulna
pilot: root mean square error of approximation (RMSEA)=0.064, 90% CI
0.043 to 0.084, Comparative Fit Index (CFI)=0.94, Tucker-Lewis Index
(TLI)=0.92. Cohort baseline: RMSEA=0.050, 90% CI 0.039 to 0.062,
CFI=0.96, TLI=0.95. Uganda: RMSEA=0.039, 90% CI 0.028 to 0.050,
CFI=0.95, TLI=0.94). The 9-item rapid form captures diverse needs. A
two-factor structure was the most appropriate but fell short of adequate
fit (Khulna pilot: RMSEA=0.092, 90% CI 0.000 to 0.158, CFI=0.93,
TLI=0.89). Hypothesised associations between the MPNS scores and other
constructs were comparable between the MPNS-36 and MPNS-SF in all
populations, and replicated, with attenuation, in the MPNS-R. Internal
consistency remained acceptable.

Conclusions
The MPNS-SF offers a reliable and valid measure of adolescent girls’
menstrual hygiene experience while reducing participant burden, to
support implementation and improve measurement in menstrual health
research. The MPNS-R provides a brief measure with poorer structural
validity, suited to short surveys and including menstrual health within
broader research topics.
Healing the Past by Nurturing the Future: trauma-aware, healing-informed care to improve support for Aboriginal and Torres Strait Islander families – implementation and evaluation study protocol
Authors: Jones Kimberley Ann , Henderson Helen , Bright Tess , Segal Leonie , Mauerhofer Olivia , Lake Katherine Jane , Julian Rebekah , Duncan Jhodie , Raymond Anita , Jones Amanda , Cameron Danielle , Fergie Doseena , Andrews Shawana , Stewart Skye , Atkinson Caroline , Elliot Alison , Crawford Belinda , Mohammed Janine , Bundle Gina , Hirvonen Tanja , Gnanamanickam Emmanuel , Davis Elise , Gee Graham , Herrman Helen , McLachlan Helen , Fisher Jane , Lovett Raymond , Campbell Sandy , Forster Della Anne , Clark Yvonne , Atkinson Judith , Marriott Rhonda , Chamberlain Catherine 
Published: July 2024

IntroductionComplex trauma can have serious impacts on the health and well-being of Aboriginal and Torres Strait Islander families. The perinatal period represents a ‘critical window’ for recovery and transforming cycles of trauma into cycles of healing. The Healing the Past by Nurturing the Future (HPNF) project aims to implement and evaluate a programme of strategies to improve support for Aboriginal and Torres Strait islander families experiencing complex trauma.MethodThe HPNF programme was codesigned over 4 years to improve awareness, support, recognition and assessment of trauma. Components include (1) a trauma-aware, healing-informed training and resource package for service providers; (2) trauma-awareness resources for parents; (3) organisational readiness assessment; (4) a database for parents and service providers to identify accessible and appropriate additional support and (5) piloting safe recognition and assessment processes. The programme will be implemented in a large rural health service in Victoria, Australia, over 12 months. Evaluation using a mixed-methods approach will assess feasibility, acceptability, cost, effectiveness and sustainability. This will include service user and provider interviews; service usage and cost auditing; and an administrative linked data study of parent and infant outcomes.AnalysisQualitative data will be analysed using reflexive thematic analysis. Quantitative and service usage outcomes will be described as counts and proportions. Evaluation of health outcomes will use interrupted time series analyses. Triangulation of data will be conducted and mapped to the Consolidated Framework for Implementation Research and Reach, Effectiveness, Adoption, Implementation and Maintenance frameworks to understand factors influencing feasibility, acceptability, effectiveness, cost and sustainability.Ethics and disseminationApproval granted from St Vincent’s Melbourne Ethics Committee (approval no. 239/22). Data will be disseminated according to the strategy outlined in the codesign study protocol, in-line with the National Health and Medical Research Council Aboriginal and Torres Strait Islander Research Excellence criteria.
Impact of defocus incorporated multiple segments (DIMS) spectacle lenses for myopia control on quality of life of the children: a qualitative study
Authors: Fatimah Mobashir , Agarkar Sumita , Narayanan Anuradha 
Published: July 2024

ObjectiveTo assess the impact of DIMS (defocus incorporated multiple segments) spectacle lenses on the quality of life of children using it.MethodsSeparate in-depth interviews were conducted with children using DIMS as a myopia control strategy for at least 1 month and their parents based on prepared guides. The recorded audio of the interviews was transcribed, and the significant data points were coded using a hybrid approach, that is, both the inductive and deductive coding methods were used to identify themes. The generated codes were further grouped, categorised and finally fitted as per relevance into the subdomains of the four domains of the WHO Quality of Life—Brief framework, namely the domains of social relationships, physical, psychological and environmental health.ResultsA total of 29 interviews were conducted, 15 with children (mean age: 12.47±2.13 years) and 14 with parents. Thematic analysis was done and a total of 63 codes were generated with 2, 16, 17 and 28 codes aligning to the domains of social relationships, environmental, psychological and physical health, respectively. Most parents did not notice any change in their child’s visual behaviour, yet children did experience symptoms such as peripheral blurred vision, eyestrain, headache, haloes and more during the adaptation period. High-cost, scratch-prone nature and difficulty in procurement were a few concerns raised by parents.ConclusionsParticipants were satisfied with most of the facets of social relationships, physical and psychological health domains. However, a few facets such as quality, accessibility and finance of the environmental health domain need improvement.
Deodorant pad for ulcerated breast cancer: safety and efficacy
Authors: Ishiba Toshiyuki , Ishida Hirohiko , Inoue Michiaki , Tazoe Yuki , Sakai Mami , Fujita Yuki , Kida Hiroko , Kosaka Taijiro , Ishihara Sakiko , Nara Miyako , Adachi Mio , Saita Chiaki , Goto Risa , Iwamoto Naoko , Nakatsugawa Noriko , Toi Masakazu , Aruga Tomoyuki 
Published: July 2024

ObjectivesAPOLLO study, ‘efficacy and safety of the deodorAnt Pad against Odour and uLceration for LOcally advanced breast cancer’, aimed to assess the safety and efficacy of wearing a deodorant pad in patients with locally advanced breast cancer (LABC) with an ulceration.MethodsKomagome Pads were previously developed by Juntendo University and Kao Corporation. In test A, a conventional pad consisting of gauze, a commercially available diaper, pad, etc and the Komagome Pad were compared over 3 days to assess their efficacy and possible improvements for short-term use. In test B, the Komagome Pad was used continuously for 1 month to evaluate its safety during long-term use.ResultsThis study included 14 patients in test A and nine in test B. In odour evaluation using sensory testing in test A, nine patients reported more significant efficacy in odour suppression with the Komagome Pad. The odour intensity of the Komagome Pad was lower on the gas chromatography-mass spectrometry. The group with a high level of exudation reported significantly higher satisfaction with the Komagome Pad. In test B, no adverse events were observed.ConclusionsA new deodorant pad for LABC demonstrated high safety and deodorant efficacy.
Special features of postoperative long-term follow-up patients with retinopathy of prematurity
Authors: Thang Le Hoang , Evgenievich Sidorenko Evgeniy , Ivanovich Sidorenko Evgeniy , Igorevich Krapivkin Alexey , Andreevna Kushchuk Olga , Vladimirovich Miguel Dmitry , Valerievna Ermolaeva Elena , Evgenievna Loskutova Victoria 
Published: July 2024

Background: Retinopathy of prematurity (ROP), leading to a high percentage of visual disability, continues to be one of the most complex and unresolved problems of pediatric ophthalmology. Some patients, despite successful surgical treatment and regression of ROP, lose their vision by the age of 25–35 years from the long-term consequences of ROP. That is why patients after surgical treatment of ROP, including those with peripheral chorioretinal dystrophy, need lifelong clinical follow-up in order to on time diagnose reactive conditions in the long-term postoperative period, leading to a significant loss of visual function. Methods: This paper presents a special case of a patient with stage 4 ROP and her long-term clinical and functional outcome. Conclusions: As a result of regular dynamic monitoring of the patient, using modern highly informative research methods, we promptly detected the formation of an exudative component of the macular area, which made it possible to prevent retinal detachment and loss of vision. Strengths of this study: This study presented a clinical case of a patient with ROP and long-term patient follow-up. This shows the importance of long-term monitoring of patients after treatment and the importance of combining treatment methods.
MST: Topology-Aware Message Aggregation for Exascale Graph Processing of Traversal-Centric Algorithms
Authors: Gan Xinbiao , Li Tiejun , Xiong Feng , Yang Bo , Chen Xinhai , Gong Chunye , Li Shijie , Lu Kai , Li Qiao , Zhang Yiming 
Published: July 2024

This article presents MST, a communication-efficient message library for fast graph traversal on exascale clusters. The key idea is to follow the multi-level network topology to perform topology-aware message aggregation, where small messages are gathered and scattered at each level of domain. To facilitate message aggregation, we equip MST with flexible buffer management including active buffer switching and dynamic buffer expansion. We implement MST on the newest-generation Tianhe supercomputer and evaluated its performance using various traversal-centric algorithms on both synthetic trillion-scale graphs and real-world big graphs. The results show that MST-based graph traversal is orders of magnitude faster than that based on Active Messages Library (AML). For the Graph500-BFS benchmark, MST-based Tianhe (with 77.2 K nodes) outperforms the Fugaku supercomputer (with 148.5 K nodes) by 18.53%, while Fugaku is ranked No. 1 in the latest Graph500-BFS ranking (June 2023). MST also greatly improves graph processing performance on other commercial large-scale computing systems at the National Supercomputing Center in Changsha (NSCC) and WuzhenLight.
Asparagine Dependency Is a Targetable Metabolic Vulnerability in TP53-Altered Castration-Resistant Prostate Cancer
Authors: Yoo Young A. , Quan Songhua , Yang William , Guo Qianyu , Rodríguez Yara , Chalmers Zachary R. , Dufficy Mary F. , Lackie Barbara , Sagar Vinay , Unno Kenji , Truica Mihai I. , Chandel Navdeep S. , Abdulkadir Sarki A. 
Published: July 2024

Abstract
TP53 tumor suppressor is frequently altered in lethal, castration-resistant prostate cancer (CRPC). However, to date there are no effective treatments that specifically target TP53 alterations. Using transcriptomic and metabolomic analyses, we have shown here that TP53-altered prostate cancer exhibits an increased dependency on asparagine (Asn) and overexpresses Asn synthetase (ASNS), the enzyme catalyzing the synthesis of Asn. Mechanistically, the loss or mutation of TP53 transcriptionally activated ASNS expression, directly and via mTORC1-mediated ATF4 induction, driving de novo Asn biosynthesis to support CRPC growth. TP53-altered CRPC cells were sensitive to Asn restriction by knockdown of ASNS or L-asparaginase treatment to deplete the intracellular and extracellular sources of Asn, respectively, and cell viability was rescued by Asn addition. Notably, pharmacological inhibition of intracellular Asn biosynthesis using a glutaminase inhibitor and depletion of extracellular Asn with L-asparaginase significantly reduced Asn production and effectively impaired CRPC growth. This study highlights the significance of ASNS-mediated metabolic adaptation as a synthetic vulnerability in CRPC with TP53 alterations, providing a rationale for targeting Asn production to treat these lethal prostate cancers.
Significance: TP53-mutated castration-resistant prostate cancer is dependent on asparagine biosynthesis due to upregulation of ASNS and can be therapeutically targeted by approaches that deplete intracellular and extracellular asparagine.
Enhancing Neutrophil Cytotoxicity of a Panel of Clinical EGFR Antibodies by Fc Engineering to IgA3.0
Authors: Chan Chilam , Jansen J.H. Marco , Hendriks Ilona S.T. , van der Peet Ida C. , Verdonschot Meggy E.L. , Passchier Elsemieke M. , Tsioumpekou Maria , Nederend Maaike , Klomp Sharon A. , Valerius Thomas , Peipp Matthias , Leusen Jeanette H.W. , Olofsen Patricia A. 
Published: July 2024

Abstract
EGFR plays an essential role in cellular signaling pathways that regulate cell growth, proliferation, and survival and is often dysregulated in cancer. Several monoclonal IgG antibodies have been clinically tested over the years, which exert their function via blocking the ligand binding domain (thereby inhibiting downstream signaling) and inducing Fc-related effector functions, such as antibody-dependent cellular cytotoxicity (ADCC) and antibody-dependent cellular phagocytosis (ADCP). However, these IgG antibodies do not optimally recruit neutrophils, which are the most abundant white blood cell population in humans. Therefore, we reformatted six therapeutic EGFR antibodies (cetuximab, panitumumab, nimotuzumab, necitumumab, zalutumumab, and matuzumab) into the IgA3.0 format, which is an IgA2 isotype adapted for clinical application. Reformatting these antibodies preserved Fab-mediated functions such as EGFR binding, growth inhibition, and ligand blockade. In addition, whole leukocyte ADCC was significantly increased when using this panel of IgA3.0 antibodies compared with their respective IgG counterparts, with no major differences between IgA3.0 antibodies. In vivo, IgA3.0 matuzumab outperformed the other antibodies, resulting in the strongest suppression of tumor outgrowth in a long intraperitoneal model. We showed that neutrophils are important for the suppression of tumor outgrowth. IgA3.0 matuzumab exhibited reduced receptor internalization compared with the other antibodies, possibly accounting for its superior in vivo Fc-mediated tumor cell killing efficacy. In conclusion, reformatting EGFR antibodies into an IgA3.0 format increased Fc-mediated killing while retaining Fab-mediated functions and could therefore be a good alternative for the currently available antibody therapies.