bluuebunny/crossref_metadata_2025_split huggingface dataset:
Neurofind: using deep learning to make individualised inferences in brain-based disorders
Authors: Vieira S. , Baecker L. , Pinaya W. H. L. , Garcia-Dias R. , Scarpazza C. , Calhoun V. , Mechelli A. 
Published: February 2025

Abstract
Within precision psychiatry, there is a growing interest in normative models given their ability to parse heterogeneity. While they are intuitive and informative, the technical expertise and resources required to develop normative models may not be accessible to most researchers. Here we present Neurofind, a new freely available tool that bridges this gap by wrapping sound and previously tested methods on data harmonisation and advanced normative models into a web-based platform that requires minimal input from the user. We explain how Neurofind was developed, how to use the Neurofind website in four simple steps (www.neurofind.ai), and provide exemplar applications. Neurofind takes as input structural MRI images and outputs two main metrics derived from independent normative models: (1) Outlier Index Score, a deviation score from the normative brain morphology, and (2) Brain Age, the predicted age based on an individual’s brain morphometry. The tool was trained on 3362 images of healthy controls aged 20–80 from publicly available datasets. The volume of 101 cortical and subcortical regions was extracted and modelled with an adversarial autoencoder for the Outlier index model and a support vector regression for the Brain age model. To illustrate potential applications, we applied Neurofind to 364 images from three independent datasets of patients diagnosed with Alzheimer’s disease and schizophrenia. In Alzheimer’s disease, 55.2% of patients had very extreme Outlier Index Scores, mostly driven by larger deviations in temporal-limbic structures and ventricles. Patients were also homogeneous in how they deviated from the norm. Conversely, only 30.1% of schizophrenia patients were extreme outliers, due to deviations in the hippocampus and pallidum, and patients tended to be more heterogeneous than controls. Both groups showed signs of accelerated brain ageing.
Tumor cell-derived EMP1 is essential for cancer-associated fibroblast infiltration in tumor microenvironment of triple-negative breast cancer
Authors: Wang Qi , Li Dandan , Ma Haixiu , Li Zengyan , Wu Juan , Qiao Jinwan , Liu Jun , Zhao Jing , Ma Ronghua , Tian Lin , Zhang Lei , Yang Jianye , Wang Jianing , Qin Shanshan , Su Zhanhai 
Published: February 2025

Abstract
The role of epithelial membrane protein 1 (EMP1) in tumor microenvironment (TME) remodeling has not yet been elucidated. In addition, the biological function of EMP1 in triple-negative breast cancer (TNBC) is largely unclear. In this study, we examined the infiltration landscape of cell types in the TME of breast cancer, and found that EMP1 expression was positively correlated with stromal and microenvironmental scores. Infiltration analysis and immunohistochemical (IHC) staining of serial sections confirmed the critical role of EMP1 in cancer-associated fibroblast (CAF) infiltration. Cell co-culture assays, xenograft tumor experiments, loss-of-function, gain-of-function, RNA sequencing studies, and rescue assays were performed to confirm the role of EMP1 in CAF infiltration in vitro and in vivo. These findings revealed that EMP1 depletion in TNBC cells resulted in considerable inhibition of CAF infiltration in vivo and in vitro. Mechanistically, EMP1 knockdown induced a substantial decrease in IL6 secretion from TNBC through the NF-κB signaling pathway, hindering CAF proliferation and subsequently inhibiting TNBC progression and metastasis. These cumulative results indicate that EMP1 functions as an oncogene in TNBC by mediating the cell communication of TNBC and CAFs. Targeted inhibition of EMP1 by suppressing CAF infiltration is a promising strategy for TNBC treatment.
Flow and ischemic changes in retina and choroid across diabetic retinopathy spectrum: a SS-OCTA study
Authors: Yang Qianhui , Teo Kelvin Y. C. , Hong Yueheng , Tan Bingyao , Schmetterer Leopold , Cheung Chui Ming Gemmy , Wong Tien Yin , Tan Siew Wei Gavin 
Published: February 2025

Abstract

Purpose
To examine changes in retinal and choroidal vasculature in diabetes mellitus across the range of diabetic retinopathy (DR) severities using optical coherence tomography angiography (OCTA) and compare the patterns of vascular changes.

Methods
We conducted a cross-sectional study enrolling 296 patients (498 eyes) with diabetes mellitus. Swept-Source OCT Angiography variables in both retina and choroid, including perfusion density (PD), vessel density (VD), large vessel density (LVD) in both superficial and deep layer of retina and CC flow voids (FD) density of the choroid were quantified. Correlations between OCTA parameters and DR severity, visual acuity and studied factors were performed.

Results
Totally 498 eyes including 176 had no DR, 160 had mild NPDR, 98 had moderate NPDR, 11 had severe NPDR, 41 had PDR with PRP, and 12 had PDR without PRP. Choriocapillaris (CC) flow voids density increased with increasing DR severity (17.06% vs 17.41% vs 17.60% vs 17.62% vs 18.05% vs 18.41%, p-trend = 0.0004), FAZ area increased with DR severity in both superficial and deep layer (superficial layer p trend=0.0027; deep layer p trend=0.0022). Visual acuity correlated negatively with CC flow voids (Pearson’s ρ = 0.09, p = 0.04) and superficial FAZ area (Pearson’s ρ = 0.22, p < 0.001), while inversely correlated with SCP PD (Pearson’s ρ = −0.15, p < 0.001) and VD (Pearson’s ρ = −0.15, p < 0.001), as well as DCP PD (Pearson’s ρ = −0.21, p < 0.001) and VD (Pearson’s ρ = −0.19, p < 0.001).

Conclusion
Choriocapillaris ischemia increased, FAZ area enlarged, and total retina perfusion density decreased with increasing DR severity. The deep layer and large vessels may change in early stage before DR progresses to PDR. More ischemia and vessel tortuosity are correlated with worse visual acuity and higher HbA1c level. OCTA can be utilized to detect both large and small vascular changes in both the retina and choroid in DR patients.
Regulation of tryptophan-indole metabolic pathway in Porphyromonas gingivalis virulence and microbiota dysbiosis in periodontitis
Authors: Ding Jing , Tan Lingping , Wu Lingzhi , Li Jinyu , Zhang Yong , Shen Zongshan , Zhang Chi , Zhao Chuanjiang , Gao Li 
Published: February 2025

Abstract
Pathogenesis of periodontitis is marked by microbiota dysbiosis and disrupted host responses. Porphyromonas gingivalis is a keystone pathogen of periodontitis which expresses various crucial virulence factors. This study aimed to clarify the role and mechanisms of P. gingivalis tryptophan-indole metabolic pathway in the pathogenesis of periodontitis. This study showed that periodontitis patients exhibited elevated tryptophan metabolism and salivary pathogen abundance. Tryptophanase gene-deficiency altered proteome and metabolome of P. gingivalis
, inhibited P. gingivalis virulent factors expression, biofilm growth, hemin utilization, cell adhesion/invasion and pro-inflammation ability. Tryptophan-indole pathway of P. gingivalis stimulated periodontitis biofilm formation and induced oral microbiota dysbiosis. In periodontitis mice, this pathway of P. gingivalis aggravated alveolar bone loss and gingival tissue destruction, causing oral and gut microbiota dysbiosis. This study indicates that the tryptophan-indole pathway serves as a significant regulator of P. gingivalis virulence and oral microbiota dysbiosis, which is also associated with gut dysbiosis.
Syntonic phototherapy versus part time occlusion for treatment of refractive amblyopia
Authors: Mohamed Sanaa Ahmed , Abdel-Wahab Khalil Adel Mohammed , Aljaghmani Maha Emhammed Almokhtar 
Published: February 2025

Abstract
To evaluate the effectiveness of syntonic phototherapy and compare it with partial time occlusion to improve visual acuity in cases of refractive amblyopia. This study is a prospective, comparative, and randomized study. It included 40 patients. Their mean age ± SD was 14.45 ± 10.03 years (Range: 6–45 years). Twenty patients were subjected to partial time occlusion of the sound eye, and 20 received syntonic phototherapy treatment.The study revealed that there was statistically significant improvement in visual functions, UCVA, BCVA, AOP, and functional visual field in patients who were subjected to syntonic phototherapy, whereas the improvement of UCVA and BCVA in patients who were subjected to conventional treatment was satisfactory but less than that reported by syntonic therapy. Visual acuity increased significantly in patients with amblyopia after syntonic phototherapy as compared to partial occlusion therapy.
Precision biochar yield forecasting employing random forest and XGBoost with Taylor diagram visualization
Authors: Uppalapati Sudhakar , Paramasivam Prabhu , Kilari Naveen , Chohan Jasgurpreet Singh , Kanti Praveen Kumar , Vemanaboina Harinadh , Dabelo Leliso Hobicho , Gupta Rupesh 
Published: February 2025

Abstract
Waste-to-energy conversion via pyrolysis has attracted increasing attention recently owing to its multiple uses. Among the products of this process, biochar stands out for its versatility, with its yield influenced by various factors. Extensive and labor-intensive experimental testing is sometimes necessary to properly grasp the output distribution from various feedstocks. Nonetheless, data-driven predictive models using large-scale historical experiment records can provide insightful analysis of projected yields from a variety of biomass materials, hence overcoming the challenges of empirical modeling. As such, five modern approaches available in modern machine learning are employed in this study to develop the biochar yield prediction models. The Lasso regression, Tweedie regression, random forest, XGBoost, and Gradient boosting regression were employed. Out of these five XGBoost was superior with a training mean squared error (MSE) of 1.17 and a test MSE of 2.94. The XGBoost-based biochar yield model shows excellent performance with a strong predictive accuracy of the R2 values as 0.9739 (training) and 0.8875 (test). The mean absolute percentage error value was only 2.14% in the training phase and 3.8% in the testing phase. Precision prognostic technologies have broad effects on sectors including biomass logistics, conversion technologies, and effective biomass utilization as renewable energy. Leveraging SHAP based on cooperative game theory, the study shows that while ash and moisture lower biochar yield, FPT, nitrogen, and carbon content significantly boost it. Small variables like heating rate and volatile matter have a secondary impact on production efficiency.
Evaluation of magnetic resonance spectroscopy total sodium concentration measures, and associations with microstructure and physical impairment in cervical myelopathy
Authors: Solanky Bhavana S. , Prados Ferran , Tur Carmen , Grussu Francesco , Al-Ahmad Selma , Yang Xixi , Bianchi Alessia , Kanber Baris , Russo Antonino , Russo Vittorio , Choi David , Panicker Jalesh N. , Wheeler-Kingshott Claudia A. M. Gandini 
Published: February 2025

Abstract
Spinal cord injury causes a cascade of physiological responses, which may trigger a subsequent neurotoxic increase in intracellular sodium. This can lead to neurodegeneration, both at and beyond the site of injury, causing clinical symptoms and loss of function. However, in vivo measurements of tissue sodium remain challenging. Here we utilise sodium magnetic resonance spectroscopy (23Na-MRS) at 3T to measure tissue sodium concentration (TSC) and its association with microstructural measures and macromolecular MRI metrics in the cervical spinal cord, distal to the site of injury. Twenty people with cervical myelopathy and twenty healthy controls, were studied. Associations with motor and sensory impairments were explored using ASIA and jOAMEQ scores. No significant difference in TSC in the cervical myelopathy group (39 ± 10 mM) relative to healthy controls (35 ± 13 mM) was found. However, patients had a significantly lower cord-cross-sectional area than controls (70 ± 9 mm2 vs. 82 ± 9 mm2, p < 0.001). Lower-extremity function positively correlated with intracellular volume fraction (p = 0.031). In conclusion, using 23Na-MRS, TSC in cervical myelopathy patients was successfully measured. Differences in TSC relative to healthy controls did not reach significance, despite a significant reduction in cord-cross-sectional area. However, lower intracellular volume fraction, indicating reduced neurite density distal to the site of injury, was associated with physical impairment.
Impact of asthma control on quality of life among palestinian children
Authors: Aldirawi Ali , Al-Qudimat Ahmad R. , Al Rawwad Tamara , Alhalaiqa Fadwa , Alwawi Abdallah , Jin Yan , Abuzerr Samer , Hammad Eman , Rjoub Lina 
Published: February 2025

Abstract
Asthma is a chronic respiratory disease that significantly affects children, impacting their health-related quality of life. This study aimed to explore the relationship between asthma control and quality of life among pediatric asthma patients in the West Bank, Palestine. A descriptive, cross-sectional study was conducted among 220 pediatric patients with asthma and their mothers, recruited from four governmental hospitals. Data were collected using self-administered questionnaires that included demographic information, an asthma control test, and the Pediatric Asthma Quality of Life questionnaire. The final analysis included 182 children with a mean age of 8 years. The results showed that 71.9% of the children had uncontrolled asthma, with poor health-related quality of life reported by approximately 70% of this group. In contrast, only 2.7% of children with controlled asthma reported reduced quality of life. The findings indicate a strong association between asthma control and health-related quality of life. Healthcare policies should prioritize educational programs for children and their parents to improve asthma management and overall well-being.
High precision, high time-cadence measurements of the MgII index of solar activity by the GOES-R Extreme Ultraviolet Irradiance Sensor 2: EUVS-C initial flight performance
Authors: E McClintock William , Snow Martin , Eden Thomas , Eparvier Francis , Machol Janet , Woodraska Donald 
Published: February 2025

EUVS-C is one component of the Extreme Ultraviolet Irradiance Sensor (EUVS) instrument. EUVS together with the X-ray sensor (XRS) comprise the Extreme Ultraviolet and X-ray Irradiances Sensors (EXIS) investigation (Machol et al. 2020) aboard the GOES-R satellite series which includes GOES-16, -17, -18, and -19. From their vantage points in geostationary orbit, the EUVS-C instruments measure the solar Mg II Index, also referred to as the Mg II core-to-wing-ratio, which is a proxy for chromosphere activity and correlates with solar extreme ultraviolet (EUV) emission. Mg II produces two bright chromosphere emission lines appearing in the sun’s spectrum at 279.55 nm and 280.71 nm (Mg II k and h) that appear in the cores of their respective photospheric absorption lines. Measuring the ratio of emission from the core (chromsopheric) to that from the wings (photospheric) provides an index that is relatively insensitive to changes in instrument performance. In 2005, Snow & McClintock used 0.1nm resolution data to show that the intrinsic solar variability in the index (as opposed to instrument noise) is on the order of 0.2% on time scales 5-10 minutes. EUVS-C is designed to exceed these performance requirements. A companion paper describes the instrument design and its pre-flight calibration. This paper describes the operational implementation for the algorithm that produces the Index, flight calibrations, and the initial instrument flight performance. Each EUVS-C currently operating (GOES-16, -17, and -18) is providing high time-cadence (3 seconds), high precision (1 part in 104) Index determinations. Spectral shifts arising from spacecraft orbital motion introduce a systematic 0.1% diurnal variation in absolute index values. Additionally, wavelength dependent radiometric responsivity degradation leads to a systematic increase in the reported index on a timescale of years at an average rate of 0.2% per year. These systematic effects can be mitigated with additional post data processing.
A Comprehensive Approach to Clinical Decision Support in the Return of Genome Informed Risk Assessments to Primary Care Pediatricians
Authors: Karavite Dean , Terek Shannon , Connolly John J. , Harr Margaret , Muthu Naveen , Hakonarson Hakon , Grundmeier Robert W. 
Published: February 2025

Abstract
Background Primary care pediatricians play an important role in genetic testing, including referrals, test ordering, responding to results, assessing risk, treatment, and managing care. As genetic testing rapidly evolves to include new tests identifying patients at risk for certain conditions, alert-based clinical decision support is insufficient in assisting pediatric primary care providers in working with patients, parents, genetics, and other specialties. Supporting pediatricians in the return of these results requires addressing gaps in genetics training and integrating genetics into practice with education, information resources, and specialized tools.
Objectives This study aimed to capture requirements for developing systems and processes to support primary care pediatricians in the return of genome-informed risk assessments.
Methods We performed a requirements analysis to inform the design of clinical decision support tools and processes for pediatric providers of patients who received a genome informed risk assessment, a novel test that combines polygenic risk scores with patient and family histories to deliver a risk assessment for common medical conditions. We developed an interview guide consisting of scenario presentations, questionnaires, and semi-structured questions to elicit provider responses on a broad set of requirements to manage results with patients and caregivers.
Results Twenty providers from 10 primary care pediatric practices within a single health system participated in the study. The findings demonstrated that providers feel responsible to be involved in the process of returning results but require a support system that integrates education, provider and patient information resources, effective communication with genetics, and electronic health record decision support tools that can accommodate a range of clinical scenarios and provider workflow preferences.
Conclusion Supporting providers with the return of genetic testing results such as the genome informed risk assessment requires a comprehensive approach to decision support consisting of education, communication, and a comprehensive and integrated set of electronic health record tools.
Outcome bei kongenitaler Tränenwegstenose
Authors: Mulaj Bardh , Patzelt Sarah , Chaloupka Karla , Gerth-Kahlert Christina 
Published: February 2025

Zusammenfassung
Hintergrund Die kongenitale Tränenwegstenose, eine häufige Erkrankung bei Neugeborenen, ist durch eine Verengung des Tränenwegsystems, häufig am Ductus nasolacrimalis, gekennzeichnet. In den meisten Fällen öffnet sich der Tränenweg spontan im 1. Lebensjahr, unterstützt durch Massagen. Bei fehlender Besserung kann eine operative Sondierung erforderlich sein. Ziel dieser Studie war die Analyse der Erscheinungsbilder und Ergebnisse operativ behandelter Tränenwegstenosen bei Kindern in unserer Klinik.
Patienten und Methoden In einer retrospektiven Analyse wurden elektronische Krankenakten von Patienten unter 18 Jahren ausgewertet, die zwischen 2011 und 2023 wegen einer kongenitalen Tränenwegstenose behandelt wurden. Erfasst wurden demografische Daten, Symptome, Lokalisation der Stenose, operative Therapie und Ergebnisse. Zudem wurden Eltern der Patienten zur postoperativen Situation und Symptomatik befragt. Die Studie wurde von der Kantonalen Ethikkommission Zürich (BASEC2022-00830) genehmigt.
Resultate Von insgesamt 147 identifizierten Patienten (39 weiblich, 62 männlich) konnte bei 69% eine Analyse mit vorliegendem Einverständnis erfolgen. Das Alter bei Erstuntersuchung lag zwischen 8 Monaten und 12 Jahren (median 27 Monate). Eine unilaterale Stenose wurde bei 69% und eine bilaterale bei 31% festgestellt. Die häufigsten Symptome waren Epiphora (95%), verklebte Zilien (68%), muköses Sekret (23%) und Rötung der Lider/Konjunktiva (19%). Bei 11% wurde intraoperativ eine Malformation festgestellt. Eine 2. Sondierung war bei 10% notwendig, wobei das Alter zwischen 18 und 69 Monaten lag (Median 38 Monate). Eine Dakryozystorhinostomie wurde bei 4% durchgeführt (Alter 92 – 145 Monate, median 113 Monate). Nach der Operation berichteten 70,5% subjektiv und/oder objektiv über Beschwerdefreiheit, 22,7% über anhaltende Epiphora und 6,8% über verkrustete Zilien. Bei 77/101 lag eine Beantwortung des Fragebogens vor. Hierbei berichteten 92%, dass das tränende Auge nicht
mehr vorhanden war und 96% benötigten keine Therapie mehr. 97% gaben an, dass die Operation ohne Komplikationen verlief, 17% erlebten erneut tränende Augen, und 6% benötigten zusätzliche, nicht tränenwegbezogene Behandlungen.
Fazit In den meisten Fällen ist eine alleinige Sondierung und Spülung zur Heilung ausreichend. Eine temporäre Sondeneinlage ist häufiger bei älteren Kindern notwendig. Eine Intervention nach dem 18. Lebensmonat beeinflusst die Heilung nicht negativ.
Twelve-Month Outcomes of Combined Phacoemulsification with Ab Interno Canaloplasty Versus Single-Use Dual Blade Goniotomy in Glaucoma Patients
Authors: Prinz Julia , Plange Niklas , Schellhase Hannah , Walter Peter , Fuest Matthias , Koutsonas Antonis , Kuerten David 
Published: February 2025

Abstract
Background To compare the efficacy and safety of combined phacoemulsification with ab interno canaloplasty (Phaco-AbiC) versus single-use dual blade goniotomy (Phaco-DBG).
Material and Methods In this prospective consecutive case series, intraocular pressure (IOP), the number of IOP-lowering medications, the mean deviation (MD) of visual field testing, and surgery-related complications were evaluated in 25 eyes following Phaco-AbiC and 20 eyes following Phaco-DBG through 12 months of follow-up. Qualified or complete success was defined as postoperative IOP lower than 21, 18, and 16 mmHg with or without IOP-lowering medications.
Results At the 12-month follow-up, IOP was significantly reduced compared to baseline in the Phaco-AbiC (14.2 ± 2.7 versus 19.2 ± 4.7 mmHg, p < 0.001) and Phaco-DBG groups (16.7 ± 3.4 versus 19.9 ± 3.9 mmHg, p < 0.001). At the 12-month follow-up, IOP was significantly higher following Phaco-DBG than Phaco-AbiC (p = 0.011). Compared to baseline, the number of IOP-lowering medications was significantly reduced in the Phaco-AbiC (1.2 ± 1.4 versus 2.4 ± 1.0, p < 0.001) and Phaco-DBG groups (0.8 ± 0.9 versus 2.1 ± 0.9, p < 0.001) at the 12-month follow-up. For IOP lower than 16 mmHg, the complete and qualified success rate was significantly higher following Phaco-AbiC (36.0 and 76.2%, respectively) than Phaco-DBG (17.5 and 40.6%; p = 0.037; p = 0.007, respectively). No severe intra- or postoperative complications occurred.
Conclusion Both Phaco-AbiC and Phaco-DBG achieved a significant reduction in IOP and IOP-lowering medications at the 12-month follow-up. IOP was significantly lower 12 months following Phaco-AbiC than Phaco-DBG.