bluuebunny/crossref_metadata_2025_split huggingface dataset:
Single center clinical analysis of macrophage activation syndrome complicating juvenile rheumatic diseases
Authors: Huang Shuoyin , Liu Yingying , Yan Wu , Zhang Tonghao , Wang Panpan , Zhu Meifang , Zhang Xiaohua , Zhou Peng , Fan Zhidan , Yu Haiguo 
Published: May 2024

Abstract
Background
Macrophage activation syndrome (MAS), an example of secondary hemophagocytic lymphohistiocytosis, is a potentially fatal complication of rheumatic diseases. We aimed to study the clinical and laboratory characteristics, treatment schemes, and outcomes of different rheumatic disorders associated with MAS in children. Early warning indicators of MAS have also been investigated to enable clinicians to make a prompt and accurate diagnosis.

Methods
Fifty-five patients with rheumatic diseases complicated by MAS were enrolled between January 2017 and December 2022. Clinical and laboratory data were collected before disease onset, at diagnosis, and after treatment with MAS, and data were compared between patients with systemic juvenile idiopathic arthritis (sJIA), Kawasaki disease (KD), and systemic lupus erythematosus (SLE). A random forest model was established to show the importance score of each variable with a significant difference.

Results
Most (81.8%) instances of MAS occurred during the initial diagnosis of the underlying disease. Compared to the active stage of sJIA, the platelet count, erythrocyte sedimentation rate, and fibrinogen level in sJIA-MAS were significantly decreased, whereas ferritin, ferritin/erythrocyte sedimentation rate, aspartate aminotransferase, alanine aminotransferase, lactate dehydrogenase, and D-dimer levels were significantly increased. Ferritin level, ferritin/erythrocyte sedimentation rate, and platelet count had the greatest predictive value for sJIA-MAS. The level of IL-18 in the sJIA-MAS group was significantly higher than in the active sJIA group, whereas IL-6 levels were significantly lower. Most patients with MAS were treated with methylprednisolone pulse combined with cyclosporine, and no deaths occurred.

Conclusions
Thrombocytopenia, ferritin levels, the ferritin/erythrocyte sedimentation rate, and elevated aspartate aminotransferase levels can predict the occurrence of MAS in patients with sJIA. Additionally, our analysis indicates that IL-18 plays an important role in the pathogenesis of MAS in sJIA-MAS.
Decadal analysis of measles epidemiological data in India (2011–2020)
Authors: Agiwal Varun , Chaudhuri Sirshendu , Kumar Maddela Vinay , Yasheswini Palle Venkata 
Published: May 2024

Abstract
Background
Despite India being one of the largest contributors to the measles burden, crucial epidemiological information is significantly lacking. We have analyzed the national-level representative data between 2011 and 2020 to estimate the national- and state-level incidence, first dose vaccine coverage, and mortality; and developed a prediction model to examine the trend of the disease.

Methods
We extracted the Health Management Information System (HMIS) for monthly aggregated measles cases, deaths, and child immunization (9–11 months) for first dose measles vaccine coverage across all states & Union Territories (UT). Population information & projections were extracted based on Census 2011. A multilevel fixed effect panel data model was used to predict measles incidence rate, assuming measles vaccination coverage as a predictor while accounting for time fixed effects.

Results
Total 558,536 measles cases and 4209 measles deaths were reported in India between 2010 and 2020. The incidence rate was highest in 2013 (628.8/million population), followed by a significant decline to reach 52.0/million in 2020. Measles vaccination coverage for the first dose was 84.1% in 2011 to 91.3% in 2019. Higher vaccination coverage was significantly correlated (r = 0.7, p = 0.02) with decline of measles incidence rate. The case fatality rate (CFR) was least in 2014 (0.13%) but upsurged consistently reaching to 3.3% in 2020. The predictive model indicates that with a first-dose vaccine coverage of 93.5%, and keeping other factors constant, the national measles incidence is projected to reach zero by 2025.

Conclusion
Measles incidence is declining in India due to higher vaccination coverage, yet the rise in death rates emphasizes the need for continued collaborative efforts to achieve a measles-free nation.
Vulnerable conditions syndemic, depression, and suicidal ideation among school children in China: cross-sectional census findings
Authors: Wang Hanqian , Lu Jingjing , Zhao Honghui , Li Lu , Zhou Xudong 
Published: May 2024

Abstract
Background
Mental health issues (depression and suicidal ideation) are increasingly common in children and emerge as escalating public health concerns. The syndemics that underline the importance of risk factor clustering provides a framework for intervention, but there is a lack of research on syndemics involving the adverse interactions of children’s mental health problems. This study therefore examined the cumulative and synergistic effects of vulnerable conditions on depression and suicidal ideation among children in China.

Methods
A mental health screening census of students in grades 5–12 was conducted from November 2022 to January 2023 in Nanling County, Anhui Province, China. The prevalence and co-occurrence of vulnerable conditions (unfavorable parental marital status, left-behind experience, bullying victimization, and self-harm behavior), depression, and suicidal ideation and the cumulative and synergistic effects of vulnerable conditions on depression and suicidal ideation were explored.

Results
Nearly a quarter of students (24.8%) reported at least two syndemic conditions. Overall, the prevalence of depression and suicidal ideation were 20.2% and 24.2% respectively. The odds of depression and suicidal ideation were higher for children with one or more vulnerable conditions and were ten times higher for children with three or more vulnerable conditions compared with those without any vulnerable condition. These four vulnerable conditions can increase the odds of depression and suicidal ideation by interacting synergistically with each other.

Conclusion
Our findings signal the importance of addressing mental health syndemics among children in China by simultaneously considering concurrent vulnerable conditions.
scCDC: a computational method for gene-specific contamination detection and correction in single-cell and single-nucleus RNA-seq data
Authors: Wang Weijian , Cen Yihui , Lu Zezhen , Xu Yueqing , Sun Tianyi , Xiao Ying , Liu Wanlu , Li Jingyi Jessica , Wang Chaochen 
Published: May 2024

AbstractIn droplet-based single-cell and single-nucleus RNA-seq assays, systematic contamination of ambient RNA molecules biases the quantification of gene expression levels. Existing methods correct the contamination for all genes globally. However, there lacks specific evaluation of correction efficacy for varying contamination levels. Here, we show that DecontX and CellBender under-correct highly contaminating genes, while SoupX and scAR over-correct lowly/non-contaminating genes. Here, we develop scCDC as the first method to detect the contamination-causing genes and only correct expression levels of these genes, some of which are cell-type markers. Compared with existing decontamination methods, scCDC excels in decontaminating highly contaminating genes while avoiding over-correction of other genes.
Study protocol: group-based psychoeducation for relatives of patients with bipolar disorder—a large scale real-world randomized controlled parallel group trial, the R-bipolar RCT
Authors: Stokholm Julie Ravneberg , Vinberg Maj , Faurholt-Jepsen Maria , Kessing Lars Vedel 
Published: May 2024

Abstract
Background
Relatives of patients with bipolar disorder (BD) often experience emotional burden with stress and depressive symptoms that again increase the likelihood of destabilization and relapses in the patient. The effects of group-based psychoeducation have not been investigated in large-scale real-world settings. We are currently conducting a large-scale real-world randomized controlled parallel group trial (RCT) to test whether group-based psychoeducation for 200 relatives to patients with BD improves mood instability and other critical outcomes in relatives and the corresponding patients with BD.

Methods
The trial is designed as a two-arm, parallel-group randomized trial with a balanced randomization 1:1 to either group-based psychoeducation or a waiting list for approximately 4 months and subsequent group-based psychoeducation. The primary outcome measure is mood instability calculated based on daily smartphone-based mood self-assessments. Other relevant outcomes are measured, including patients’ reported outcomes, assessing self-assessed burden, self-efficacy, and knowledge about BD.

Discussion
This protocol describes our currently ongoing randomized controlled trial (RCT) that aims at investigating group-based psychoeducation as an intervention for relatives of individuals diagnosed with bipolar disorder (BD). The study is the first large-scale real-world RCT to focus on a relatively short intervention of psychoeducation (6 sessions of 2 h each) in a large group of relatives (approximately 30 participants per group). With this focus, we wish to test an intervention that is feasible to implement in real-life psychiatric settings with limited budgets and time. It is also the first study to use mood instability in relatives as the primary outcome measure and to investigate whether mood instability and other affective symptoms in patients and relatives covary. It could be considered as limitations, that the trial is not blinded and does not include long-term follow-up.

Trial registration
ClinicalTrials.gov NCT06176001. Registered on 2023–12-19. The study is approved by the data agency (P-2021–809). The project was allowed to be initiated without permission from the Scientific Ethical Committees for the Capital Region, because it according to section 1, paragraph 4 of the Committee Act was not defined as a health scientific intervention study (case number 21063013).
Influence of metabolic syndrome on prognosis of patients with surgically treated esophageal cancer: a meta-analysis
Authors: Zhang Zhao , Huang Congcong , Xu Mengshan 
Published: May 2024

Abstract
Background
Metabolic syndrome (MetS) has been related to the increased incidence of esophageal cancer (EC). The aim of the study was to evaluate the influence of MetS on prognosis of patients with surgically treated EC in a systematic review and meta-analysis.

Methods
An extensive search was conducted on PubMed, Embase, Web of Science, Wanfang, and CNKI to identify relevant cohort studies. Random-effects models were employed to combine the findings, taking into account the potential influence of heterogeneity.

Results
Seven cohort studies involving 4332 patients with stage I-III EC who received surgical resection were included. At baseline, 608 (14.0%) patients had MetS. Pooled results suggested that MetS were associated with a higher risk of postoperative complications (risk ratio [RR]: 1.30, 95% confidence interval [CI]: 1.03 to 1.64, p = 0.03; I2 = 0%). However, the overall survival (RR: 1.07, 95% CI: 0.75 to 1.52, p = 0.71; I2 = 80%) and progression-free survival (RR: 1.27, 95% CI: 0.53 to 3.00, p = 0.59; I2 = 80%) were not significantly different between patients with and without MetS. Subgroup analyses suggested that the results were not significantly modified by study design (prospective or retrospective), histological type of EC (squamous cell carcinoma or adenocarcinoma), or diagnostic criteria for MetS (p values indicating subgroup difference all > 0.05).

Conclusion
Although MetS may be associated with a moderately increased risk of postoperative complications in patients with EC under surgical resection, the long-term survival may not be different between patients with and without MetS.
Possibilities and efficiency of MSC co-transfection for gene therapy
Authors: Christoffers Sina , Seiler Lisa , Wiebe Elena , Blume Cornelia 
Published: May 2024

AbstractMesenchymal stem/stromal cells (MSCs) are not only capable of self-renewal, trans-differentiation, homing to damaged tissue sites and immunomodulation by secretion of trophic factors but are also easy to isolate and expand. Because of these characteristics, they are used in numerous clinical trials for cell therapy including immune and neurological disorders, diabetes, bone and cartilage diseases and myocardial infarction. However, not all trials have successful outcomes, due to unfavourable microenvironmental factors and the heterogenous nature of MSCs. Therefore, genetic manipulation of MSCs can increase their prospect. Currently, most studies focus on single transfection with one gene. Even though the introduction of more than one gene increases the complexity, it also increases the effectivity as different mechanism are triggered, leading to a synergistic effect. In this review we focus on the methodology and efficiency of co-transfection, as well as the opportunities and pitfalls of these genetically engineered cells for therapy.
Graphical abstract
AiZynthFinder 4.0: developments based on learnings from 3 years of industrial application
Authors: Saigiridharan Lakshidaa , Hassen Alan Kai , Lai Helen , Torren-Peraire Paula , Engkvist Ola , Genheden Samuel 
Published: May 2024

AbstractWe present an updated overview of the AiZynthFinder package for retrosynthesis planning. Since the first version was released in 2020, we have added a substantial number of new features based on user feedback. Feature enhancements include policies for filter reactions, support for any one-step retrosynthesis model, a scoring framework and several additional search algorithms. To exemplify the typical use-cases of the software and highlight some learnings, we perform a large-scale analysis on several hundred thousand target molecules from diverse sources. This analysis looks at for instance route shape, stock usage and exploitation of reaction space, and points out strengths and weaknesses of our retrosynthesis approach. The software is released as open-source for educational purposes as well as to provide a reference implementation of the core algorithms for synthesis prediction. We hope that releasing the software as open-source will further facilitate innovation in developing novel methods for synthetic route prediction. AiZynthFinder is a fast, robust and extensible open-source software and can be downloaded from https://github.com/MolecularAI/aizynthfinder.
Ursonic acid from medicinal herbs inhibits PRRSV replication through activation of the innate immune response by targeting the phosphatase PTPN1
Authors: Yang Yuanqi , Gao Yanni , Sun Haifeng , Bai Juan , Zhang Jie , Zhang Lujie , Liu Xing , Sun Yangyang , Jiang Ping 
Published: May 2024

AbstractPorcine reproductive and respiratory syndrome (PRRS), caused by the PRRS virus (PRRSV), has caused substantial economic losses to the global swine industry due to the lack of effective commercial vaccines and drugs. There is an urgent need to develop alternative strategies for PRRS prevention and control, such as antiviral drugs. In this study, we identified ursonic acid (UNA), a natural pentacyclic triterpenoid from medicinal herbs, as a novel drug with anti-PRRSV activity in vitro. Mechanistically, a time-of-addition assay revealed that UNA inhibited PRRSV replication when it was added before, at the same time as, and after PRRSV infection was induced. Compound target prediction and molecular docking analysis suggested that UNA interacts with the active pocket of PTPN1, which was further confirmed by a target protein interference assay and phosphatase activity assay. Furthermore, UNA inhibited PRRSV replication by targeting PTPN1, which inhibited IFN-β production. In addition, UNA displayed antiviral activity against porcine epidemic diarrhoea virus (PEDV) and Seneca virus A (SVA) replication in vitro. These findings will be helpful for developing novel prophylactic and therapeutic agents against PRRS and other swine virus infections.
New progress in roles of TGF-β signaling crosstalks in cellular functions, immunity and diseases
Authors: Gu Shuchen , Derynck Rik , Chen Ye-Guang , Feng Xin-Hua 
Published: May 2024

AbstractThe family of secreted dimeric proteins known as the Transforming Growth Factor-β (TGF-β) family plays a critical role in facilitating intercellular communication within multicellular animals. A recent symposium on TGF-β Biology - Signaling, Development, and Diseases, held on December 19–21, 2023, in Hangzhou, China, showcased some latest advances in our understanding TGF-β biology and also served as an important forum for scientific collaboration and exchange of ideas. More than twenty presentations and discussions at the symposium delved into the intricate mechanisms of TGF-β superfamily signaling pathways, their roles in normal development and immunity, and the pathological conditions associated with pathway dysregulation.
Kalman filter for radio source power and direction of arrival estimation
Authors: Cano Cyril , Arab Nawel , Chaumette Éric , Larzabal Pascal , El Korso Mohammed Nabil , Vin Isabelle 
Published: May 2024

AbstractImages are an important source of information for spacecraft navigation. Based on an image and a known attitude, triangulation techniques (intersection or resection) are often used for positioning and navigation. In the resection problem, an observer estimate its unknown location by using angle measurements to points at known locations (i.e., landmarks), the localization performance depending on the accuracy of the angle measurements. As a contribution to resection for spacecraft navigation, we considers the dynamic image estimation problem based on radio interferometry, i.e., image of radio source power, where the measurements are sample covariance matrices (SCMs). Considering the case where several measurements are available as well as a known dynamic linear model of image evolution, a.k.a a linear state model, the minimum mean-squared error image estimator (MMSE) is given by the Kalman filter (KF) or one of its variants. However standard Kalman-like filters are not a priori suitable for the problem at hand since the measurements (i.e., SCMs) cannot be formulated analytically as a function of state parameters to be estimated (i.e., radio source power). In fact, this lack of analytical formulation can be circumvented by a statistical linear fitting allowing the SCMs to be expressed in terms of the state. This linear fitting introduces an additive residual noise, equivalent to a measurement noise, whose covariance matrix depends on the current state, a non-standard case for a measurement model. The covariance matrix of the residual noise is derived whatever the distributions of the radio sources and of the additive noise at the samples level, unveiling the contribution of their multivariate kurtosis. The proposed method is evaluated on simulated data representative of a dynamic radio interferometry framework. The results show that the proposed method is capable of effectively tracking moving radio sources in complex scenes with theoretical guaranties when the signal multivariate kurtosis is known.
Interventions to reduce inequalities for pregnant women living with disadvantage in high-income countries: an umbrella review protocol
Authors: Vousden N. , Geddes-Barton D. , Roberts N. , Knight M. 
Published: May 2024

Abstract
Background
Women who live with disadvantages such as socioeconomic deprivation, substance misuse, poor mental health, or domestic abuse face inequalities in health before, during, and after pregnancy and for their infants through to childhood. Women do not experience these factors alone; they accumulate and interact. Therefore, there is a need for an overview of interventions that work across health and social care and target women at risk of inequalities in maternal or child health.

Methods
Systematic review methodology will be used to identify systematic reviews from high-income countries that describe interventions aiming to reduce inequalities for women who experience social disadvantage during pregnancy. We will describe the range of interventions and their effectiveness in reducing inequalities in maternal or child health. Any individual, hospital, or community-level activity specific to women during the pre-conception, antenatal, or postpartum period up to 1 year after birth will be included, regardless of the setting in which they are delivered. We will search eight electronic databases with the pre-determined search strategy and supplement them with extensive grey literature searches. We will present a narrative synthesis, taking into account the quality assessment and coverage of included studies.

Discussion
Inequalities in maternal and child health are a key priority area for national policymakers. Understanding the range and effectiveness of interventions across the perinatal period will inform policy and practice. Identifying gaps in the evidence will inform future research.

Systematic review registration
PROSPERO CRD42023455502.
Practitioner perspectives on working with older patients in opioid agonist treatment (OAT) in Norway: opportunities and challenges
Authors: Todd-Kvam John , Clausen Thomas 
Published: May 2024

Abstract
Background
Norway has a growing proportion of ageing opioid agonist treatment (OAT) patients, with 42% of the 8300 Norwegian OAT patients aged over 50 in 2022. This study aims to explore practitioners’ views and experiences from treatment of ageing OAT patients.

Methods
Data were collected as a series of semi-structured interviews with treatment staff (roles interviewed: doctor, psychologist, social worker, nurse, and learning disability nurse). Participants were recruited from three OAT outpatient clinics, one with an urban catchment area and two with a mix of urban and rural. The interviews incorporated questions on patients’ somatic and mental health, strengths and weaknesses of the service for this group, and patients’ quality of life.

Results
Older patients were perceived to be more often stable in terms of substance use and housing situation, but also experiencing some key challenges in terms of cognitive impairment, loneliness and isolation, and comorbidities. Both the practitioner-patient relationship and healthcare interactions outside OAT had the potential to impact treatment quality positively or negatively depending on how they were managed.

Conclusions
Treating older patients in a way that respects and enhances their dignity is important. We argue that this requires better services for those whose functioning is impacted by cognitive impairment/dementia, an age-informed treatment model for this patient group, along with urgent work to improve municipal-level services given practitioners describe them as unacceptable in certain areas.