bluuebunny/crossref_metadata_2025_split huggingface dataset:
A tool to automatically design multiplex PCR primer pairs for specific targets using diverse templates
Authors: Yang Lin , Ding Feng , Lin Qiang , Xie Junhua , Fan Wei , Dai Fangyin , Cui Peng , Liu Wanfei 
Published: September 2023

AbstractMultiplex PCR is an increasingly popular method for identifying species, investigating environmental diversity, and conducting phylogenetic analysis. The complexity and increasing availability of diverse templates necessitate a highly automated approach to design degenerate primer pairs for specific targets with multiple sequences. Existing tools for degenerate primer design suffer from poor maintenance, semi-automation, low adaptability, and low tolerance for gaps. We developed PMPrimer, a Python-based tool for automated design and evaluation of multiplex PCR primer pairs for specific targets using diverse templates. PMPrimer automatically designs optimal multiplex PCR primer pairs using a statistical-based template filter; performs multiple sequence alignment, conserved region identification, and primer design; and evaluates the primers based on template coverage, taxon specificity, and target specificity. PMPrimer identifies conserved regions using Shannon’s entropy method, tolerates gaps using a haplotype-based method, and evaluates multiplex PCR primer pairs based on template coverage and taxon specificity. We tested PMPrimer using datasets with diverse levels of conservation, sizes, and applications, including tuf genes of Staphylococci, hsp65 genes of Mycobacteriaceae, and 16S ribosomal RNA genes of Archaea. PMPrimer showed outstanding performance compared with existing tools and experimental validated primers. PMPrimer is available as a Python package at https://github.com/AGIScuipeng/PMPrimer.
Selecting and describing control conditions in mobile health randomized controlled trials: a proposed typology
Authors: Goldberg Simon B. , Sun Shufang , Carlbring Per , Torous John 
Published: September 2023

AbstractHundreds of randomized controlled trials (RCTs) have tested the efficacy of mobile health (mHealth) tools for a wide range of mental and behavioral health outcomes. These RCTs have used a variety of control condition types which dramatically influence the scientific inferences that can be drawn from a given study. Unfortunately, nomenclature across mHealth RCTs is inconsistent and meta-analyses commonly combine control conditions that differ in potentially important ways. We propose a typology of control condition types in mHealth RCTs. We define 11 control condition types, discuss key dimensions on which they differ, provide a decision tree for selecting and identifying types, and describe the scientific inferences each comparison allows. We propose a five-tier comparison strength gradation along with four simplified categorization schemes. Lastly, we discuss unresolved definitional, ethical, and meta-analytic issues related to the categorization of control conditions in mHealth RCTs.
A deep-learning pipeline to diagnose pediatric intussusception and assess severity during ultrasound scanning: a multicenter retrospective-prospective study
Authors: Pei Yuanyuan , Wang Guijuan , Cao Haiwei , Jiang Shuanglan , Wang Dan , Wang Haiyu , Wang Hongying , Yu Hongkui 
Published: September 2023

AbstractIleocolic intussusception is one of the common acute abdomens in children and is first diagnosed urgently using ultrasound. Manual diagnosis requires extensive experience and skill, and identifying surgical indications in assessing the disease severity is more challenging. We aimed to develop a real-time lesion visualization deep-learning pipeline to solve this problem. This multicenter retrospective-prospective study used 14,085 images in 8736 consecutive patients (median age, eight months) with ileocolic intussusception who underwent ultrasound at six hospitals to train, validate, and test the deep-learning pipeline. Subsequently, the algorithm was validated in an internal image test set and an external video dataset. Furthermore, the performances of junior, intermediate, senior, and junior sonographers with AI-assistance were prospectively compared in 242 volunteers using the DeLong test. This tool recognized 1,086 images with three ileocolic intussusception signs with an average of the area under the receiver operating characteristic curve (average-AUC) of 0.972. It diagnosed 184 patients with no intussusception, nonsurgical intussusception, and surgical intussusception in 184 ultrasound videos with an average-AUC of 0.956. In the prospective pilot study using 242 volunteers, junior sonographers’ performances were significantly improved with AI-assistance (average-AUC: 0.966 vs. 0.857, P < 0.001; median scanning-time: 9.46 min vs. 3.66 min, P < 0.001), which were comparable to those of senior sonographers (average-AUC: 0.966 vs. 0.973, P = 0.600). Thus, here, we report that the deep-learning pipeline that guides lesions in real-time and is interpretable during ultrasound scanning could assist sonographers in improving the accuracy and efficiency of diagnosing intussusception and identifying surgical indications.
Event‐based reduced‐order H∞$H_{\infty }$ estimation for switched complex networks based on T‐S fuzzy model
Authors: Sun Ying , Zhang Yaping , Mao Jingyang , Liu Shuai 
Published: September 2023

AbstractThis paper investigates the design of a reduced‐order filter for a specific class of switched complex network systems with time‐varying delays. To handle the nonlinear components of the complex network, a T‐S fuzzy model is employed to convert them into a set of linear components. To tackle the issue of heavy network load, a memory‐based adaptive trigger mechanism is proposed. In this study, a reduced‐order state estimator is designed using the T‐S fuzzy model. To demonstrate the exponential stability of the error system, a suitable Lyapunov function is constructed based on the Lyapunov stability principle. The parameter matrix of the reduced‐order estimator is determined using the linear matrix inequality and convex linearization method. Additionally, a sufficient condition for the exponential stability of the error system at the suppression level is provided. Finally, the feasibility of the proposed scheme is validated through a simulation experiment.
Dissecting the emission from LHAASO J0341+5258: Implications for future multiwavelength observations
Authors: De Sarkar Agnibha , Majumdar Pratik 
Published: September 2023

Context. The Large High Altitude Air Shower Observatory (LHAASO) has detected multiple ultra-high-energy (UHE; Eγ ≥ 100 TeV) gamma-ray sources in the Milky Way Galaxy, which are associated with Galactic “PeVatrons” that accelerate particles up to PeV (=1015 eV) energies. Although supernova remnants (SNRs) and pulsar wind nebulae (PWNe), as source classes, are considered the leading candidates, further theoretical and observational efforts are needed to find conclusive proof that can confirm the nature of these PeVatrons.
Aims. The aim of this work is to provide a phenomenological model to account for the emission observed from the direction of LHAASO J0341+5258, an unidentified UHE gamma-ray source observed by LHAASO. Further, we also aim to provide the implications of our model in order to support future observations at multiple wavelengths.
Methods. We analyzed 15 yr of Fermi-LAT data to find the high-energy (HE; 100 MeV ≤ Eγ ≤ 100 GeV) GeV gamma-ray counterpart of LHAASO J0341+5258 in the 4FGL-DR3 catalog. We explain the spectrum of the closest 4FGL source, 4FGL J0340.4+5302, by a synchro-curvature emission formalism. We explored the escape-limited hadronic interaction between protons accelerated in an old, now invisible SNR and cold protons inside associated molecular clouds (MCs) and leptonic emission from a putative TeV halo in an effort to explain the multiwavelength (MWL) spectral energy distribution (SED) observed from the LHAASO source region.
Results. The spectrum of 4FGL J0340.4+5302 is explained well by the synchro-curvature emission, which, along with its point-like nature, indicates that this object is likely a GeV pulsar. A combined lepto-hadronic emission from SNR+MC and TeV halo scenarios explains the MWL SED of the LHAASO source. In addition, we find that leptonic emission from an individual TeV halo is also consistent with the observed MWL emission. We discuss possible observational avenues that can be explored in the near future and predict the outcome of those observational efforts from the model explored in this paper.
Risk of Incident Atrial Fibrillation and Subsequent Use of Oral Anticoagulants in Patients with Dementia
Authors: Tsai Chuan-Tsai , Chan Yi-Hsin , Liao Jo-Nan , Chen Tzeng-Ji , Lip Gregory Y. H. , Chen Shih-Ann , Chao Tze-Fan 
Published: September 2023

Background Dementia and atrial fibrillation (AF) have many shared risk factors. Besides, patients with dementia are under-represented in randomized trials, and even if AF is present, oral anticoagulants (OACs) are not prescribed frequently. This study aimed to report the incidence of newly diagnosed AF in dementia patients, and the impacts of use of vitamin K antagonist (VKA; e.g., warfarin) and non-VKA OAC (NOACs) on stroke and bleeding outcomes.
Methods Our study utilized the Taiwan National Health Insurance Research Database. A total of 554,074 patients with dementia were compared with 554,074 age- and sex-matched patients without dementia regarding the risk of incident AF. Among patients with dementia who experienced incident AF, the risks of clinical events of patients treated with warfarin or NOACs were compared with those without OACs (reference group).
Results The risk of incident AF was greater for patients with dementia compared with those without (adjusted hazard ratio [aHR]: 1.054; 95% confidence interval [CI]: 1.040–1.068 for all types of dementia, aHR: 1.035; 95% CI: 1.020–1.051 for presenile/senile dementia, and aHR: 1.125; 95% CI: 1.091–1.159 for vascular dementia). Among patients with dementia and experienced incident AF, warfarin use was associated with a higher risk of ischemic stroke (aHR: 1.290; 95% CI: 1.156–1.440), intracranial hemorrhage (ICH; aHR: 1.678; 95% CI: 1.346–2.090), and major bleeding (aHR: 1.192; 95% CI: 1.073–1.323) compared with non-OACs. NOAC use was associated with a lower risk of ischemic stroke (aHR: 0.421; 95% CI: 0.352–0.503) and composite risk of ischemic stroke or major bleeding (aHR: 0.544; 95% CI: 0.487–0.608) compared with non-OACs. These results were consistent among the patients after the propensity matching.
Conclusion In this large nationwide cohort, the risk of newly diagnosed AF was higher in patients with dementia (all dementia, presenile/senile dementia, and vascular dementia) compared with those without dementia. For patients with dementia who experienced incident AF, NOAC use was associated with a better clinical outcome compared with non-OAC. Patients with dementia require a holistic approach to their care and management, including the use of NOACs to reduce the risks of clinical events.
The girl powering of global politics
Authors: Walters Rosie 
Published: September 2023

AbstractRecent years have seen unprecedented interest in girls’ activism, and yet our understanding of their politics is still limited. More broadly, children have largely been absent from International Relations scholarship, despite the centrality of childhood and our understandings of it to global politics. Where they have featured, it is often as victims of phenomena beyond their control, or as the perpetrators of crimes, but rarely as active subjects able to influence politics for the better. In this article, I review the emerging literature that aims to conceptualise girls’ agency in global politics. I show the parallels between recent work in Girlhood Studies and in feminist and postcolonial IR, in exploring the potential for feminist activism within and against neoliberalism. Finally, I outline how a ‘transnational girlhoods’ approach might enable feminist scholars to explore how girls across a range of different contexts are challenging inequalities
Decreasing prevalence of atopic dermatitis in Swedish schoolchildren: three repeated population-based surveys
Authors: af Klinteberg Maja , Winberg Anna , Andersson Martin , Rönmark Eva , Hedman Linnea 
Published: September 2023

Abstract

Background
The prevalence of atopic dermatitis (AD) has increased over several decades and now affects about one-fifth of all children in high-income countries (HICs). While the increase continues in lower-income countries, the prevalence of AD might have reached a plateau in HICs.

Objectives
To investigate trends in the prevalence of AD and atopic comorbidity in schoolchildren in Sweden.

Methods
The study population consisted of three cohorts of children (median age 8 years) in Norrbotten, Sweden, for 1996 (n = 3430), 2006 (n = 2585) and 2017 (n = 2785). An identical questionnaire that included questions from the International Study of Asthma and Allergies in Childhood (ISAAC) protocol was used in all three cohorts. Trends in AD prevalence were estimated, as well as trends in atopic comorbidity. AD prevalence was estimated both according to the ISAAC definition of AD and by adding the reported diagnosis by a physician (D-AD).

Results
The prevalence of AD decreased in the last decade, from 22.8% (1996) and 21.3% (2006) to 16.3% (2017; P &lt; 0.001). The prevalence of D-AD was lower, but the same pattern of decrease was seen, from 9.3% (1996) and 9.4% (2006) to 5.7% (2017; P &lt; 0.001). In all three cohorts, AD was more common among girls than boys (18.9% vs. 13.8% in 2017; P &lt; 0.001). Children from the mountain inlands had a higher prevalence of AD than children from coastal cities (22.0% vs. 15.1% in 2017; P &lt; 0.001). In comparing D-AD, there were no significant differences between the sexes or between inland or coastal living. Concomitant asthma increased over the years from 12.2% (1996) to 15.8% (2006) to 23.0% (2017; P &lt; 0.001). Concomitant allergic rhinitis and allergic sensitization increased from 1996 (15.0% and 27.5%) to 2006 (24.7% and 49.5%) but then levelled off until 2017 (21.0% and 46.7%).

Conclusions
The prevalence of AD among schoolchildren in Sweden decreased over the study period, whereas atopic comorbidity among children with AD increased. Although a decrease was seen, AD is still common and the increase in atopic comorbidity among children with AD, especially the increase in asthma, is concerning.
Widespread alternative splicing dysregulation occurs presymptomatically in CAG expansion spinocerebellar ataxias
Authors: Shorrock Hannah K , Lennon Claudia D , Aliyeva Asmer , Davey Emily E , DeMeo Cristina C , Pritchard Caroline E , Planco Lori , Velez Jose M , Mascorro-Huamancaja Alexandra , Shin Damian S , Cleary John D , Berglund J Andrew 
Published: September 2023

Abstract
The spinocerebellar ataxias (SCAs) are a group of dominantly inherited neurodegenerative diseases, several of which are caused by CAG expansion mutations (SCAs 1, 2, 3, 6, 7 and 12) and more broadly belong to the large family of over 40 microsatellite expansion diseases. While dysregulation of alternative splicing is a well defined driver of disease pathogenesis across several microsatellite diseases, the contribution of alternative splicing in CAG expansion SCAs is poorly understood. Furthermore, despite extensive studies on differential gene expression, there remains a gap in our understanding of presymptomatic transcriptomic drivers of disease. We sought to address these knowledge gaps through a comprehensive study of 29 publicly available RNA-sequencing datasets.
We identified that dysregulation of alternative splicing is widespread across CAG expansion mouse models of SCAs 1, 3 and 7. These changes were detected presymptomatically, persisted throughout disease progression, were repeat length-dependent, and were present in brain regions implicated in SCA pathogenesis including the cerebellum, pons and medulla. Across disease progression, changes in alternative splicing occurred in genes that function in pathways and processes known to be impaired in SCAs, such as ion channels, synaptic signalling, transcriptional regulation and the cytoskeleton. We validated several key alternative splicing events with known functional consequences, including Trpc3 exon 9 and Kcnma1 exon 23b, in the Atxn1154Q/2Q mouse model. Finally, we demonstrated that alternative splicing dysregulation is responsive to therapeutic intervention in CAG expansion SCAs with Atxn1 targeting antisense oligonucleotide rescuing key splicing events.
Taken together, these data demonstrate that widespread presymptomatic dysregulation of alternative splicing in CAG expansion SCAs may contribute to disease onset, early neuronal dysfunction and may represent novel biomarkers across this devastating group of neurodegenerative disorders.
Molecular subtypes of epilepsy associated with post-surgical seizure recurrence
Authors: Hershberger Courtney E , Louis Shreya , Busch Robyn M , Vegh Deborah , Najm Imad , Bazeley Peter , Eng Charis , Jehi Lara , Rotroff Daniel M 
Published: September 2023

AbstractApproximately 50% of individuals who undergo resective epilepsy surgery experience seizure recurrence. The heterogenous post-operative outcomes are not fully explained by clinical, imaging and electrophysiological variables. We hypothesized that molecular features may be useful in understanding surgical response, and that individuals with epilepsy can be classified into molecular subtypes that are associated with seizure freedom or recurrence after surgical resection. Pre-operative blood samples, brain tissue and post-operative seizure outcomes were collected from a cohort of 40 individuals with temporal lobe epilepsy, 23 of whom experienced post-operative seizure recurrence. Messenger RNA and microRNA extracted from the blood and tissue samples were sequenced. The messenger RNA and microRNA expression levels from the blood and brain were each subjected to a novel clustering approach combined with multiple logistic regression to separate individuals into genetic clusters that identify novel subtypes associated with post-operative seizure outcomes. We then compared the microRNAs and messenger RNAs from patient blood and brain tissue that were significantly associated with each subtype to identify signatures that are similarly over- or under-represented for an outcome and more likely to represent endophenotypes with common molecular aetiology. These target microRNAs and messenger RNAs were further characterized by pathway analysis to assess their functional role in epilepsy. Using blood-derived microRNA and messenger RNA expression levels, we identified two subtypes of epilepsy that were significantly associated with seizure recurrence (clusters A1 and B4) (adjusted P &lt; 0.20). A total of 551 microRNAs and 2486 messenger RNAs were associated with clusters A1 and B4, respectively (adjusted P &lt; 0.05). Clustering of brain–tissue messenger RNA expression levels revealed an additional subtype (C2) associated with seizure recurrence that had high overlap of dysregulated messenger RNA transcripts with cluster B4. Clusters A1, B4 and C2 also shared significant overlap of subjects, which altogether suggests a coordinated mechanism by which microRNA and messenger RNA transcripts may be related to seizure recurrence. Epileptic subtypes A1, B4 and C2 reveal both known and novel microRNA and messenger RNA targets in seizure recurrence. Furthermore, targets identified in A1 and B4 are quantifiable in pre-operative blood samples and could potentially serve as biomarkers for surgical resection outcomes.
Invasive Pneumococcal Disease and Potential Impact of Pneumococcal Conjugate Vaccines Among Adults, Including Persons Experiencing Homelessness—Alaska, 2011–2020
Authors: Steinberg Jonathan , Bressler Sara S , Orell Laurie , Thompson Gail C , Kretz Anthony , Reasonover Alisa L , Bruden Dana , Bruce Michael G , Fischer Marc 
Published: September 2023

Abstract

Background
Adults aged ≥65 years, adults with certain underlying medical conditions, and persons experiencing homelessness are at increased risk for invasive pneumococcal disease (IPD). Two new pneumococcal conjugate vaccines, 15-valent pneumococcal conjugate vaccine (PCV15) and 20-valent pneumococcal conjugate vaccine (PCV20), were recently approved for use in US adults. We describe the epidemiology of IPD among Alaska adults and estimate the proportion of IPD cases potentially preventable by new vaccines.

Methods
We used statewide, laboratory-based surveillance data to calculate and compare IPD incidence rates and 95% confidence intervals (CIs) among Alaska adults aged ≥18 years during 2011–2020 and estimate the proportion of IPD cases that were caused by serotypes in PCV15 and PCV20.

Results
During 2011–2020, 1164 IPD cases were reported among Alaska adults for an average annual incidence of 21.3 cases per 100 000 adults per year (95% CI, 20.1–22.5). Incidence increased significantly during the study period (P &lt; .01). IPD incidence among Alaska Native adults was 4.7 times higher than among non-Alaska Native adults (95% CI, 4.2–5.2). Among adults experiencing homelessness in Anchorage, IPD incidence was 72 times higher than in the general adult population (95% CI, 59–89). Overall, 1032 (89%) Alaska adults with IPD had an indication for pneumococcal vaccine according to updated vaccination guidelines; 456 (39%) and 700 (60%) cases were caused by serotypes in PCV15 and PCV20, respectively.

Conclusions
Use of PCV15 and PCV20 could substantially reduce IPD among adults in Alaska, including Alaska Native adults and adults experiencing homelessness.
“We adjusted for race”: now what? A systematic review of utilization and reporting of race in American Journal of Epidemiology and Epidemiology, 2020–2021
Authors: Swilley-Martinez Monica E , Coles Serita A , Miller Vanessa E , Alam Ishrat Z , Fitch Kate Vinita , Cruz Theresa H , Hohl Bernadette , Murray Regan , Ranapurwala Shabbar I 
Published: September 2023

Abstract
Race is a social construct, commonly used in epidemiologic research to adjust for confounding. However, adjustment of race may mask racial disparities, thereby perpetuating structural racism. We conducted a systematic review of articles published in Epidemiology and American Journal of Epidemiology between 2020 and 2021 to (1) understand how race, ethnicity, and similar social constructs were operationalized, used, and reported; and (2) characterize good and poor practices of utilization and reporting of race data on the basis of the extent to which they reveal or mask systemic racism. Original research articles were considered for full review and data extraction if race data were used in the study analysis. We extracted how race was categorized, used—as a descriptor, confounder, or for effect measure modification (EMM)—and reported if the authors discussed racial disparities and systemic bias–related mechanisms responsible for perpetuating the disparities. Of the 561 articles, 299 had race data available and 192 (34.2%) used race data in analyses. Among the 160 US-based studies, 81 different racial categorizations were used. Race was most often used as a confounder (52%), followed by effect measure modifier (33%), and descriptive variable (12%). Fewer than 1 in 4 articles (22.9%) exhibited good practices (EMM along with discussing disparities and mechanisms), 63.5% of the articles exhibited poor practices (confounding only or not discussing mechanisms), and 13.5% were considered neither poor nor good practices. We discuss implications and provide 13 recommendations for operationalization, utilization, and reporting of race in epidemiologic and public health research.