bluuebunny/crossref_metadata_2025_split huggingface dataset:
Pathogen-derived mechanical cues potentiate the spatio-temporal implementation of plant defense
Authors: Léger Ophélie , Garcia Frédérick , Khafif Mehdi , Carrere Sebastien , Leblanc-Fournier Nathalie , Duclos Aroune , Tournat Vincent , Badel Eric , Didelon Marie , Le Ru Aurélie , Raffaele Sylvain , Barbacci Adelin 
Published: December 2022

Abstract
Background
The ongoing adaptation of plants to their environment is the basis for their survival. In this adaptation, mechanoperception of gravity and local curvature plays a role of prime importance in finely regulating growth and ensuring a dynamic balance preventing buckling. However, the abiotic environment is not the exclusive cause of mechanical stimuli. Biotic interactions between plants and microorganisms also involve physical forces and potentially mechanoperception. Whether pathogens trigger mechanoperception in plants and the impact of mechanotransduction on the regulation of plant defense remains however elusive.

Results
Here, we found that the perception of pathogen-derived mechanical cues by microtubules potentiates the spatio-temporal implementation of plant immunity to fungus. By combining biomechanics modeling and image analysis of the post-invasion stage, we reveal that fungal colonization releases plant cell wall-born tension locally, causing fluctuations of tensile stress in walls of healthy cells distant from the infection site. In healthy cells, the pathogen-derived mechanical cues guide the reorganization of mechanosensing cortical microtubules (CMT). The anisotropic patterning of CMTs is required for the regulation of immunity-related genes in distal cells. The CMT-mediated mechanotransduction of pathogen-derived cues increases Arabidopsis disease resistance by 40% when challenged with the fungus Sclerotinia sclerotiorum.

Conclusions
CMT anisotropic patterning triggered by pathogen-derived mechanical cues activates the implementation of early plant defense in cells distant from the infection site. We propose that the mechano-signaling triggered immunity (MTI) complements the molecular signals involved in pattern and effector-triggered immunity.
Diastolic dysfunction and sex-specific progression to HFpEF: current gaps in knowledge and future directions
Authors: van Ommen A. M. L. N. , Canto E. Dal , Cramer Maarten J. , Rutten F. H. , Onland-Moret N. C. , Ruijter H. M. den 
Published: December 2022

AbstractDiastolic dysfunction of the left ventricle (LVDD) is equally common in elderly women and men. LVDD is a condition that can remain latent for a long time but is also held responsible for elevated left ventricular filling pressures and high pulmonary pressures that may result in (exercise-induced) shortness of breath. This symptom is the hallmark of heart failure with preserved ejection fraction (HFpEF) which is predominantly found in women as compared to men within the HF spectrum. Given the mechanistic role of LVDD in the development of HFpEF, we review risk factors and mechanisms that may be responsible for this sex-specific progression of LVDD towards HFpEF from an epidemiological point-of-view and propose future research directions.
Mass screening and treatment (MSaT) for identifying and treating asymptomatic cases of malaria-malaria elimination demonstration project (MEDP), Mandla, Madhya Pradesh
Authors: Singh Akansha , Rajvanshi Harsh , Singh Mrigendra P. , Bhandari Sneha , Nisar Sekh , Poriya Rajan , Telasey Vinay , Jayswar Himanshu , Mishra Ashok K. , Das Aparup , Kaur Harpreet , Lal Altaf A. , Bharti Praveen K. 
Published: December 2022

Abstract
Background
Mass screening and treatment (MSaT) aims at reducing the spread of malaria in communities by identifying and treating infected persons regardless of the symptoms. This study was conducted to identify and treat asymptomatic cases using MSaT approaches in the community.

Methods
Three rounds of MSaT using cluster combination approaches were carried out during September 2018 to December 2019 to identify and treat asymptomatic malaria cases in the community. All individuals who were present in the household were screened using RDT irrespective of malaria related symptoms. Simultaneously thick and thin blood smear and blood spot were collected for further analysis using microscopy and diagnostic PCR done in a subset of the samples.

Results
Logistic regression analysis revealed that asymptomatic malaria cases significantly less among the older age groups compared with < 5 years children (OR ranged between 0.52 and 0.61; p < 0.05), lowest in cluster 4 (OR = 0.01; p < 0.0001); during third round of MSaT survey (OR = 0.11; p < 0.0001) and significantly higher in moderate to high endemic areas (OR = 88.30; p < 0.0001).

Conclusion
Over the three rounds of MSaT, the number of asymptomatic cases were significantly less in the older age groups, and during third round. Similarly, the asymptomatic cases were significantly less in the low endemic area with API < 1 (cluster four). Therefore, the malaria elimination programme may consider the MSaT strategy to identify asymptomatic cases that would be otherwise missed by routine fever based surveillance. This MSaT strategy would help accomplish the malaria elimination goal in an expedited manner.
Direct 3D printed biocompatible microfluidics: assessment of human mesenchymal stem cell differentiation and cytotoxic drug screening in a dynamic culture system
Authors: Riester Oliver , Laufer Stefan , Deigner Hans-Peter 
Published: December 2022

Abstract
Background
In vivo-mimicking conditions are critical in in vitro cell analysis to obtain clinically relevant results. The required conditions, comparable to those prevalent in nature, can be provided by microfluidic dynamic cell cultures. Microfluidics can be used to fabricate and test the functionality and biocompatibility of newly developed nanosystems or to apply micro- and nanoelectromechanical systems embedded in a microfluidic system. However, the use of microfluidic systems is often hampered by their accessibility, acquisition cost, or customization, especially for scientists whose primary research focus is not microfluidics.

Results
Here we present a method for 3D printing that can be applied without special prior knowledge and sophisticated equipment to produce various ready-to-use microfluidic components with a size of 100 µm. Compared to other available methods, 3D printing using fused deposition modeling (FDM) offers several advantages, such as time-reduction and avoidance of sophisticated equipment (e.g., photolithography), as well as excellent biocompatibility and avoidance of toxic, leaching chemicals or post-processing (e.g., stereolithography). We further demonstrate the ease of use of the method for two relevant applications: a cytotoxicity screening system and an osteoblastic differentiation assay. To our knowledge, this is the first time an application including treatment, long-term cell culture and analysis on one chip has been demonstrated in a directly 3D-printed microfluidic chip.

Conclusion
The direct 3D printing method is tested and validated for various microfluidic components that can be combined on a chip depending on the specific requirements of the experiment. The ease of use and production opens up the potential of microfluidics to a wide range of users, especially in biomedical research. Our demonstration of its use as a cytotoxicity screening system and as an assay for osteoblastic differentiation shows the methods potential in the development of novel biomedical applications. With the presented method, we aim to disseminate microfluidics as a standard method in biomedical research, thus improving the reproducibility and transferability of results to clinical applications.

Graphical Abstract
Macrophage cell membrane-based nanoparticles: a new promising biomimetic platform for targeted delivery and treatment
Authors: Wu Yuesong , Wan Shengli , Yang Shuo , Hu Haiyang , Zhang Chunxiang , Lai Jia , Zhou Jiahan , Chen Wang , Tang Xiaoqin , Luo Jiesi , Zhou Xiaogang , Yu Lu , Wang Long , Wu Anguo , Fan Qingze , Wu Jianming 
Published: December 2022

AbstractSynthetic nanoparticles with surface bioconjugation are promising platforms for targeted therapy, but their simple biological functionalization is still a challenging task against the complex intercellular environment. Once synthetic nanoparticles enter the body, they are phagocytosed by immune cells by the immune system. Recently, the cell membrane camouflage strategy has emerged as a novel therapeutic tactic to overcome these issues by utilizing the fundamental properties of natural cells. Macrophage, a type of immune system cells, plays critical roles in various diseases, including cancer, atherosclerosis, rheumatoid arthritis, infection and inflammation, due to the recognition and engulfment function of removing substances and pathogens. Macrophage membranes inherit the surface protein profiles and biointerfacing properties of source cells. Therefore, the macrophage membrane cloaking can protect synthetic nanoparticles from phagocytosis by the immune cells. Meanwhile, the macrophage membrane can make use of the natural correspondence to accurately recognize antigens and target inflamed tissue or tumor sites. In this review, we have summarized the advances in the fabrication, characterization and homing capacity of macrophage membrane cloaking nanoparticles in various diseases, including cancers, immune diseases, cardiovascular diseases, central nervous system diseases, and microbial infections. Although macrophage membrane-camouflaged nanoparticles are currently in the fetal stage of development, there is huge potential and challenge to explore the conversion mode in the clinic.
Does postoperative chemotherapy improve overall survival of patients with ypT1-2N0 cancer?
Authors: Su Pengfei , Zhang Yingjing , Yu Tian , Jiang Lin , Kang Weiming , Liu Yuqin , Yu Jianchun 
Published: December 2022

Abstract
Background
Perioperative chemotherapy combined with curative gastrectomy has been increasingly represented the standard therapeutic strategy for resectable gastric cancer (GC). However, it is still unclear whether postoperative chemotherapy has a survival benefit for ypT1-2N0 gastric cancer patients who have undergone preoperative chemotherapy followed curative gastrectomy.

Methods
The data of patients who undergone neoadjuvant chemotherapy followed by gastrectomy and had pathological classification of ypT1–2N0 between March 2016 and December 2020 at Peking Union Medical College Hospital were retrospectively reviewed. Chi-square test was adopted to compare the difference between the patients with postoperative chemotherapy (pCHT) and without postoperative chemotherapy (no pCHT). Survival curves for overall survival (OS) were estimated using the Kaplan-Meier method, and the log-rank test was used to compare survival difference. Univariate and multivariate analyses for prognostic factors were based on the Cox regression.

Results
A total of 134 patients met the inclusion criteria and 56 (41.8%) of them have undergone postoperative chemotherapy. There were no statistically significant differences in demographic and clinicopathologic characteristics between pCHT group and no pCHT group (all p > 0.05). Postoperative chemotherapy was not associated with a significant improvement in overall survival (OS) (Hazard ratio [HR] 0.815, 95% confidence interval [CI] 0.403–1.650; p = 0.474). Subgroup analyses demonstrated survival was equivalent between pCHT and no CHT group in ypT1N0 patients (HR 0.832, CI 0.222–3.121; p = 0.786) and ypT2N0 patients (HR 1.284, CI 0.564–2.924; p = 0.551). Multivariable analysis identified that clinical T stage independently influenced prognosis (cT3 vs. cT2: HR 2.875, 95% CI 0.998–8.281, p = 0.050; cT4 vs. cT2: HR 7.382, 95% CI 2.569–21.211, p < 0.001). In clinical T3–4 patients, there was an overall survival benefit for postoperative chemotherapy (HR 0.270, 95% CI 0.114–0.634; p = 0.006). No survival benefit of postoperative chemotherapy was identified in clinical T2 patients (HR 0.689, 95% CI 0.200–2.372; p = 0.579). Furthermore, postoperative chemotherapy was proved to be an independently positive prognostic factor for clinical T3–4 patients (HR 0.132, 95% CI 0.051–0.345; p < 0.001).

Conclusion
Postoperative chemotherapy might offer survival benefit to patients with ypT1-2N0 gastric cancer whose clinical T stage was T3–4 before preoperative chemotherapy.
Health-related quality of life, continuity of care and patient satisfaction: long-term outcomes of former patients of the Tuebingen Transition Program (TTP) – a retrospective cohort study
Authors: Boeker Luca Samuel , Kuemmerle-Deschner Jasmin Beate , Saur Sebastian Jonas , Klotsche Jens , Erbis Gabriele , Hansmann Sandra 
Published: December 2022

Abstract
Background
A significant number of patients in pediatric rheumatology suffer from ongoing disease activity into adulthood and thus need to be transferred into adult care. Transition as a structured individual process of preparation and patient empowerment can reduce risks of adverse long-term outcomes. The aim of this study was to measure long-term transition outcomes such as health-related quality of life (HR-QoL), patient satisfaction, and continuity of care in former patients of the interdisciplinary Tuebingen Transition Program (TTP).

Methods
In an iterative team process, a standardized questionnaire was developed including the EQ-5D-5L to measure HR-QoL, visual analogue scales to measure various items of patient satisfaction, further questions on continuity of care and physical activity and physician global assessment (PGA) to determine disease activity. HR-QoL and physical activity were compared to data from the average German population. Data was analyzed descriptively, and a logistic regression analysis was performed to identify possible predictive factors for negative outcomes.

Results
Response rate was 28.8% (85/295), 70.6% were female and median age was 24.1 years. 70.6% were diagnosed with juvenile idiopathic arthritis (JIA). Overall, HR-QoL was high (79.8 on the EQ VAS), yet lower than in the average population. The study cohort was more physically active than the respective average age groups. Mean patient satisfaction with pediatric care (8.4; standard deviation (SD) 1.7) and with the transition program (7.9; SD 2.6) was higher than with adult care (7.7; SD 2.2). 76.5% of participants received regular rheumatologic care after transfer. After excluding all participants in remission, the drop-out rate was 4.7%. A low PGA at the time of transfer was associated with higher HR-QoL and patient satisfaction after transfer.

Conclusions
HR-QoL of adult patients after successful transfer to adult rheumatology is reduced compared to the general population but physical activity and achievement of clinical remission could help to prevent negative long-term outcomes. Patient satisfaction and self-management of TTP patients were generally high, whereas youth-specific issues and their impact on the disease mandate greater attention. Treatment discontinuation rates were low and mostly due to remission. Further studies should focus on the identification of early predictors of long-term outcome to improve the process and outcome of transition.
Identification of circulating miRNAs differentially expressed in patients with Limb-girdle, Duchenne or facioscapulohumeral muscular dystrophies
Authors: García-Giménez José Luis , García-Trevijano Elena R. , Avilés-Alía Ana I. , Ibañez-Cabellos José Santiago , Bovea-Marco Miquel , Bas Teresa , Pallardó Federico V. , Viña Juan R. , Zaragozá Rosa 
Published: December 2022

Abstract
Background
Limb-girdle muscular dystrophy (LGMD) is a rare neuromuscular disease including a growing and heterogeneous number of subtypes with variable phenotype. Their clinical and histopathological characteristics frequently overlap with other neuromuscular dystrophies. Our goal was to identify, by a non-invasive method, a molecular signature including biochemical and epigenetic parameters with potential value for patient prognosis and stratification.

Results
Circulating miRNome was obtained by smallRNA-seq in plasma from LGMD patients (n = 6) and matched-controls (n = 6). Data, validated by qPCR in LGMD samples, were also examined in other common muscular dystrophies: Duchenne (DMD) (n = 5) and facioscapulohumeral muscular dystrophy (FSHD) (n = 4). Additionally, biochemical and clinical parameters were analyzed. miRNome analysis showed that thirteen differentially expressed miRs could separate LGMD vs control group by hierarchical clustering. Most of differentially expressed miRs in LGMD patients were up-regulated (miR-122-5p, miR-122b-3p, miR-6511a-3p, miR-192-5p, miR-574-3p, mir-885-3p, miR-29a-3p, miR-4646-3p, miR-203a-3p and miR-203b-5p) whilst only three of sequenced miRs were significantly down-regulated (miR-19b-3p, miR-7706, miR-323b-3p) when compared to matched controls. Bioinformatic analysis of target genes revealed cell cycle, muscle tissue development, regeneration and senescence as the most affected pathways. Four of these circulating miRs (miR-122-5p, miR-192-5p, miR-19b-3p and miR-323b-3p), together with the myomiR miR-206, were further analysed by qPCR in LGMD, DMD and FSHD. The receiver operating characteristic curves (ROC) revealed high area under the curve (AUC) values for selected miRs in all groups, indicating that these miRs have good sensitivity and specificity to distinguish LGMD, DMD and FSHD patients from healthy controls. miR-122-5p, miR-192-5p and miR-323-3p were differentially expressed compared to matched-controls in all groups but apparently, each type of muscular dystrophy showed a specific pattern of miR expression. Finally, a strong correlation between miRs and biochemical data was only found in LGMD patients: while miR-192-5p and miR-122-5p negatively correlated with CK, miR-192-5p positively correlated with vitamin D3 and ALP.

Conclusions
Although limited by the small number of patients included in this study, we propose here a specific combination of circulating miR-122-5p/miR-192-5p/miR-323-3 and biochemical parameters as a potential molecular signature whose clinical value for LGMD patient prognosis and stratification should be further confirmed in a larger cohort of patients.
NetAct: a computational platform to construct core transcription factor regulatory networks using gene activity
Authors: Su Kenong , Katebi Ataur , Kohar Vivek , Clauss Benjamin , Gordin Danya , Qin Zhaohui S. , Karuturi R. Krishna M. , Li Sheng , Lu Mingyang 
Published: December 2022

AbstractA major question in systems biology is how to identify the core gene regulatory circuit that governs the decision-making of a biological process. Here, we develop a computational platform, named NetAct, for constructing core transcription factor regulatory networks using both transcriptomics data and literature-based transcription factor-target databases. NetAct robustly infers regulators’ activity using target expression, constructs networks based on transcriptional activity, and integrates mathematical modeling for validation. Our in silico benchmark test shows that NetAct outperforms existing algorithms in inferring transcriptional activity and gene networks. We illustrate the application of NetAct to model networks driving TGF-β-induced epithelial-mesenchymal transition and macrophage polarization.
Truvari: refined structural variant comparison preserves allelic diversity
Authors: English Adam C. , Menon Vipin K. , Gibbs Richard A. , Metcalf Ginger A. , Sedlazeck Fritz J. 
Published: December 2022

AbstractThe fundamental challenge of multi-sample structural variant (SV) analysis such as merging and benchmarking is identifying when two SVs are the same. Common approaches for comparing SVs were developed alongside technologies which produce ill-defined boundaries. As SV detection becomes more exact, algorithms to preserve this refined signal are needed. Here, we present Truvari—an SV comparison, annotation, and analysis toolkit—and demonstrate the effect of SV comparison choices by building population-level VCFs from 36 haplotype-resolved long-read assemblies. We observe over-merging from other SV merging approaches which cause up to a 2.2× inflation of allele frequency, relative to Truvari.
Comparison between two methods of the immediate post-placental insertion of copper intrauterine device in vaginal birth—a protocol for a randomized clinical trial
Authors: Herculano Thuany Bento , Surita Fernanda Garanhani , Juliato Cássia Raquel Teatin , Rehder Patrícia Moretti 
Published: December 2022

Abstract
Background
Ensuring effective and long-term contraception in the immediate postpartum period is an effective strategy for reducing unplanned pregnancies. In the meantime, the intrauterine device (IUD) is an excellent option. The aim of our study was to evaluate the best way to insert post-placental IUDs in the immediate postpartum period. Discomfort during insertion, expulsion rate, uterine perforation rate, and proper positioning 40–60 days postpartum will be analyzed.

Methods
Randomized, controlled, open clinical trial. The study group will be composed of women between 18 and 43 years old who are admitted for vaginal birth at the Women’s Hospital of the State University of Campinas and who wish to use the IUD as a contraceptive method. The sample will be randomized into two insertion groups: manual and forceps. To calculate the sample size, the method of comparing the proportion between 2 groups was used, setting the level of significance alpha at 5% (alpha=0.05) and the power of the sample at 80% (beta=0.20). Based on the results, it was estimated that a sample of n=186 women (n=93 with manual insertion and n=93 with forceps) would be representative for comparison of expulsion between the 2 groups. All participants will undergo a postpartum consultation 40–60 days after birth with transvaginal ultrasound to assess the proper placement of the IUD.

Discussion
Insertion of an IUD in the immediate postpartum period has been considered a good option to increase coverage and access to contraception, and its benefit outweighs the inconvenience of a higher expulsion rate.

Trial registration
This study was approved by the Ethics and Research Commission of UNICAMP (CAAE: 50497321.4.0000.5404) and the Brazilian Registry of Clinical Trials (REBEC) (number RBR-4j62jv6). This is the first version of the study protocol approved on 11/12/2021 prior to the start of participant recruitment.