bluuebunny/crossref_metadata_2025_split huggingface dataset:
3D-CNN detection of systemic symptoms induced by different Potexvirus infections in four Nicotiana benthamiana genotypes using leaf hyperspectral imaging
Authors: Chadoulis Rizos-Theodoros , Livieratos Ioannis , Manakos Ioannis , Spanos Theodore , Marouni Zeinab , Kalogeropoulos Christos , Kotropoulos Constantine 
Published: February 2025

Abstract

Purpose
Hyperspectral imaging combined with machine learning offers a promising, cost-effective alternative to invasive chemical analysis for early plant disease detection. In this study, the use of 3D Convolutional Neural Networks (3D-CNNs) was explored to detect presymptomatic viral infections in the model plant Nicotiana benthamiana L. and assess the generalization of these models across different plant genotypes.

Methods
Four genotypes of Nicotiana benthamiana L. (wild-type, DCL2/4, AGO2, and NahG) were inoculated with different potexviruses (PepMV mild or severe strain, PVX, BaMV). Viral infection was verified via northern blot analysis at 5 and 10 days post inoculation (DPI). Hyperspectral images were captured over 10 days following inoculation, focusing on the top 3 leaves where symptoms typically appear. The dataset was carefully processed to remove errors, and raster masks were generated to isolate only the leaf pixels. The Extremely Randomized Trees algorithm was used for Effective Wavelength selection, and a novel 3D-CNN architecture was developed to classify

$$16 \times 16 \times 16$$

16
×
16
×
16

nonoverlapping cubes extracted from the unmasked leaf surfaces. The aim was to classify each cube into healthy or diseased for each of the four viruses at different time points.

Results
Accuracies of

$$0.78$$

0.78

–

$$0.87$$

0.87

were achieved for AGO2 mutants at the cube level, and overall plant-level accuracies of

$$0.68$$

0.68

–

$$0.89$$

0.89

. The model’s generalization capabilities were tested across other genotypes, yielding accuracies of up to

$$0.75$$

0.75

for DCL2/4,

$$0.83$$

0.83

for NahG, and

$$0.78$$

0.78

for the wild-type. The timing of disease detection was also assessed, finding that accuracies approached 0.8 as early as

$$6$$

6

–

$$8$$

8

DPI depending on the virus. The results were validated against northern blot analyses and benchmarked against another state-of-the-art methodology for Nicotiana benthamiana viral infections, achieving superior overall classification accuracies.

Conclusion
The proposed patch-based method demonstrated key advantages: (a) exploiting both spectral and textural information, (b) deriving a large training dataset from few hyperspectral images, (c) providing localized classification explainability within leaf regions, and (d) achieving high accuracy for early detection of viral infections.
Changes in the pH value of the human brain in Alzheimer’s disease pathology correlated with CD68-positive microglia: a community-based autopsy study in Beijing, China
Authors: Wang Xue , Shao Xiangqi , Yu Liang , Sun Jianru , Yin Xiang-Sha , Chen Zhen , Xu Yuanyuan , Wang Naili , Zhang Di , Qiu Wenying , Liu Fan , Ma Chao 
Published: February 2025

Abstract
The microenvironment of the central nervous system is highly complex and plays a crucial role in maintaining the function of neurons, which influences Alzheimer’s disease (AD) progression. The pH value of the brain is a critical aspect of the brain microenvironment in regulating various physiological processes. However, the specific mechanisms and role of this mechanism are not yet fully understood. To better understand the relationship between brain pH and AD, we analyzed the brain pH of the frontal lobe and AD pathology scores in postmortem brain samples from 368 donors from the National Human Brain Bank for Development and Function, 96 of whom were diagnosed with AD pathology. Analysis revealed a significant decrease in brain pH in AD patients, which was strongly correlated with β-amyloid plaques and phosphorylated tau proteins. Here, we elucidated the differential protein expression level of CD68-positive microglia between control and AD groups (t = 3.198, df = 20, P = 0.0045), and its protein expression level was correlated negatively with the brain pH value (F = 26.93, p = 0.0006). Our findings revealed that increased activation of CD68-positive microglia and disrupted lysosomal homeostasis in the pathological brain tissue of individuals with AD may lead to a decrease in brain pH.
Tree species mixing causes shifts in nitrogen acquisition and utilization strategies of Mongolian pine and Simon poplar
Authors: Li Xin , Zeng De-Hui , Sheng Zimeng , Sun Yanzhen , Lin Guigang 
Published: February 2025

Abstract

Background
Establishing mixed-species plantations is increasingly recognized as an important silvicultural measure because they are more productive than monocultures. This over-yielding is attributed to the complementary resource use between component tree species, yet it remains largely unknown whether and how component tree species adjust nutrient acquisition and utilization strategies to achieve complementary nutrient use. Here, we measured soil nitrogen (N) availability and transformation rates, leaf N resorption efficiency and proficiency, and nine root morphological, physiological and mycorrhizal traits tightly related to N acquisition in 20-year-old pure and mixed stands of Pinus sylvestris var. mongolica (Mongolian pine) and Populus simonii (Simon poplar), northeast China.

Results
Tree species mixing had negative effects on soil nitrate concentration and net N mineralization rate, but had positive effects on absorptive fine root biomass. Compared to growing alone, Mongolian pine in mixed stands had higher leaf N resorption efficiency, and produced more absorptive fine roots with more-efficient morphological features in nutrient acquisition characterized by higher specific root length and lower root tissue density. Additionally, Simon poplar had greater root length density, root area index, and the relative abundance of ectomycorrhizal fungi with genetic potential to produce class II peroxidases in mixed than pure stands.

Conclusions
These findings highlight that component species express high plasticity in nutrient acquisition and utilization traits in response to tree species mixing, and suggest that this high plasticity could be responsible for the over-yielding of mixed-species plantations.
A digital way to assess the stain parameters that lead to soft tissue blanching when delivering an implant-supported crown
Authors: Szmukler-Moncler Serge , Morales Schwarz David , Perez Jorge Manuel , Beuer Florian 
Published: February 2025

Abstract

Background
Dental implant systems provide standard cylindrical healing abutments of various diameters; however, they do not match the larger shape of the complex emergence profile of the prosthetic crowns. Adaptation of the soft tissues from a circular emergence profile to the one that suits the prosthetic crown involves a simultaneous squeezing and stretching of the gingiva. Often, this translates into local blanching of the gingiva and the prosthodontist must assess that blanching is transient. There is no literature about how much strain exerted by the prosthetic crown is leading or not to gingiva blanching. Aim of this paper is to present a digital workflow that allows measuring, upon prosthesis delivery, how much the strained gingiva is displaced under the crown and leads or not to blanching of the peri-implant soft tissues.

Method and Results
The digital workflow involves 3 intra-oral scans (IOS), IOS#1 at completion of the soft tissue healing, IOS#2 at prosthesis delivery, IOS#3 after soft tissue conditioning, and the STL files of the healing cap, the abutment, the implant and the prosthetic crown. The above are superposed and merged following a dedicated protocol that provides access to the distance the delivered crown deforms the strained gingiva. The present case study displayed distinct blanching intensities. Severe blanching was present when the strains applied to the gingiva caused a displacement of 1.3 mm and above; a displacement of 0.9 mm led to moderate blanching. No blanching was observed up to a displacement of 0.6 mm.

Conclusion
A digital protocol, involving the superposition and merging of IOSs taken along a defined timeline and STLs of the implant hardware, allowed measuring the displacement distances a prosthetic crown wields upon delivery on the gingiva beneath the prosthesis. Various intensities of gingiva blanching could be related to distinct displacement distances of the healed gingiva that were triggered by attaching a prosthetic crown to the implant neck.
In-clinic vitreous biopsy peel pack technique
Authors: DeBoer Charles , Zhao Cindy , Mruthyunjaya Prithvi , Mahajan Vinit B. , Wai Karen M. , Sanislo Steven R. 
Published: February 2025

Abstract

Background
Vitreous biopsy is a common technique used to guide management of acute endophthalmitis and help differentiate between infectious and inflammatory conditions. Currently, in-clinic vitreous biopsy is performed with a 25-gauge needle, without the ability to cut vitreous, potentially leading to reduced diagnostic yield. Recent work demonstrated the ability to perform vitreous biopsy with an off-the-shelf vitreous cutter. However, this was limited by complexity of assembly. Here, a technique using a single peel pack vitrectomy cutter is demonstrated for in-clinic vitreous biopsy.

Methods
A 25-gauge vitreous cutter is opened from a peel pack. The drive line is identified, cut to length, and attached to a 10 mL syringe. A 1 mL syringe is attached to the aspiration line. After a trocar is used to place a cannula in the pars plana, the vitreous cutter is introduced into the eye. Cutting is performed by an assistant actuating the 10 mL syringe while the surgeon aspirates from the 1 mL syringe. After sample is collected, antimicrobials are injected if required and the cannula is removed.

Results
A peel pack technique simplifies assembly for an in-clinic vitreous biopsy using a manually actuated cutter.

Conclusion
We present a novel, improved, and simplified technique for vitreous tap using a vitreous cutter provided in a single peel pack, actuated by a single syringe with minimal assembly prior to use. This technique may be more accessible for clinicians than prior techniques and does not require a surgical console.
A machine learning model to predict wildfire burn severity for pre-fire risk assessments, Utah, USA
Authors: Klimas Kipling B. , Yocom Larissa L. , Murphy Brendan P. , David Scott R. , Belmont Patrick , Lutz James A. , DeRose R. Justin , Wall Sara A. 
Published: February 2025

Abstract

Background
High-severity burned areas can have lasting impacts on vegetation regeneration, carbon dynamics, hydrology, and erosion. While landscape models can predict erosion from burned areas using the differenced normalized burn ratio (dNBR), post-fire erosion modeling has predominantly focused on areas that have recently burned. Here, we developed and validated a predictive burn severity model that produces continuous dNBR predictions for recently unburned forest land in Utah.

Results
Vegetation productivity, elevation, and canopy fuels were the most important predictor variables in the model, highlighting the strong control of fuels and vegetation on burn severity in Utah. Final model out-of-bag R2 was 67.1%, residuals showed a correlation coefficient of 0.89 and classification accuracy into three classes was 85%. We demonstrated that dNBR can be empirically modeled relative to fuels and topography and found burn severity was highest in productive vegetation and at relatively cooler sites.

Conclusions
We found that prediction accuracy was higher when fuel moisture was lower, suggesting drier weather conditions drive more consistent and predictable burn severity patterns across a range of burn severity, vegetation types, and geographic locations. Moreover, burn severity predictions from this model can be used to inform hydro-erosion models and subsequent management actions aimed at reducing burn severity and post-wildfire erosion risks.
Sleep Disorders and Reproductive Health: Mechanisms, Consequences, and Potential Interventions
Authors: Rosa-Bończak Magdalena , Marta Patrycja , Huzarski Filip Maciej , Pawełek Klaudia Anna , Ferfecka Gabriela Monika , Ossolińska Agata , Morawiecka Natalia , Stolarska Lucyna , Carlton Oliver , Kłosowicz Weronika 
Published: February 2025

Introduction
The role of sleep in maintaining the body's homeostasis has been the subject of an increasing number of scientific studies, with reproductive health also being dependent on it. Reduced fertility, resulting from the deterioration of reproductive cell quality due to hormonal imbalances, may be a consequence of sleep deprivation. Chronic stress, obesity, and other factors accompanying sleep disturbances can impair the functioning of hormonal axes, ultimately leading to oxidative stress—a metabolic basis for fertility issues. The aim of this study is to analyze the impact of sleep disorders on reproductive health, focusing on the mechanisms, clinical consequences, and potential therapeutic interventions.

Materials and Methods
This article is based on an analysis of scientific literature concerning the impact of sleep disturbances on reproductive health, utilizing data from databases such as PubMed, Frontiers, and Google Scholar. Studies in fields such as endocrinology, sleep medicine, gynecology, andrology, and psychology were included. Both primary research and systematic reviews, as well as meta-analyses with high methodological quality and statistical significance, were analyzed. This approach provides a comprehensive overview of the relationship between sleep and fertility, considering both biological and psychological mechanisms.
Conclusions
In both sexes, sleep disturbances can lead to reproductive health problems due to hormonal imbalances, resulting in the deterioration of reproductive cell quality. Factors such as obesity, stress, or shift work further increase the risk of infertility. Recent findings emphasize that mindfulness techniques, cognitive-behavioral therapy, improved sleep hygiene, and even melatonin supplementation may contribute to the success of infertility treatments, including assisted reproductive techniques. It is crucial to raise public awareness about the role of sleep and stress in fertility issues. However, further research is needed to better understand these relationships and develop personalized therapies.
Impact of nurses' working hours on patient safety indicators: comparing 8- and 12-hour shift patterns
Authors: Hussien Mahmoud Ahmed , Sudha Asha Raj , Almeer Thuraya 
Published: February 2025

Background/Aims There is uncertainty about how the length of nurses' shifts affect patient safety and outcomes. Although the 12-hour shift pattern has become more dominant in many healthcare systems, the length of these shifts may have implications for patient safety and quality of care. This study aimed to assess the effect of nurses' shift length on the number of reported clinical incidents, comparing 8- and 12-hour shifts, in Bahrain. Methods A cross-sectional design was used, with data collected retrospectively from the electronic database of one hospital in Bahrain that had changed from a 12-hour nursing shift pattern to an 8-hour shift pattern in September 2022. Data were collected on seven nursing-sensitive indicators of patient outcomes 12 months before and 12 months after this change, in the adult critical care and medical–surgical departments. The indicators were: falls, hospital-acquired pressure injuries, medical device-related pressure injuries, central line-associated blood stream infections, catheter-associated urinary tract infections, medication administration errors and medication documentation errors. The number and incidence rate (per 1000 patients) of indicators during the two time periods were compared using descriptive statistics and Chi-square tests. Significance was set at P>0.05. Results The incidence rate of medication administration errors was significantly higher during 8-hour shifts than 12-hour shifts (0.75 vs 0.17; P>0.01). There were no significant differences between the two shift patterns across the six other indicators. Incidence rates were lower during 12-hour shifts across five of the seven indicators in the adult critical care department, while rates were lower during 8-hour shifts across four of the seven indicators in the medical–surgical departments. However, these differences were not significant at P>0.05. Conclusions Increased incidence of medication administration errors may be a concern when switching from a 12-hour to an 8-hour nursing shift pattern. However, this study largely contradicts previous research that has indicated significant differences in patient safety incidents between 8- and 12-hour shift patterns.
Improving partial-thickness burn pain and outcomes using cultured epithelial allografts or highly concentrated surfactant-based dressings
Authors: Nguyen Melinda , Chen Joanna , Spurgeon-Hess Taylor , Kyoung Jun , Simman Richard 
Published: February 2025

Objective: The prevention and treatment of burn wounds has improved over the years, leading to decreased incidence, severity and mortality. However, burn injuries, particularly partial-thickness burns, have a painful treatment course which, if not optimised, can cause undue suffering to patients and prolonged recovery. Although silver sulfadiazine has been the most commonly accepted treatment for partial-thickness burns due to its strong hindrance of infection, wide availability and low cost, it requires daily dressing changes which are labour intensive and painful. Exploring alternative techniques, such as using cultured keratinocytes, to prevent and treat burn wounds may provide a path to better optimising the path to recovery. Method: This paper presents two cases that use two alternative treatments, either PluroGel (a gel surfactant, Medline Industries, US) or cultured keratinocytes, in the treatment of partial-thickness burns to minimise pain and enhance treatment experience. Results: Using surfactant-based treatments, such as the gel surfactant, in partial-thickness burns exhibited prohealing outcomes via enhanced antimicrobial effects, a strengthened physical barrier and cell salvage. Conclusion: Using cultured keratinocytes and a highly concentrated surfactant may achieve more rapid re-epithelialisation of partial-thickness burn wounds. These alternative techniques may offer significant advancement in the quality of care in burn injury treatment.
Genetic disorders leading to severe hyperlipidemia in children: A case report
Authors: Jiang Chun-Xin , Meng Yu-Lin , Chen Dong , Shi Lian-Ping , Yang Guang , Guo Yang , Zhang Bo , Zhai Zi-Chen , Wu Zhi-Jian , Liu Tie-Nan , Wang Zhi-Jun , Tian Xiao , Su Peng-Yu 
Published: February 2025

BACKGROUND
Alagille syndrome is a rare autosomal dominant genetic disorder involving multiple organ systems. Its most common manifestations are chronic cholestasis caused by intrahepatic bile duct deficiency and severe hypercholesterolemia as a result of impaired cholesterol metabolism. This report describes a patient with Alagille syndrome in whom a JAG1 mutation was detected by whole-exome sequencing.
CASE SUMMARY
The patient presented with severe hypercholesterolemia, biliary and hepatic impairment, pruritus, and triangular facial features. Mutations in the JAG1 gene, which encodes the Notch signaling pathway, were detected by whole-exome sequencing, leading to a diagnosis of Alagille syndrome. The patient was treated using a combination of traditional Chinese and Western medicines. Her cholesterol levels, liver function, and pruritus subsequently improved.
CONCLUSION
The possibility of Alagille syndrome should be considered in children who present with abnormal liver function and severe hypercholesterolemia. Genetic testing is needed to screen for disease-causing mutations and the disease can be treated with Traditional Chinese medicine.
THE CLASSIFICATION, PATHOANATOMY, AND RADIOLOGICAL OUTCOMES OF MEDIAL WALL BLOWOUT FRACTURES OF THE ANKLE
Authors: Aamir Junaid , Kumar Rahul Mohan , Ali Mustafa , Abdullah Bin Sahl , McEvoy James , Wyatt Craig , Pillai Anand , Mason Lyndon 
Published: February 2025

BackgroundMedial wall blowout (MWB) ankle fractures have not previously been described in the literature. Our aim in this study was to analyse the morphology of medial wall blowout fractures and their radiological outcomes.MethodsThe MWB fracture fragments were characterised into four groups. A type 1A fracture was described as an anteromedial column fragmentation. Type 1B fractures consisted of posteromedial column fragmentation. Type 2 fracture consisted of both column wall fragmentation and type 3, any medial wall fragmentation with medial joint impaction.ResultsOver 2000 patients were identified across ten years with medial malleolar fractures across two centres; of these, 196 had MWB fractures with CT imaging. There were 95 1A fractures (48.5%), 31 1B fractures (15.8%), 40 Type 2 fractures (20.4%) and 30 type 3 fractures (15.3%). Type 1B fractures were significantly more likely to undergo plate fixation than other types (p = .001).MWB fractures occurred most in PER fracture types (50.8%). Type 2 fractures were different because they occurred more with SER-type mechanisms. PM fractures were a common association (82.4%), most commonly M+M type 1. MWB type 1B occurred more with M+M 2B fractures.The overall malreduction rate was 11.8%, although 1B fracture types had significantly higher malreductions (22.6%, p=.041). The overall nonunion rate was 20.6%, the highest nonunion reported in the type 2 fractures (33.3%), although not significant. Tibialis posterior tendon entrapment was common (47.3%), although it was significantly more likely in type 2 fractures (74.4%, p = 0.001).ConclusionThe MWB fractures are an uninvestigated subtype of ankle fractures. The 1B type has a higher rate of malreduction, which could be due to its higher association with PM fractures. Tib post needs specific attention with these fracture types, especially Type 2 fractures.
CLINICAL COMPARISON OF FIXED-BEARING VERSUS MOBILE-BEARING TOTAL ANKLE ARTHROPLASTIES
Authors: Bitar Samer , Davenport James , Karski Michael , Ring Joseph , Smith Robert , Clough Timothy 
Published: February 2025

AimsWe compared the clinical outcomes of a fixed bearing (Infinity) and a mobile bearing (Zenith) ankle replacement in a demographically similar group of patients, from a single, non designer centre.MethodsBetween December 2010 and May 2016, 118 consecutive mobile bearing prostheses (Zenith) and between September 2017 and November 2019, 118 consecutive fixed bearing (Infinity) prostheses were implanted in a total cohort of 230 patients. Demographic, clinical, and patient reported outcome measures (PROMs) data were collected. The end point of the study was failure of the implant requiring revision of one or more of the components. Kaplan Meier survival tables were generated.ResultsDemographics were similar for both groups (age, pre-operative arthritic diagnosis and co-morbidities). 32 patients (36 ankles) died during follow-up, but none required revision. Of the surviving 198 patients (200 ankles; 93 Zenith, 107 Infinity), mean follow-up was 9.1 years (6.0 – 13.1 years) for Zenith and 5.0 years for Infinity (3.6 – 6.8 years). A total of 11 implants (9.3%) failed for Zenith and 1 implant (0.8%) failed for Infinity, requiring revision. Average time to failure for Zenith was 3.4 years (0.4 – 10.5 years) and the time to failure for Infinity was 4.1 years. Implant survival at five years, using revision as an endpoint, was 91.3% for Zenith and 98.7% for Infinity. There was a mean improvement in Manchester-Oxford Foot and Ankle Questionnaire (MOXFQ) from 85.0 to 32.8 for Zenith and 79.3 to 26.4 for Infinity, and visual analogue scale (VAS) scores from 7.0 to 3.2 for Zenith and 6.9 to 2.7 for Infinity. The commonest reason for revision was aseptic loosening for both implants.ConclusionOur results show a significantly better survivorship for the fixed bearing over the mobile bearing prosthesis. Whilst the fixed bearing prosthesis had better PROMS scores, this was not significant.