bluuebunny/crossref_metadata_2025_split huggingface dataset:
Identifying Potential Bioactive Components and Targets of Shaofuzhuyu Decoction in Treating Endometriosis Using serum Pharmacochemistry and Network Pharmacology
Authors: Li Qiyao , Liu Jing , Ding Lin , Yang Dongxia , Piao Chengyu , Yu Yang , Wu Xiuhong 
Published: August 2024

Objective To evaluate the underlying pharmacodynamics and therapeutic mechanism of Shaofuzhuyu Decoction (SFZYD) in treating Endometriosis (EMs). Methods Ultra-performance liquid chromatography-quadrupole time-of-flight mass spectrometry (UPLC-Q-TOF-MS) was employed to identify prototype ingredients of SFZYD in serum samples of EMs model rats. SFZYD was screened by Network Pharmacology for potential bioactive components, targets and key pathways in vivo according to the prototype components in blood. Subsequently, the binding activities of the potential bioactive compounds and key targets were tested by molecular docking techniques. Results 170 components of SFZYD were characterized in vitro using UPLC-Q-TOF-MS, and a total of 40 prototype ingredients of SFZYD were identified in rat serum. Network pharmacology predicted 90 protein targets and 193 pathways associated with EMs based on these prototypes. Five components of SFZYD were screened as potential biological activities, and four core targets were identified, these components were trans-4-hydroxycinnamic acid, ethyl p-methoxycinnamate, ferulic acid, protoferulic acid, and 3,5-O-dicaffeoylquinic acid, while the identified core targets were ESR1, EGFR, SRC, and MAPK1. Vigorous binding activities between potential bioactive components and the core targets were demonstrated by molecular docking studies. Conclusion The present study elucidated that 13 active components in SFZYD act to treat EMs by regulating four core targets, ESR1, EGFR, SRC and MAPK1, through multiple signalling pathways, and have multi-target, multi-component and synergistic effects, which may serve as a reference and basis for the development of new drugs for treating EMs.
Comparing the effects of lower limb orthoses on knee pain, function, quality of life, and knee joint alignment in people with medial knee osteoarthritis
Authors: Mahmoodi Maede , Arazpour Mokhtar , Mousavi Mohammad Ebrahim 
Published: August 2024

Introduction The purpose of this study was to compare the impact of three types of orthoses (knee orthosis, ankle foot orthosis (AFO), and foot orthosis) on knee alignment, pain, function, and quality of life in individuals with medial knee osteoarthritis (MKOA). Method Thirty patients took part in this study and were randomly assigned to three groups ( n = 10 in each group) based on the type of intervention. Knee function was assessed using the knee injury and osteoarthritis outcome score (KOOS) questionnaire, and knee alignment was evaluated by measuring angles using the images of bony prominence (AMI) method. Results After using knee orthosis and AFO, all subscales of KOOS showed significant improvement ( p < .05). However, there was no significant difference in the results after using foot orthosis ( p > .05). Conclusion The findings indicate that knee orthosis or AFO for 6 weeks can improve clinical outcomes for individuals with MKOA. This suggests that clinicians can consider using knee orthosis and AFO among the available treatment options to improve clinical outcomes.
A rapid transition from subduction to Barrovian metamorphism: geochronology of mafic–ultramafic relicts of oceanic crust in the Central Alps, Switzerland
Authors: Lemke Kim , Rubatto Daniela , Hermann Jörg 
Published: August 2024

AbstractRelicts of subducted oceanic lithosphere provide key information for the tectonic reconstructions of convergent margins. In the Central Alps, such relicts occur as isolated mafic–ultramafic lenses within the migmatites of the southern Adula nappe and Cima-Lunga unit. Analysis of the major-, minor-, and accessory minerals of these ophiolitic relicts, combined with zircon and rutile U–Pb ages and zircon oxygen isotopes, allows the reconstruction of different stages of their complex evolution. The mafic–ultramafic suite in Valle di Moleno consists of chlorite-harzburgites associated with metarodingites and retrogressed eclogites. Relic omphacite and kyanite in retrogressed eclogites provide evidence for subduction-related metamorphism. Increasing XPrp in the garnet mantle towards the rim documents heating during high-pressure metamorphism up to 800–850 °C. Polyphase inclusions and chemical zoning in garnet suggest fluid-assisted melting during high-pressure metamorphism dated at 31.0 ± 0.9 Ma. In Val Cama, chlorite-harzburgites, metarodingites and calcsilicate-metasediments occur. Detrital zircon ages in the metasediment suggest a Mesozoic deposition. The metarodingite-metaperidotite-metasediment association and the low δ18O signatures of zircon (δ18O 3.0–3.7‰), inherited from seafloor metasomatism of the protoliths, show that the rocks are derived from former altered oceanic crust. Amphibolite facies metamorphism related to the Central Alps Barrovian evolution in Val Cama occurred at 28.8 ± 1.5 Ma. The combined data from Moleno and Cama indicate a rapid transition (~ 2 Ma) from subduction to collisional metamorphism with corresponding exhumation rates of 3–6 cm/year. Fast exhumation tectonics may have been favored by slab break-off or slab extraction. U–Pb dating of rutile from both localities yields ages of ~ 20 Ma, suggesting that these rocks remained at amphibolite-facies conditions for about 10 Ma and underwent a second fast exhumation of 3 cm/year associated with vertical movements along the Insubric line.
Assessing in-field pesticide effects under European regulation and its implications for biodiversity: a workshop report
Authors: Solé Magali , Brendel Stephan , Aldrich Annette , Dauber Jens , Ewald Julie , Duquesne Sabine , Gottschalk Eckhard , Hoffmann Jörg , Kuemmerlen Mathias , Leake Alastair , Matezki Steffen , Meyer Stefan , Nabel Moritz , Natal-da-Luz Tiago , Pieper Silvia , Piselli Dario , Rigal Stanislas , Roß-Nickoll Martina , Schäffer Andreas , Settele Josef , Sigmund Gabriel , Sotherton Nick , Wogram Jörn , Messner Dirk 
Published: August 2024

Abstract
Background
Biodiversity loss is particularly pronounced in agroecosystems. Agricultural fields cover about one-third of the European Union and are crucial habitats for many species. At the same time, agricultural fields receive the highest pesticide input in European landscapes. Non-target species, including plants and arthropods, closely related to targeted pests, are directly affected by pesticides. Direct effects on these lower trophic levels cascade through the food web, resulting in indirect effects via the loss of food and habitat for subsequent trophic levels. The overarching goals of the European pesticide legislation require governments to sufficiently consider direct and indirect effects on plants and arthropods when authorising pesticides. This publication provides an overview of a workshop's findings in 2023 on whether the current pesticide risk assessment adequately addresses these requirements.

Results
Effects due to in-field exposure to pesticides are currently not assessed for plants and inadequately assessed for arthropods, resulting in an impairment of the food web support and biodiversity. Deficiencies lie within the risk assessment, as defined in the terrestrial guidance document from 2002. To overcome this problem, we introduce a two-step assessment method feasible for risk assessors, that is to determine (i) whether a pesticide product might have severe impacts on plants or arthropods and (ii) whether these effects extend to a broad taxonomic spectrum. When each step is fulfilled, it can be concluded that the in-field exposure of the pesticide use under assessment could lead to unacceptable direct effects on non-target species in-field and thus subsequent indirect effects on the food web. While our primary focus is to improve risk assessment methodologies, it is crucial to note that risk mitigation measures, such as conservation headlands, exist in cases where risks from in-field exposure have been identified.

Conclusions
We advocate that direct and indirect effects caused by in-field exposure to pesticides need to be adequately included in the risk assessment and risk management as soon as possible. To achieve this, we provide recommendations for the authorities including an evaluation method. Implementing this method would address a major deficiency in the current in-field pesticide risk assessment and ensure better protection of biodiversity.
The reliability and validity of rapid transcranial magnetic stimulation mapping for muscles under active contraction
Authors: Chowdhury Nahian S. , Chang Wei-Ju , Cavaleri Rocco , Chiang Alan K.I. , Schabrun Siobhan M. 
Published: August 2024

AbstractRapid mapping is a transcranial magnetic stimulation (TMS) mapping method which can significantly reduce data collection time compared to traditional approaches. However, its validity and reliability has only been established for upper-limb muscles during resting-state activity. Here, we determined the validity and reliability of rapid mapping for non-upper limb muscles that require active contraction during TMS: the masseter and quadriceps muscles. Eleven healthy participants attended two sessions, spaced two hours apart, each involving rapid and ‘traditional’ mapping of the masseter muscle and three quadriceps muscles (rectus femoris, vastus medialis, vastus lateralis). Map parameters included map volume, map area and centre of gravity (CoG) in the medial-lateral and anterior-posterior directions. Low to moderate measurement errors (%SEMeas = 10–32) were observed across muscles. Relative reliability varied from good-to-excellent (ICC = 0.63–0.99) for map volume, poor-to-excellent (ICC = 0.11–0.86) for map area, and fair-to-excellent for CoG (ICC = 0.25–0.8) across muscles. There was Bayesian evidence of equivalence (BF’s > 3) in most map outcomes between rapid and traditional maps across all muscles, supporting the validity of the rapid mapping method. Overall, rapid TMS mapping produced similar estimates of map parameters to the traditional method, however the reliability results were mixed. As mapping of non-upper limb muscles is relatively challenging, rapid mapping is a promising substitute for traditional mapping, however further work is required to refine this method.
External validation of the CARDOT score for predicting respiratory complications after thoracic surgery
Authors: Pipanmekaporn Tanyong , Kitswat Pakaros , Leurcharusmee Prangmalee , Runraksar Thanaporn , Bunchungmongkol Nutchanart , Khorana Jiraporn , Tantraworasin Apichat , Lapisatepun Panuwat , Saokaew Surasak 
Published: August 2024

Abstract
Background
The CARDOT scores have been developed for prediction of respiratory complications after thoracic surgery. This study aimed to externally validate the CARDOT score and assess the predictive value of preoperative neutrophil-to-lymphocyte ratio (NLR) for postoperative respiratory complication.

Methods
A retrospective cohort study of consecutive thoracic surgical patients at a single tertiary hospital in northern Thailand was conducted. The development and validation datasets were collected between 2006 and 2012 and from 2015 to 2021, respectively. Six prespecified predictive factors were identified, and formed a predictive score, the CARDOT score (chronic obstructive pulmonary disease, American Society of Anesthesiologists physical status, right-sided operation, duration of surgery, preoperative oxygen saturation on room air, thoracotomy), was calculated. The performance of the CARDOT score was evaluated in terms of discrimination by using the area under the receiver operating characteristic (AuROC) curve and calibration.

Results
There were 1086 and 1645 patients included in the development and validation datasets. The incidence of respiratory complications was 15.7% (171 of 1086) and 22.5% (370 of 1645) in the development and validation datasets, respectively. The CARDOT score had good discriminative ability for both the development and validation datasets (AuROC 0.789 (95% CI 0.753–0.827) and 0.758 (95% CI 0.730–0.787), respectively). The CARDOT score showed good calibration in both datasets. A high NLR (≥ 4.5) significantly increased the risk of respiratory complications after thoracic surgery (P < 0.001). The AuROC curve of the validation cohort increased to 0.775 (95% CI 0.750–0.800) when the score was combined with a high NLR. The AuROC of the CARDOT score with the NLR showed significantly greater discrimination power than that of the CARDOT score alone (P = 0.008).

Conclusions
The CARDOT score showed a good discriminative performance in the external validation dataset. An addition of a high NLR significantly increases the predictive performance of CARDOT score. The utility of this score is valuable in settings with limited access to preoperative pulmonary function testing.
YELLOW RoUTIne prospective cohort study protocol: insight in the dynamics of bacteria in the elderly bladder
Authors: Wang Ruo Chen , Van Buul Laura W. , Geerlings Suzanne E. , De Greeff Sabine C. , Haenen Anja , Halonen Kati , Notermans Daan W. , Reuland E. Ascelijn , Smalbrugge Martin , Twisk Jos W. R. , Schneeberger Caroline 
Published: August 2024

Abstract
Background
Asymptomatic bacteriuria (ASB) – the presence of bacteria in urine without urinary tract infection (UTI) related signs & symptoms (S&S) – is common in the elderly bladder and is not considered pathogenic for UTI. We hypothesise that colonisation with non-uropathogenic bacteria could protect the bladder from invasion of more harmful bacteria. The exact role and dynamics of bacteriuria in the relation to the development of a UTI is still unknown. We aim to provide insight into the course of bacteriuria in the elderly bladder and its relation to UTI in frail older adults.

Methods and analysis
A prospective observational cohort study is being conducted in Dutch nursing homes (NHs) between February 2024 and December 2025. Urine samples and case report forms (CRF) on UTI-related S&S will be collected from each consenting NH resident every 3 months for a follow-up period of 18 months. Whenever a UTI-suspicion occurs in between the 3 monthly time points, additional data and a urine sample will be collected. Urine samples undergo several urinalyses (e.g. dipstick and bacterial culture). Additional molecular analysis will be conducted on a selection of cultured Escherichia coli (E. coli) for virulence genes.
Primary analyses will be conducted between residents with and without ASB at each time point. The primary outcome is UTI incidence during follow-up. In secondary analyses we will also take into account the low versus high presence of virulence genes of the E. coli.

Discussion
The combination of high ASB prevalence and a reduced ability of frail older adults to express UTI-related S&S may lead to UTI misdiagnosis and inappropriate antibiotic use. To our knowledge, this is the first study to investigate the dynamics and role of bacteriuria in the elderly bladder and their potential protective effect on the development of UTI.
The study findings with comprehensive analysis of epidemiological, clinical and molecular data could set the fundamental base for future guidelines and studies, and contribute to improving prevention, diagnosis and treatment of UTI in frail older adults, in addition to contributing to antibiotic stewardship in NHs.
Special supplement issue on quality assurance and enrichment of biological and biomedical ontologies and terminologies
Authors: Cui Licong , Agrawal Ankur 
Published: August 2024

AbstractOntologies and terminologies serve as the backbone of knowledge representation in biomedical domains, facilitating data integration, interoperability, and semantic understanding across diverse applications. However, the quality assurance and enrichment of these resources remain an ongoing challenge due to the dynamic nature of biomedical knowledge. In this editorial, we provide an introductory summary of seven articles included in this special supplement issue for quality assurance and enrichment of biological and biomedical ontologies and terminologies. These articles span a spectrum of topics, such as development of automated quality assessment frameworks for Resource Description Framework (RDF) resources, identification of missing concepts in SNOMED CT through logical definitions, and developing a COVID interface terminology to enable automatic annotations of COVID-19 related Electronic Health Records (EHRs). Collectively, these contributions underscore the ongoing efforts to improve the accuracy, consistency, and interoperability of biomedical ontologies and terminologies, thus advancing their pivotal role in healthcare and biomedical research.
Integrating causal pathway diagrams into practice facilitation to address colorectal cancer screening disparities in primary care
Authors: Ike Brooke , Johnson Ashley , Meza Rosemary , Cole Allison 
Published: August 2024

Abstract
Background
Colorectal cancer (CRC) is the second leading cause of cancer death and the second most common cancer diagnosis among the Hispanic population in the United States. However, CRC screening prevalence remains lower among Hispanic adults than among non-Hispanic white adults. To reduce CRC screening disparities, efforts to implement CRC screening evidence-based interventions in primary care organizations (PCOs) must consider their potential effect on existing screening disparities. More research is needed to understand how to leverage existing implementation science methodologies to improve health disparities. The Coaching to Improve Colorectal Cancer Screening Equity (CoachIQ) pilot study explores whether integrating two implementation science tools, Causal Pathway Diagrams and practice facilitation, is a feasible and effective way to address CRC screening disparities among Hispanic patients.

Methods
We used a quasi-experimental, mixed methods design to evaluate feasibility and assess initial signals of effectiveness of the CoachIQ approach. Three PCOs received coaching from CoachIQ practice facilitators over a 12-month period. Three non-equivalent comparison group PCOs received coaching during the same period as participants in a state quality improvement program. We conducted descriptive analyses of screening rates and coaching activities.

Results
The CoachIQ practice facilitators discussed equity, facilitated prioritization of QI activities, and reviewed CRC screening disparities during a higher proportion of coaching encounters than the comparison group practice facilitator. While the mean overall CRC screening rate in the comparison PCOs increased from 34 to 41%, the mean CRC screening rate for Hispanic patients did not increase from 30%. In contrast, the mean overall CRC screening rate at the CoachIQ PCOs increased from 41 to 44%, and the mean CRC screening rate for Hispanic patients increased from 35 to 39%.

Conclusions
The CoachIQ program merges two implementation science methodologies, practice facilitation and causal pathway diagrams, to help PCOs focus quality improvement efforts on improving CRC screening while also reducing screening disparities. Results from this pilot study demonstrate key differences between CoachIQ facilitation and standard facilitation, and point to the potential of the CoachIQ approach to decrease disparities in CRC screening.
Total elbow replacement in England: a protocol for analysis of National Joint Registry and Hospital Episode Statistics data
Authors: Hamoodi Zaid , Sayers Adrian , Whitehouse Michael R. , Rangan Amar , Kearsley-Fleet Lianne , Sergeant Jamie C. , Watts Adam C. 
Published: August 2024

Abstract
Introduction
Primary total elbow replacement (TER) services in England are being restructured with the goal of centralising care to specialised centres. It is important to monitor the impact of this service redesign. This protocol outlines an intended analysis to provide detailed descriptions of the patients who are receiving primary TER, where and by whom TER is being performed, and what the current surgical practices for TER are in England before the reconfiguration.

Methods
This analysis will use the National Joint Registry (NJR) elbow dataset and link it with NHS England Hospital Episode Statistics-Admitted Patient Care (HES-APC). It will include eligible patients from the start of the NJR elbow dataset in April 2012 to December 2022. The main objective is to determine the incidence of TER in England. Age-sex standardised rates will be calculated for groups including different ethnicities, and socioeconomic backgrounds, using the mid-year population data provided by the Office for National Statistics. This planned analysis will summarise patient characteristics such as age, sex, body mass index (BMI), hand dominance, American Society of Anaesthesiologists (ASA) grade, indication for TER, socioeconomic status, and patient co-morbidities. It will also examine implant fixation type, classification, brand/type, and changes over time in implant types used in England. Additionally, it will explore the characteristics and volume of the surgeons and hospitals providing primary TER services, including the grade of the primary surgeons, funding source for surgery, and admission type. The analysis will cover the number of procedures performed by surgeons and hospitals annually in England and in each region of England. Finally, the planned analysis will summarise the elective wait time, postoperative length of stay, and any serious adverse events or re-admissions within 30 and 90 days after the TER.

Discussion
This protocol describes the first deep dive analysis into the NJR elbow dataset to describe the incidence of TER surgery in England and the characteristics of patients who are receiving it. This analysis will summarise current primary TER practices in England before service reconfigurations. The impact of reconfiguration can be monitored by comparing future practice to the outcomes from this study.
Trial registration ClinicalTrials.gov, NCT06355011. Registered 02 April 2024, https://clinicaltrials.gov/ct2/show/NCT06355011.
Altered brain connectivity in mild cognitive impairment is linked to elevated tau and phosphorylated tau, but not to GAP-43 and Amyloid-β measurements: a resting-state fMRI study
Authors: Sadeghi Mohammad , Azargoonjahromi Ali , Nasiri Hamide , Yaghoobi Arash , Sadeghi Maryam , Chavoshi Seyedeh Saeideh , Baghaeikia Shilan , Mahzari Nastaran , Valipour Arina , Razeghi Oskouei Romina , Shahkarami Farshad , Amiri Fatemeh , Mayeli Mahsa 
Published: August 2024

AbstractMild Cognitive Impairment (MCI) is a neurological condition characterized by a noticeable decline in cognitive abilities that falls between normal aging and dementia. Along with some biomarkers like GAP-43, Aβ, tau, and P-tau, brain activity and connectivity are ascribed to MCI; however, the link between brain connectivity changes and such biomarkers in MCI is still being investigated. This study explores the relationship between biomarkers like GAP-43, Aβ, tau, and P-tau, and brain connectivity. We enrolled 25 Participants with normal cognitive function and 23 patients with MCI. Levels of GAP-43, Aβ1–42, t-tau, and p-tau181p in the CSF were measured, and functional connectivity measures including ROI-to-voxel (RV) correlations and the DMN RV-ratio were extracted from the resting-state fMRI data. P-values below 0.05 were considered significant. The results showed that in CN individuals, higher connectivity within the both anterior default mode network (aDMN) and posterior DMN (pDMN) was associated with higher levels of the biomarker GAP-43. In contrast, MCI individuals showed significant negative correlations between DMN connectivity and levels of tau and P-tau. Notably, no significant correlations were found between Aβ levels and connectivity measures in either group. These findings suggest that elevated levels of GAP-43 indicate increased functional connectivity in aDMN and pDMN. Conversely, elevated levels of tau and p-tau can disrupt connectivity through various mechanisms. Thus, the accumulation of tau and p-tau can lead to impaired neuronal connectivity, contributing to cognitive decline.