bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Similarity-based Time Series Source Dataset Selection Method for Transfer Learning
Authors: Zhang Zongxi , Zhou Kejian , Wang Xiaohu , Zhu Ming , Gao Jiahao , Mei Jie , Huang Qinqing 
Published: February 2023

Abstract
Source datasets are selected with high similarity to target datasets to improve the effect of transfer learning. The low similarity between the source and target datasets may lead to negative transfer. This paper proposes a similarity-based time series source dataset selection method for transfer learning. First, to reduce the complexity of the operation, we use Dynamic time-warped barycentric averaging to obtain the prototype signals of each dataset and convert the dataset similarity calculation into the similarity calculation between the prototype signals. The dynamic time warping (DTW) algorithm, commonly used to calculate time-series signal similarity, does not consider the effect of signal complexity and the amount of data the dataset contains on the signal similarity calculation. This article makes improvements to the above issues. Experiments are carried out on 20-time series datasets archived by the University of California Riverside. Experimental results show that the average transfer effect of source datasets selected by the proposed method is better than the commonly used dataset similarity measurement method based on DTW.
Performance Analysis of Machine Learning Methods
Authors: Liang Dinghai , Jin Xuan , Yuan Yuchen , Zou Ruyuan 
Published: February 2023

Abstract
Machine Learning has been studied worldwide for its functions in data science and artificial intelligence (AI) fields. Previous works have shown the excellent performance of machine learning methods in image classification. This paper uses various machine learning methods for fashion product classification. This paper aims to analyze the result of predictions for all classes and the first three ranked classes, and meanwhile, compare and discuss Support Vector Machine (SVM), K Nearest Neighbor (KNN), Convolution Neural Network (CNN), Contrastive Language-Image Pre-training (CLIP) methods’ performance. The results show that the F-Score is increased if just predicted for the first three ranked classes, and among SVM, KNN, and CNN models, CNN is the best in both conditions. From the performance of all four models, CLIP was the best model with better learning ability. Besides, the results suggest that an imbalanced dataset may harm predictions, and the CLIP method yields the best result. In the future, CLIP methods may be more likely recommended in an image classification problem with lots of classes, and an imbalanced dataset adjusted will provide new insights into unsolved and unimproved classification problems.
Application of multi-beam bathymetry system in shallow water area
Authors: Guo Qiang , Fu Chuanyu , Chen Yikang , Zhang Yu 
Published: February 2023

Abstract
Multi-beam bathymetry technology plays an important role in ocean, river and lake surveying and mapping. According to the measurement principle and technical requirements of MS8200 multi-beam bathymetry system, this paper introduces the composition and working principle of the system, the installation and calibration of the system, and the data in the post-processing process, the sea area and terrain characteristics near Wenchang Qinglan Port are taken as the research object to discuss the dual multi-beam bathymetric technology and data processing process, and compare the data of single multi-beam in the same sea area. The research results show that the dual probe of multibeam bathymetry system can better reflect the topographic features of the seafloor compared with the single probe, and shorten the time of mapping, reduce the labor intensity and improve the measurement efficiency, and provide data reference for the stability and reliability evaluation study of the dual probe of multibeam bathymetry system.
Design of a radiation shield applied to surface air temperature monitoring
Authors: Dai Wei , Tan Mengqing , Zhu Huanan 
Published: February 2023

Abstract
Due to the solar radiation effect, the current thermometric
instruments may produce a radiation error of about 1°C. In
this paper, a new radiation shield was designed. Initially, a
Computational Fluid Dynamics (CFD) method was employed to create the
radiation shield structure. Then, the CFD method was used to
quantify the radiation errors of the radiation shield under various
environmental conditions. Next, a Multi-layer Perceptron (MLP)
network was employed to form a radiation error correction approach
for this radiation shield. Finally, the air temperature observation
experiments were performed to verify the accuracy of the new
radiation shield. A 076B fan aspirated radiation shield was served
as an air temperature reference during experiments. The mean
absolute error, root mean square error, and correlation coefficient
between the radiation error results provided by the correction
approach and the measured radiation error results given by the
experiments are 0.012°C, 0.015°C, and 0.796°C,
respectively.
A 128-channel time-to-digital converter based on the 24-phase shift-clock sampling method for RPC
Authors: Xue Zhengwei , Liang Hao , Li Jiaxuan , Ge Jiajin , Li Quanyin 
Published: February 2023

Abstract
The Resistive Plate Chamber (RPC) are widely used in high
energy physics (HEP) experiments. In recent years, new designs and
application scenarios of RPCs abound, and an advanced
time-to-digital converter (TDC) system is in demand. The TDC
implemented in the field-programmable gate array (FPGA) is widely
used in HEP experiments with changeable conditions as a flexible
time measurement method. This article presents a multi-phase
shift-clock sampling FPGA-based TDC with 128 channels. The TDC
module is implemented in a Xilinx Kintex-7 FPGA. The sampling clock
period (2.22 ns) is subdivided into 24 phases to achieve finer time
resolution. The TDC performance measurements show that the
root-mean-square (RMS) time resolution of the TDC module in the time
interval measurement is 45.3 ∼ 57.7 ps, and the integral
nonlinearity (INL) is smaller than 0.2368 least significant bit
(LSB). In addition, some target designs are made to adapt to the
application scenarios. This article also shows measurement results
acquired from an RPC by this TDC. This TDC was used to measure the
RPC efficiency plateau and the TOT of the RPC readout signal.
Holistic similarity-based prediction of phosphorylation sites for understudied kinases
Authors: Ma Renfei , Li Shangfu , Parisi Luca , Li Wenshuo , Huang Hsien-Da , Lee Tzong-Yi 
Published: February 2023

AbstractPhosphorylation is an essential mechanism for regulating protein activities. Determining kinase-specific phosphorylation sites by experiments involves time-consuming and expensive analyzes. Although several studies proposed computational methods to model kinase-specific phosphorylation sites, they typically required abundant experimentally verified phosphorylation sites to yield reliable predictions. Nevertheless, the number of experimentally verified phosphorylation sites for most kinases is relatively small, and the targeting phosphorylation sites are still unidentified for some kinases. In fact, there is little research related to these understudied kinases in the literature. Thus, this study aims to create predictive models for these understudied kinases. A kinase–kinase similarity network was generated by merging the sequence-, functional-, protein-domain- and ‘STRING’-related similarities. Thus, besides sequence data, protein–protein interactions and functional pathways were also considered to aid predictive modelling. This similarity network was then integrated with a classification of kinase groups to yield highly similar kinases to a specific understudied type of kinase. Their experimentally verified phosphorylation sites were leveraged as positive sites to train predictive models. The experimentally verified phosphorylation sites of the understudied kinase were used for validation. Results demonstrate that 82 out of 116 understudied kinases were predicted with adequate performance via the proposed modelling strategy, achieving a balanced accuracy of 0.81, 0.78, 0.84, 0.84, 0.85, 0.82, 0.90, 0.82 and 0.85, for the ‘TK’, ‘Other’, ‘STE’, ‘CAMK’, ‘TKL’, ‘CMGC’, ‘AGC’, ‘CK1’ and ‘Atypical’ groups, respectively. Therefore, this study demonstrates that web-like predictive networks can reliably capture the underlying patterns in such understudied kinases by harnessing relevant sources of similarities to predict their specific phosphorylation sites.
Association of homelessness and skin conditions: a Danish population-based cohort study
Authors: Nilsson Sandra F , Ali Zarqa , Laursen Thomas M , Thyssen Jacob P , Egeberg Alexander  , Nordentoft Merete , Hjorthøj Carsten , Thomsen Simon F 
Published: February 2023

Abstract

Background
Research has linked homelessness with an increased risk of skin conditions. However, representative studies of diagnosis-specific information on skin conditions in people experiencing homelessness are lacking.

Objectives
To examine the association between homelessness and diagnosed skin conditions, prescribed medication and type of ­consultation.

Methods
This cohort study included data from the Danish nationwide health, social and administrative registers from 1 January 1999 to 31 December 2018. All people of Danish origin living in Denmark and aged at least 15 years at some point during the study period were included. Homelessness, measured by homeless shelter contacts, was the exposure. The outcome was any diagnosis of a skin disorder and specific skin disorders recorded in the Danish National Patient Register. Information on diagnostic consultation type (i.e. dermatological, nondermatological and emergency room) and dermatological prescriptions was studied. We estimated adjusted incidence rate ratio (aIRR) (adjusted for sex, age and calendar year) and cumulative incidence.

Results
In total, 5 054 238 individuals (50.6% female) were included in the study population, accounting for 73 477 258 person-years at risk, with a start mean (SD) age of 39.4 (21.1) years. Of the total number of individuals, 759 991 (15.0%) received a skin diagnosis and 38 071 (0.7%) experienced homelessness. A 2.31-times [95% confidence interval (CI) 2.25–2.36] higher IRR of any diagnosed skin condition was associated with homelessness, higher for nondermatological and emergency room consultations. Homelessness was associated with a reduced IRR of a skin neoplasm diagnosis (aIRR 0.76, 95% CI 0.71–8.82) compared with no homelessness. By the end of follow-up, 2.8% (95% CI 2.5–3.0) of individuals experiencing homelessness had a skin neoplasm diagnosis vs. 5.1% (95% CI 4.9–5.3) of individuals not experiencing homelessness. Five or more shelter contacts during the first year from first contact was associated with the highest aIRR of any diagnosed skin condition (7.33, 95% CI 5.57–9.65) compared with no contacts.

Conclusions
Individuals experiencing homelessness have high rates of most diagnosed skin conditions, but a lower occurrence of skin cancer diagnosis. Diagnostic and medical patterns for skin disorders differed clearly between people experiencing homelessness and individuals without these experiences. The time after first homeless shelter contact is an important window of opportunity for mitigating and preventing skin disorders.
Aglycosylated extracellular loop of inwardly rectifying potassium channel 4.1 (KCNJ10) provides a target for autoimmune neuroinflammation
Authors: Nicot Arnaud B , Harb Jean , Garcia Alexandra , Guillot Flora , Mai Hoa-Le , Mathé Camille V , Morille Jérémy , Vallino Amélie , Dugast Emilie , Shah Sita P , Lefrère Fabienne , Moyon Mélinda , Wiertlewski Sandrine , Le Berre Ludmilla , Renaudin Karine , Soulillou Jean-Paul , van Pesch Vincent , Brouard Sophie , Berthelot Laureline , Laplaud David-Axel 
Published: February 2023

AbstractMultiple sclerosis is an autoimmune disease of the central nervous system. Yet, the autoimmune targets are still undefined. The extracellular e1 sequence of KCNJ10, the inwardly rectifying potassium channel 4.1, has been subject to fierce debate for its role as a candidate autoantigen in multiple sclerosis. Inwardly rectifying potassium channel 4.1 is expressed in the central nervous system but also in peripheral tissues, raising concerns about the central nervous system-specificity of such autoreactivity. Immunization of C57Bl6/J female mice with the e1 peptide (amino acids 83–120 of Kir4.1) induced anti-e1 immunoglobulin G- and T-cell responses and promoted demyelinating encephalomyelitis with B cell central nervous system enrichment in leptomeninges and T cells/macrophages in central nervous system parenchyma from forebrain to spinal cord, mostly in the white matter. Within our cohort of multiple sclerosis patients (n = 252), 6% exhibited high anti-e1 immunoglobulin G levels in serum as compared to 0.7% in the control cohort (n = 127; P = 0.015). Immunolabelling of inwardly rectifying potassium channel 4.1-expressing white matter glia with the anti-e1 serum from immunized mice increased during murine autoimmune neuroinflammation and in multiple sclerosis white matter as compared with controls. Strikingly, the mouse and human anti-e1 sera labelled astrocytoma cells when N-glycosylation was blocked with tunicamycin. Western blot confirmed that neuroinflammation induces Kir4.1 expression, including its shorter aglycosylated form in murine experimental autoencephalomyelitis and multiple sclerosis. In addition, recognition of inwardly rectifying potassium channel 4.1 using mouse anti-e1 serum in Western blot experiments under unreduced conditions or in cells transfected with the N-glycosylation defective N104Q mutant as compared to the wild type further suggests that autoantibodies target an e1 conformational epitope in its aglycosylated form. These data highlight the e1 sequence of inwardly rectifying potassium channel 4.1 as a valid central nervous system autoantigen with a disease/tissue-specific post-translational antigen modification as potential contributor to autoimmunity in some multiple sclerosis patients.
The Coronavirus Disease 2019 Rebound Study: A Prospective Cohort Study to Evaluate Viral and Symptom Rebound Differences in Participants Treated With Nirmatrelvir Plus Ritonavir Versus Untreated Controls
Authors: Pandit Jay A , Radin Jennifer M , Chiang Danielle C , Spencer Emily G , Pawelek Jeff B , Diwan Mira , Roumani Leila , Mina Michael J 
Published: February 2023

Abstract

Background
The uptake of nirmatrelvir plus ritonavir (NPR) in patients with coronavirus disease 2019 (COVID-19) has been limited by concerns around the rebound phenomenon despite the scarcity of evidence around its epidemiology. The purpose of this study was to prospectively compare the epidemiology of rebound in NPR-treated and untreated participants with acute COVID-19 infection.

Methods
We designed a prospective, observational study in which participants who tested positive for COVID-19 and were clinically eligible for NPR were recruited to be evaluated for either viral or symptom clearance and rebound. Participants were assigned to the treatment or control group based on their decision to take NPR. Following initial diagnosis, both groups were provided 12 rapid antigen tests and asked to test on a regular schedule for 16 days and answer symptom surveys. Viral rebound based on test results and COVID-19 symptom rebound based on patient-reported symptoms were evaluated.

Results
Viral rebound incidence was 14.2% in the NPR treatment group (n = 127) and 9.3% in the control group (n = 43). Symptom rebound incidence was higher in the treatment group (18.9%) compared to controls (7.0%). There were no notable differences in viral rebound by age, gender, preexisting conditions, or major symptom groups during the acute phase or at the 1-month interval.

Conclusions
This preliminary report suggests that rebound after clearance of test positivity or symptom resolution is higher than previously reported. However, notably we observed a similar rate of rebound in both the NPR treatment and control groups. Large studies with diverse participants and extended follow-up are needed to better understand the rebound phenomena.
Phosphodiesterase 8 governs cAMP/PKA-dependent reduction of L-type calcium current in human atrial fibrillation: a novel arrhythmogenic mechanism
Authors: Grammatika Pavlidou Nefeli , Dobrev Shokoufeh , Beneke Kira , Reinhardt Franziska , Pecha Simon , Jacquet Eric , Abu-Taha Issam H , Schmidt Constanze , Voigt Niels , Kamler Markus , Schnabel Renate B , Baczkó Istvan , Garnier Anne , Reichenspurner Hermann , Nikolaev Viacheslav O , Dobrev Dobromir , Molina Cristina E 
Published: February 2023

Abstract

Aims
Atrial fibrillation (AF) is associated with altered cAMP/PKA signaling and an AF-promoting reduction of L-type Ca2+-current (ICa,L), the mechanisms of which are poorly understood. Cyclic-nucleotide phosphodiesterases (PDEs) degrade cAMP and regulate PKA-dependent phosphorylation of key calcium-handling proteins, including the ICa,L-carrying Cav1.2α1C subunit. The aim was to assess whether altered function of PDE type-8 (PDE8) isoforms contributes to the reduction of ICa,L in persistent (chronic) AF (cAF) patients.

Methods and results
mRNA, protein levels, and localization of PDE8A and PDE8B isoforms were measured by RT-qPCR, western blot, co-immunoprecipitation and immunofluorescence. PDE8 function was assessed by FRET, patch-clamp and sharp-electrode recordings. PDE8A gene and protein levels were higher in paroxysmal AF (pAF) vs. sinus rhythm (SR) patients, whereas PDE8B was upregulated in cAF only. Cytosolic abundance of PDE8A was higher in atrial pAF myocytes, whereas PDE8B tended to be more abundant at the plasmalemma in cAF myocytes. In co-immunoprecipitation, only PDE8B2 showed binding to Cav1.2α1C subunit which was strongly increased in cAF. Accordingly, Cav1.2α1C showed a lower phosphorylation at Ser1928 in association with decreased ICa,L in cAF. Selective PDE8 inhibition increased Ser1928 phosphorylation of Cav1.2α1C, enhanced cAMP at the subsarcolemma and rescued the lower ICa,L in cAF, which was accompanied by a prolongation of action potential duration at 50% of repolarization.

Conclusion
Both PDE8A and PDE8B are expressed in human heart. Upregulation of PDE8B isoforms in cAF reduces ICa,L via direct interaction of PDE8B2 with the Cav1.2α1C subunit. Thus, upregulated PDE8B2 might serve as a novel molecular mechanism of the proarrhythmic reduction of ICa,L in cAF.
A scoping review of evidence-based guidance and guidelines published by general practice professional organizations
Authors: O’Brien Emer , Duffy Seamus , Harkins Velma , Smith Susan M , O’Herlihy Noirin , Walsh Aisling , Clyne Barbara , Wallace Emma 
Published: February 2023

Abstract

Background
General practitioners (GPs) need robust, up-to-date evidence to deliver high-quality patient care. There is limited literature regarding the role of international GP professional organizations in developing and publishing clinical guidelines to support GPs clinical decision making.

Objective
To identify evidence-based guidance and clinical guidelines produced by GP professional organizations and summarize their content, structure, and methods of development and dissemination.

Methods
Scoping review of GP professional organizations following Joanna Briggs Institute guidance. Four databases were searched and a grey literature search was conducted. Studies were included if they were: (i) evidence-based guidance documents or clinical guidelines produced de novo by a national GP professional organization, (ii) developed to support GPs clinical care, and (iii) published in the last 10 years. GP professional organizations were contacted to provide supplementary information. A narrative synthesis was performed.

Results
Six GP professional organizations and 60 guidelines were included. The most common de novo guideline topics were mental health, cardiovascular disease, neurology, pregnancy and women’s health and preventive care. All guidelines were developed using a standard evidence-synthesis method. All included documents were disseminated through downloadable pdfs and peer review publications. GP professional organizations indicated that they generally collaborate with or endorse guidelines developed by national or international guideline producing bodies.

Conclusion
The findings of this scoping review provide an overview of de novo guideline development by GP professional organizations and can support collaboration between GP organizations worldwide thus reducing duplication of effort, facilitating reproducibility, and identifying areas of standardization.

Protocol registration
Open Science Framework: https://doi.org/10.17605/OSF.IO/JXQ26.
Methylation of CENP-A/Cse4 on arginine 143 and lysine 131 regulates kinetochore stability in yeast
Authors: Tran Nguyen Tra My , Munhoven Arno , Samel-Pommerencke Anke , Kshirsagar Rucha , Cuomo Alessandro , Bonaldi Tiziana , Ehrenhofer-Murray Ann E 
Published: February 2023

Abstract
Post-translational modifications on histones are well known to regulate chromatin structure and function, but much less information is available on modifications of the centromeric histone H3 variant and their effect at the kinetochore. Here, we report two modifications on the centromeric histone H3 variant CENP-A/Cse4 in the yeast Saccharomyces cerevisiae, methylation at arginine 143 (R143me) and lysine 131 (K131me), that affect centromere stability and kinetochore function. Both R143me and K131me lie in the core region of the centromeric nucleosome, near the entry/exit sites of the DNA from the nucleosome. Unexpectedly, mutation of Cse4-R143 (cse4-R143A) exacerbated the kinetochore defect of mutations in components of the NDC80 complex of the outer kinetochore (spc25-1) and the MIND complex (dsn1-7). The analysis of suppressor mutations of the spc25-1 cse4-R143A growth defect highlighted residues in Spc24, Ndc80, and Spc25 that localize to the tetramerization domain of the NDC80 complex and the Spc24-Spc25 stalk, suggesting that the mutations enhance interactions among NDC80 complex components and thus stabilize the complex. Furthermore, the Set2 histone methyltransferase inhibited kinetochore function in spc25-1 cse4-R143A cells, possibly by methylating Cse4-K131. Taken together, our data suggest that Cse4-R143 methylation and Cse4-K131 methylation affect the stability of the centromeric nucleosome, which is detrimental in the context of defective NDC80 tetramerization and can be compensated for by strengthening interactions among NDC80 complex components.