bluuebunny/crossref_metadata_2025_split huggingface dataset:
Relationship between dietary pattern and depressive symptoms: an international multicohort study
Authors: Wu Hanzhang , Gu Yeqing , Meng Ge , Zhang Qing , Liu Li , Wu Hongmei , Zhang Shunming , Zhang Tingjing , Wang Xuena , Zhang Juanjuan , Sun Shaomei , Wang Xing , Zhou Ming , Jia Qiyu , Song Kun , Chang Hong , Huang Tao , Niu Kaijun 
Published: June 2023

Abstract
Background
Several previous studies have shown that dietary patterns are associated with the incidence of depressive symptoms. However, the results have been inconsistent. This study aimed to prospectively investigate the association between dietary patterns and the risk of depressive symptoms in two large cohort studies.

Methods
The Tianjin Chronic Low-grade Systemic Inflammation and Health (TCLSIH) cohort study included a total of 7,094 participants living in Tianjin, China from 2013 to 2019, and the UK Biobank cohort study includes 96,810 participants who were recruited from 22 assessment centers across the UK taken between 2006 and 2010. All participants were free of a history of cardiovascular disease (CVD), cancer, and depressive symptoms at baseline. Dietary patterns at baseline were identified with factor analysis based on responses to a validated food frequency questionnaire in TCLSIH or Oxford WebQ in UK Biobank. Depressive symptoms were evaluated using the Chinese version of the Zung Self-Rating Depression Scale (SDS) in TCLSIH or hospital inpatient records in UK Biobank. Cox proportional hazards regression models were used to estimate the association between dietary patterns and depressive symptoms.

Results
A total of 989, and 1,303 participants developed depressive symptoms during 17,410 and 709,931 person-years of follow-up. After adjusting for several potential confounders, the multivariable HRs (95% CIs) of the depressive symptoms were 0.71 (0.57, 0.88) for traditional Chinese dietary pattern, 1.29 (1.07, 1.55) for processed animal offal included animal food dietary pattern, and 1.22 (1.02, 1.46) for sugar rich dietary pattern in TCLSIH (all Q4 vs Q1). In the UK Biobank, the HRs (95% CIs) of depressive symptoms were 1.39 (1.16, 1.68) for processed food dietary pattern (Q4 vs Q1), 0.90 (0.77, 1.00) for healthy dietary pattern (Q3 vs Q1), and 0.89 (0.75, 1.05) for meat dietary pattern (Q4 vs Q1) in the final adjusted model.

Conclusion
Dietary patterns rich in processed foods were associated with a higher risk of depressive symptoms, and following a traditional Chinese dietary pattern or healthy dietary pattern was associated with a lower risk of depressive symptoms, whereas meat dietary pattern was not associated.
Knee acoustic emissions as a noninvasive biomarker of articular health in patients with juvenile idiopathic arthritis: a clinical validation in an extended study population
Authors: Goossens Quentin , Locsin Miguel , Gharehbaghi Sevda , Brito Priya , Moise Emily , Ponder Lori A , Inan Omer T , Prahalad Sampath 
Published: June 2023

Abstract
Background
Joint acoustic emissions from knees have been evaluated as a convenient, non-invasive digital biomarker of inflammatory knee involvement in a small cohort of children with Juvenile Idiopathic Arthritis (JIA). The objective of the present study was to validate this in a larger cohort.

Findings
A total of 116 subjects (86 JIA and 30 healthy controls) participated in this study. Of the 86 subjects with JIA, 43 subjects had active knee involvement at the time of study. Joint acoustic emissions were bilaterally recorded, and corresponding signal features were used to train a machine learning algorithm (XGBoost) to classify JIA and healthy knees. All active JIA knees and 80% of the controls were used as training data set, while the remaining knees were used as testing data set. Leave-one-leg-out cross-validation was used for validation on the training data set. Validation on the training and testing set of the classifier resulted in an accuracy of 81.1% and 87.7% respectively. Sensitivity / specificity for the training and testing validation was 88.6% / 72.3% and 88.1% / 83.3%, respectively. The area under the curve of the receiver operating characteristic curve was 0.81 for the developed classifier. The distributions of the joint scores of the active and inactive knees were significantly different.

Conclusion
Joint acoustic emissions can serve as an inexpensive and easy-to-use digital biomarker to distinguish JIA from healthy controls. Utilizing serial joint acoustic emission recordings can potentially help monitor disease activity in JIA affected joints to enable timely changes in therapy.
Inhibition of the MEK/ERK pathway suppresses immune overactivation and mitigates TDP-43 toxicity in a Drosophila model of ALS
Authors: Yue Wenkai , Deng Xue , Wang Zhao , Jiang Mingsheng , Hu Rirong , Duan Yongjia , Wang Qiangqiang , Cui Jihong , Fang Yanshan 
Published: June 2023

AbstractTDP-43 is an important DNA/RNA-binding protein that is associated with age-related neurodegenerative diseases such as amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD); however, its pathomechanism is not fully understood. In a transgenic RNAi screen usingDrosophilaas a model, we uncovered that knockdown (KD) ofDsor1(theDrosophilaMAPK kinasedMEK) suppressed TDP-43 toxicity without altering TDP-43 phosphorylation or protein levels. Further investigation revealed that theDsor1downstream generl(dERK) was abnormally upregulated in TDP-43 flies, and neuronal overexpression ofdERKinduced profound upregulation of antimicrobial peptides (AMPs). We also detected a robust immune overactivation in TDP-43 flies, which could be suppressed by downregulation of the MEK/ERK pathway in TDP-43 fly neurons. Furthermore, neuronal KD of abnormally increased AMPs improved the motor function of TDP-43 flies. On the other hand, neuronal KD ofDnr1, a negative regulator of theDrosophilaimmune deficiency (IMD) pathway, activated the innate immunity and boosted AMP expression independent of the regulation by the MEK/ERK pathway, which diminished the mitigating effect of RNAi-dMEKon TDP-43 toxicity. Finally, we showed that an FDA-approved MEK inhibitor trametinib markedly suppressed immune overactivation, alleviated motor deficits and prolonged the lifespan of TDP-43 flies, but did not exhibit a lifespan-extending effect in Alzheimer disease (AD) or spinocerebellar ataxia type 3 (SCA3) fly models. Together, our findings suggest an important role of abnormal elevation of the MEK/ERK signaling and innate immunity in TDP-43 pathogenesis and propose trametinib as a potential therapeutic agent for ALS and other TDP-43-related diseases.
Within- and between-therapist agreement on personalized parameters for robot-assisted gait therapy: the challenge of adjusting robotic assistance
Authors: van Dellen Florian , Aurich-Schuler T. , Labruyère Rob 
Published: June 2023

Abstract
Background
Stationary robotic gait trainers usually allow for adjustment of training parameters, including gait speed, body weight support and robotic assistance, to personalize therapy. Consequently, therapists personalize parameter settings to pursue a relevant therapy goal for each patient. Previous work has shown that the choice of parameters influences the behavior of patients. At the same time, randomized clinical trials usually do not report the applied settings and do not consider them in the interpretation of their results. The choice of adequate parameter settings therefore remains one of the major challenges that therapists face in everyday clinical practice. For therapy to be most effective, personalization should ideally result in repeatable parameter settings for repeatable therapy situations, irrespective of the therapist who adjusts the parameters. This has not yet been investigated. Therefore, the aim of the present study was to investigate the agreement of parameter settings from session to session within a therapist and between two different therapists in children and adolescents undergoing robot-assisted gait training.

Methods and results
Fourteen patients walked in the robotic gait trainer Lokomat on 2 days. Two therapists from a pool of 5 therapists independently personalized gait speed, bodyweight support and robotic assistance for a moderately and a vigorously intensive therapy task. There was a very high agreement within and between therapists for the parameters gait speed and bodyweight support, but a substantially lower agreement for robotic assistance.

Conclusion
These findings imply that therapists perform consistently at setting parameters that have a very clear and visible clinical effect (e.g. walking speed and bodyweight support). However, they have more difficulties with robotic assistance, which has a more ambiguous effect because patients may respond differently to changes. Future work should therefore focus on better understanding patient reactions to changes in robotic assistance and especially on how instructions can be employed to steer these reactions. To improve the agreement, we propose that therapists link their choice of robotic assistance to the individual therapy goals of the patients and closely guide the patients during walking with instructions.
Prevalence and clinicopathological associations of HER2 expression in non-small cell lung cancer: a retrospective study in Jordanian patients
Authors: Abu Al Karsaneh Ola , Al Anber Arwa , ALQudah Mohammad , Al-Mustafa Sahar , AlMa’aitah Hussien , Sughayer Maher 
Published: June 2023

Abstract
Background
Human epidermal growth factor receptor 2 (HER2), a promising therapeutic target, can be mutated, amplified, or overexpressed in different malignancies, including non-small cell lung cancer (NSCLC). Although these alterations showed adverse prognostic effects in many cancers, their clinical significance in NSCLC is controversial. This study primarily assessed the prevalence of HER2 protein expression in NSCLC among Jordanian patients. In addition, the possible association between HER2 protein expression and clinicopathological variables was evaluated.

Methods
A total of 100 surgically resected NSCLC cases treated at King Hussein Cancer Center (KHCC) between 2009 and 2021 were examined for HER2 protein expression using immunohistochemistry (IHC). The American Society of Clinical Oncology/College of American Pathologists (ASCO/CAP) guidelines for breast cancer were applied to interpret the results with a final score ranging from 0 to 3+, considering a score of 3 + as overexpression. Additionally, a separate subset of patients was tested for HER2 gene mutation. Fisher’s exact test was used to assess the association between HER2 scores and the other variables. Kaplan-Meier method was used to calculate survival.

Results
Of the 100 cases, Her2 overexpression (score 3+) was detected in 2 cases (2%), score 2 + in 10 cases (10%), score 1 + in 12 cases (12%), and score 0 in 76 cases (76%). The two positive cases were one adenocarcinoma and one squamous cell carcinoma; both patients were elderly male smokers. No significant association was identified between Her2 expression and age, gender, smoking, histological subtype, grade, stage, tumor size, and lymph node status. Our findings also showed no association between Her2 expression and survival; however, advanced tumor stages and positive lymph node metastasis were significantly associated with poor overall survival. All cases tested for the Her2 mutation were negative.

Conclusions
Her2 overexpression is uncommon in NSCLC among the Jordanian population. However, when the same scoring criteria are used, the rates are similar to other results found in Asian cohorts. Due to our study’s relatively small sample size, a larger one is required to investigate the prognostic value and the molecular associations between the different Her2 alterations.
Tonsillectomy reduces the family impact of periodic fever, aphthous stomatitis, pharyngitis and cervical adenitis (PFAPA) syndrome and improves health-related quality of life in affected children
Authors: Rydenman Karin , Sparud-Lundin Carina , Karlsson-Bengtsson Anna , Berg Stefan , Fasth Anders , Wekell Per 
Published: June 2023

AbstractBackgroundPeriodic fever, aphthous stomatitis, pharyngitis and cervical adenitis (PFAPA) syndrome is an autoinflammatory disorder that primarily affects young children, and typically gives rise to fever episodes that recur monthly for several years. This study investigated the impact of PFAPA syndrome on the families of affected children, the health-related quality of life (HRQOL) of children with the syndrome, and how these factors were influenced by tonsillectomy.MethodsThis prospective cohort study included 24 children with typical PFAPA syndrome that were referred for tonsillectomy, of whom 20 underwent the procedure. The control group consisted of randomly selected children from the general population. Family impact and HRQOL were measured using the standardized, validated questionnaires Pediatric Quality of Life Inventory™ (PedsQL™) Family Impact Module (FIM) and PedsQL™ 4.0 Generic Core Scales (GCS). Parents to children with PFAPA completed the questionnaires before and 6 months after their child underwent tonsillectomy, and HRQOL was measured both between and during PFAPA episodes. The Wilcoxon signed-rank test was used to compare data before and after tonsillectomy in the patient group, while the Mann–Whitney test was used for comparison of the patient and control groups.ResultsBefore tonsillectomy, children with PFAPA had significantly lower scores than the control group on the PedsQL™ FIM and the PedsQL™ 4.0 GCS during fever episodes. After tonsillectomy, all patients improved with diminished febrile episodes, which resulted in significantly higher scores regarding both family impact and HRQOL at the time of follow-up. HRQOL of in children with PFAPA improved after tonsillectomy even when compared to afebrile intervals before the procedure. The differences between PFAPA patients and controls were eliminated after tonsillectomy.ConclusionPFAPA syndrome has a profound negative impact on the families of affected children. Tonsillectomy that leads to cessation or reduction of fever episodes eases the impact of the disease on the family. HRQOL in children with PFAPA is low during febrile episodes and similar to healthy controls in between episodes. The improvement of HRQOL in patients with PFAPA after tonsillectomy compared to the afebrile intervals before tonsillectomy highlights that the constantly recurring fevers may affect the children’s well-being even between fever episodes.
A benchmark of computational pipelines for single-cell histone modification data
Authors: Raimundo Félix , Prompsy Pacôme , Vert Jean-Philippe , Vallot Céline 
Published: June 2023

Abstract
Background
Single-cell histone post translational modification (scHPTM) assays such as scCUT&Tag or scChIP-seq allow single-cell mapping of diverse epigenomic landscapes within complex tissues and are likely to unlock our understanding of various mechanisms involved in development or diseases. Running scHTPM experiments and analyzing the data produced remains challenging since few consensus guidelines currently exist regarding good practices for experimental design and data analysis pipelines.

Results
We perform a computational benchmark to assess the impact of experimental parameters and data analysis pipelines on the ability of the cell representation to recapitulate known biological similarities. We run more than ten thousand experiments to systematically study the impact of coverage and number of cells, of the count matrix construction method, of feature selection and normalization, and of the dimension reduction algorithm used. This allows us to identify key experimental parameters and computational choices to obtain a good representation of single-cell HPTM data. We show in particular that the count matrix construction step has a strong influence on the quality of the representation and that using fixed-size bin counts outperforms annotation-based binning. Dimension reduction methods based on latent semantic indexing outperform others, and feature selection is detrimental, while keeping only high-quality cells has little influence on the final representation as long as enough cells are analyzed.

Conclusions
This benchmark provides a comprehensive study on how experimental parameters and computational choices affect the representation of single-cell HPTM data. We propose a series of recommendations regarding matrix construction, feature and cell selection, and dimensionality reduction algorithms.
The regulatory role and mechanism of lncTUG1 on cartilage apoptosis and inflammation in osteoarthritis
Authors: Liu Nan-nan , Huang Yan-ping , Shao Yu-bao , Fan Xue-fei , Sun He-yan , Wang Tao-rong , Yao Tao , Chen Xiao-Yu 
Published: June 2023

AbstractsBackgroundLong-stranded non-coding RNA TUG1 is lowly expressed in osteoarthritic chondrocytes. This study aimed to elucidate the role of TUG1 in osteoarthritic cartilage damage and the underlying mechanisms.MethodsCombined database analysis, using primary chondrocytes as well as the C28/I2 cell line, was performed by qRT-PCR, Western blotting, and immunofluorescence to determine the expression of TUG1, miR-144-3p, DUSP1, and other target proteins. Dual luciferase reporter gene and RIP to verify direct interaction of TUG1 with miR-144–3-p and miR-144–3-p with DUSP1, Annexin V-FITC/PI double staining to detect apoptosis. CCK-8 to detect cell proliferation. The biological significance of TUG1, miR-144-3p, and DUSP1 was assessed in vitro experiments using siRNA for TUG1, mimic and repressor for miR-144-3p, and overexpression plasmid for DUSP1. In this study, all data were subjected to at-test or one-way analysis of variance with ap-value < 0.05 as the cutoff.ResultsTUG1 expression was closely associated with osteoarthritic chondrocyte damage, and knockdown of TUG1 significantly promoted chondrocyte apoptosis and inflammation. In the present study, we found that TUG1 inhibited chondrocyte apoptosis and inflammation by competitively binding miR-144-3p, deregulating the negative regulatory effect of miR-144-3p on DUSP1, promoting DUSP1 expression, and inhibiting the p38 MAPK signaling pathway.ConclusionsIn conclusion, our study clarifies the role of the ceRNA regulatory network of TUG1/miR-144-3p/DUSP1/P38 MAPK in OA cartilage injury and provides an experimental and theoretical basis for genetic engineering tools to promote articular cartilage repair.Graphical abstract
RETRACTED ARTICLE: Associations of composite dietary antioxidant index with cardiovascular disease mortality among patients with type 2 diabetes
Authors: Yang Chan , Yang Qiangfei , Peng Xi , Li Xinqiong , Rao Guocheng 
Published: June 2023

Abstract
To investigate the associations of composite dietary antioxidant index (CDAI) with risk of cardiovascular disease (CVD) mortality among individuals with type 2 diabetes (T2D). This prospective cohort study included 7551 patients with T2D who participated in the National Health and Nutrition Examination Survey (NHANES) from 1999 through 2018. Death statistics were gathered by connecting the cohort database to the National Death Index through December 31, 2019. Multivariable Cox proportional hazards regression models were utilized to calculate hazard ratios and 95% CIs for the relationship of CDAI with risks of CVD and all-cause mortality. Three multivariable models were built. Restricted cubic spline analyses were utilized to explore the nonlinear association of CDAI with CVD mortality, and nonlinearity was tested by the likelihood ratio test. This cohort study included data from 7551 participants with T2D (mean [SE] age, 61.4 (0.2) years; 3811 male [weighted, 50.5%] and 3740 female [weighted, 49.5%]; median CDAI level, − 2.19 [IQR, − 2.19 ~ − 0.22]). A total of 2227 all-cause deaths and 746 CVD deaths were identified during an average of 98 months of follow-up. Nonlinear associations were observed for CDAI (P < 0.05 for nonlinearity) with risk of CVD mortality among patients with T2D. Compared with participants in the first quartile of CDAI levels (< − 2.19), the hazard ratios for CVD mortality were 0.47 (95% CI 0.30–0.75) for participants in the highest CDAI level quartile. This cohort study found that higher CDAI levels were significantly associated with lower risk of CVD mortality among individuals with T2D.
Extreme thermal stability of the antiGFP nanobody – GFP complex
Authors: Kakasi Balázs , Gácsi Eszter , Jankovics Hajnalka , Vonderviszt Ferenc 
Published: June 2023

Abstract
Objective
The green fluorescent protein (GFP) and its derivatives are widely used in biomedical research. The manipulation of GFP-tagged proteins by GFP-specific binders, e.g. single-domain antibodies (nanobodies), is of increasing significance. It is therefore important to better understand the properties of antiGFP-GFP interaction in order to establish methodological applications. In this work the interaction of superfolder GFP (sfGFP) and its enhancer nanobody (aGFPenh) was characterized further.

Results
Previous calorimetric experiments demonstrated that the aGFPenh nanobody binds strongly to sfGFP with a nanomolar affinity. Here we show that this interaction results in a substantial structural stabilization of aGFPenh reflected in a significant increase of its melting temperature by almost 30 °C. The thermal stability of the sfGFP-aGFPenh complex is close to 85 °C in the pH range 7.0–8.5. For therapeutic applications thermoresistance is often an essential factor. Our results suggest that methodologies based on GFP-aGFP interaction can be applied under a wide range of physicochemical conditions. The aGFPenh nanobody seems to be suitable for manipulating sfGFP-labeled targets even in extreme thermophilic organisms.
Discriminating two bacteria via laser-induced breakdown spectroscopy and artificial neural network
Authors: Arabi Dina , Hamdy Omnia , Mohamed Mahmoud S. M. , Abdel-Salam Zienab , Abdel-Harith Mohamed 
Published: June 2023

AbstractRapid and successful clinical diagnosis and bacterial infection treatment depend on accurate identification and differentiation between different pathogenic bacterial species. A lot of efforts have been made to utilize modern techniques which avoid the laborious work and time-consuming of conventional methods to fulfill this task. Among such techniques, laser-induced breakdown spectroscopy (LIBS) can tell much about bacterial identity and functionality. In the present study, a sensitivity-improved version of LIBS, i.e. nano-enhanced LIBS (NELIBS), has been used to discriminate between two different bacteria (Pseudomonas aeruginosa and Proteus mirabilis) belonging to different taxonomic orders. Biogenic silver nanoparticles (AgNPs) are sprinkled onto the samples’ surface to have better discrimination capability of the technique. The obtained spectroscopic results of the NELIBS approach revealed superior differentiation between the two bacterial species compared to the results of the conventional LIBS. Identification of each bacterial species has been achieved in light of the presence of spectral lines of certain elements. On the other hand, the discrimination was successful by comparing the intensity of the spectral lines in the spectra of the two bacteria. In addition, an artificial neural network (ANN) model has been created to assess the variation between the two data sets, affecting the differentiation process. The results revealed that NELIBS provides higher sensitivity and more intense spectral lines with increased detectable elements. The ANN results showed that the accuracy rates are 88% and 92% for LIBS and NELIBS, respectively. In the present work, it has been demonstrated that NELIBS combined with ANN successfully differentiated between both bacteria rapidly with high precision compared to conventional microbiological discrimination techniques and with minimum sample preparation.