bluuebunny/crossref_metadata_2025_split huggingface dataset:
Liver manifestations in autosomal dominant polycystic kidney disease (ADPKD) and their impact on quality of life
Authors: Arjune Sita , Todorova Polina , Bartram Malte P , Grundmann Franziska , Müller Roman-Ulrich 
Published: November 2024

ABSTRACT

Background
ADPKD is the most prevalent monogenic kidney disease with an estimated incidence of 1:1000. The condition is characterized by the formation of kidney cysts, which can cause kidney function loss and bear a significant risk of advancing to kidney failure. This study examined the prevalence of hepatic cysts in individuals with ADPKD, and the possible influence of these cysts on liver function and quality of life. Furthermore, the relationship between hepatic cysts and genotype was analysed.

Methods
Clinical data from 880 patients with ADPKD were analysed, including longitudinal patient data, genetic information, and laboratory parameters.

Results
The prevalence of hepatic cysts in adult ADPKD patients was 81.71%, consistent with previous studies. Prevalence increased with age, particularly in male patients. No clear association was observed between ADPKD genotype and the presence of liver cysts. Among male patients with liver cysts, glutamate pyruvate transaminase (GPT) levels significantly decreased with age, while female patients showed a significant increase in gamma-glutamyl transferase (γ-GT) levels. Overall, hepatic cysts had minimal impact on liver enzymes. Quality of life assessments using the SF-12 questionnaire revealed no significant influence of hepatic cysts on physical or mental well-being. However, physical quality of life was significantly lower in patients showing polycystic liver disease as a manifestation of ADPKD compared to all other patients, both with and without liver cysts.

Conclusions
Hepatic cysts are highly prevalent in adult patients with ADPKD, increasing with age. ADPKD genotype does not appear to be associated with the presence of hepatic cysts. Liver function, as indicated by enzyme levels, is minimally affected by hepatic cysts in most ADPKD patients. The quality of life of ADPKD patients is generally unaffected by the presence of hepatic cysts, except in severe cases of polycystic liver disease (PLD). Further research is needed to develop effective treatments for severe PLD and gain a better understanding of the factors influencing hepatic cyst incidence and progression in patients with ADPKD.
Factors influencing early response of IgA nephropathy following targeted-release budesonide (TRB) treatment: preliminary results from a multicenter study
Authors: Keskinis Christodoulos , Moysidou Eleni , Kapsia Eleni , Vaios Vasilios , Bintas Christos , Trivyza Maria , Christodoulou Michalis , Lioulios Georgios , Stai Stamatia , Nikolaidou Christina , Pateinakis Panagiotis , Papasotiriou Marios , Liakopoulos Vassilios , Marinaki Smaragdi , Stangou Maria 
Published: November 2024

ABSTRACT

Background
Formation of galactose-deficient IgA1 (Gd-IgA1) immunoglobulin is the initial step in the immunological cascade leading to IgA nephropathy (IgAN). Targeted-release budesonide (TRB), an evidence-based regimen without major side-effects, has recently been approved for IgAN treatment; herein we present our preliminary real-world data regarding prompt response to TRB.

Methods
Patients with primary IgAN who remained with Uprot &gt;1 g/24 h despite conventional treatment for 6 months were started on TRB, and re-evaluated at 3 (T3) and 6 (T6) months. Reduction of proteinuria by ≥30%, at T3 and T6 was regarded as very early (VER) and early response (ER), respectively. Kidney biopsies were evaluated according to Oxford classification (MEST-C) score.

Results
Thirty-seven IgAN patients, male/female 26/11, mean ± standard deviation age 50.38 ± 14.32 years and mean time since diagnosis 45.65 ± 56.67 months, were included. Seventeen (45.94%) patients demonstrated VER, increasing to 29 (78.3%) as ER (P = .004). Patients who demonstrated VER had a shorter time interval since diagnosis compared with non-VER, 29.41 ± 6.96 vs 65.37 ± 17.64 months (P = .05), and preserved estimated glomerular filtration rate at diagnosis and T0, while time since diagnosis was the main factor associated with ER, 38.36 ± 19.6 vs 78.67 ± 18.64 months, in ER and non-ER respectively (P = .05). Patients with M0, E0, S0 and T0 had no significant changes during T0–T6, while patients with M1, E1, S1 and even T1 had significantly reduced proteinuria (P = .006, P = .0011, P &lt; .0001 and P &lt; .0001, respectively).

Conclusions
Almost half of the patients showed proteinuria reduction after TRB treatment at 3 months, and the proportion increased significantly at 6 months. Patients likely to have a prompt proteinuria reduction were relatively close to diagnosis, retained kidney function and had active lesions in kidney biopsy.
Multiparametric MRI: can we assess renal function differently?
Authors: Tournebize Corentin , Schleef Maxime , De Mul Aurélie , Pacaud Sophie , Derain-Dubourg Laurence , Juillard Laurent , Rouvière Olivier , Lemoine Sandrine 
Published: November 2024

ABSTRACT
We are lacking tools to evaluate renal performance. In this review, we presented the current knowledge and potential future applications in nephrology of new magnetic resonance imaging (MRI) techniques, focusing on diffusion-weighted (DWI) MRI, blood oxygen level-dependent (BOLD) MRI, and magnetic resonance relaxometry (T1 and T2 mapping). These sequences are sensitive to early changes in biological processes such as perfusion, oxygenation, edema, or fibrosis without requiring contrast medium injection and avoids irradiation and nephrotoxicity. Combining these different sequences into the so-called “multiparametric MRI” enables noninvasive, repeated exploration of renal performance on each kidney separately. DWI MRI, which evaluates the movement of water molecules, is a promising tool for noninvasive assessment of interstitial fibrosis and the cortical restricted diffusion has a prognostic value for the deterioration of renal function in diabetic nephropathy. BOLD MRI is sensitive to changes in renal tissue oxygenation based on the paramagnetic properties of deoxyhemoglobin and is of particular interest in the setting of renal artery stenosis to assess tissue oxygenation in the post-stenotic kidney. This sequence can be used for predicting degradation of renal function in chronic kidney diseases (CKD) and might be useful in preclinical studies to assess nephroprotective and nephrotoxic effects of drugs in development. T1 and T2 relaxation times change with tissue water content and might help assessing renal fibrosis. A corticomedullary dedifferentiation in T1 has been observed in CKD and negatively correlates with glomerular filtration rate. Data on the significance of T2 values in renal imaging is more limited. Multiparametric MRI has the potential to provide a better understanding of renal physiology and pathophysiology, a better characterization of renal lesions, an earlier and more sensitive detection of renal disease, and an aid to personalized patient-centered therapeutic decision-making. Further data and clinical trials are needed to allow its routine application in clinical practice.
Partial Enteral Nutrition in the Management of Crohn’s Disease: A Systematic Review and Meta-Analysis
Authors: Jatkowska Aleksandra , White Bernadette , Gkikas Konstantinos , Seenan John Paul , MacDonald Jonathan , Gerasimidis Konstantinos 
Published: November 2024

Abstract

Background
Exclusive enteral nutrition is an established treatment for active Crohn’s disease but the role of partial enteral nutrition (PEN) in the broader management of the disease is less clear. This systematic review and meta-analysis reviewed the literature on the role of PEN in Crohn’s disease management.

Methods
This review was conducted following Cochrane recommendations. The protocol was registered on PROSPERO. Findings were reported following the PRISMA guidelines.

Results
Sixty-four articles were identified, of which 11 reported data from randomized control trials. Good quality evidence suggests that PEN may be used as a maintenance and induction therapy, particularly at high dosages and/or alongside exclusion diets. A higher dosage of PEN is associated with a lower risk of subsequent disease relapse, with benefits observed at intakes above 35% of energy requirements (35%-50% PEN: OR [95% confidence intervals (CI)]: 0.42 [0.27-0.65]; &gt; 50% PEN: OR [95% CI]: 0.27 [0.08-0.88]). Low-quality evidence suggests that postoperative use of PEN may prevent disease recurrence or enhance treatment outcomes when used as adjunct therapy to biologics. PEN can improve nutritional parameters, showing efficacy comparable to EEN in pediatric patients (weight: OR [95% CI]: −0.04 [−0.32, 0.25]). The effect of PEN on improving patients’ quality of life is comparable to that of EEN and anti-tumor necrosis factor alpha therapies.

Conclusions
Partial enteral nutrition may help in various aspects of Crohn’s disease management but much of the current evidence is of low quality. Well-designed randomized control trials are required to confirm findings from current literature and before clinical recommendations can be made.
Prognostic impact of mild renal dysfunction in patients undergoing valve surgery
Authors: Kim Kitae , Kim Taeksu , Yoon Sungsil , Kim Hong Rae , Kim Ho Jin , Kang Pil Je , Yoo Jae Suk , Jung Sung-Ho , Chung Cheol Hyun , Kim Joon Bum 
Published: November 2024

Abstract

OBJECTIVES
To analyse the impact of mild renal dysfunction on the prognosis of patients undergoing valve surgery.

METHODS
A total of 6210 consecutive patients (3238 women; mean age 59.2 ± 12.7 years) who underwent left-sided heart valve surgery between 2000 and 2022 were included in the study cohort. The primary outcome was all-cause death, and the secondary outcome was a composite of death, reoperation, stroke and heart failure. The restricted cubic spline function was utilized to investigate the association between estimated glomerular filtration rate and clinical outcomes, which was validated using inverse probability of treatment weighting-adjusted analysis.

RESULTS
Severities of baseline renal dysfunction were none in 1520 (24.5%), mild in 3557 (57.3%), moderate in 977 (15.7%), severe in 59 (1.0%) and end-stage in 97 (1.6%). Clinical outcomes varied significantly according to the degree of baseline renal dysfunction. The restricted cubic spline function curve showed a non-linear association, indicating that the significantly adverse effects of low estimated glomerular filtration rate on clinical outcomes were diminished in cases of mild renal dysfunction. This finding was corroborated by inverse probability of treatment weighting-adjusted analysis, and subgroup analyses did not show significant differences in clinical outcomes according to the presence of mild renal dysfunction (all-cause mortality, hazard ratio: 1.08; 95% confidence interval 0.90–1.28; P = 0.413; composite outcome, hazard ratio: 1.06; 95% confidence interval 0.92–1.21; P = 0.421).

CONCLUSIONS
In patients undergoing valve surgery, long-term clinical outcomes were significantly associated with the degree of baseline renal function impairment but not with the presence of mild renal dysfunction, demonstrating a non-linear association between baseline renal function and postoperative outcomes.
Nonobese young females with polycystic ovary syndrome are at high risk for long-term cardiovascular disease
Authors: Zhao Xingping , Wang Jie , Sun Dan , Xu Dabao , Lu Yao 
Published: November 2024

Abstract

Aims
Whether polycystic ovary syndrome (PCOS) is an independent risk factor for long-term cardiovascular disease (CVD) is unclear, and the risk of CVD in easily overlooked young nonobese PCOS patients is unknown. This study aimed to investigate the associations of PCOS with CVD and identify the management priorities.

Methods and results
Three thousand and eight hundred sixty-four participants (645 with PCOS) from UK Biobank were recruited from 2006 to 2010. The cumulative incidences of the CVD were calculated and compared between patients with and without PCOS via the log-rank test. Cox proportional risk regression models were used to assess the relationships of PCOS with CVD and the impact of PCOS treatments on CVD risk. Polygenic risk scores and linkage disequilibrium score regression were used to assess the genetic-level associations. Then, proteomics subgroup cohort was conducted to explore the significant biomarker involved in the PCOS–CVD associations. Compared with participants without PCOS, participants with PCOS had greater risks of CVD [hazard ratio (HR) = 1.77, 95% confidence interval (CI) = 1.19–2.65], coronary artery disease (HR = 2.27, 95% CI = 1.35–3.81), and myocardial infarction (HR = 2.08, 95% CI = 1.11–3.90) independent of genetic risk, especially for young nonobese PCOS patients (Pfor interaction &lt; 0.05). Current commonly used treatments did not affect CVD incidence. Proteomics cohort revealed that discoidin, CUB, and LCCL domain-containing protein 2 (DCBLD2) may be specific CVD biomarker for patients with PCOS.

Conclusion
Patients with PCOS had an increased risk of CVD, and young nonobese PCOS patients should be prioritized for CVD risk management. These findings support the necessity of clinical surveillance and suggest DCBLD2 as a possible CVD biomarker in females with PCOS.
Environmental factors and potential probiotic lineages shape the active prokaryotic communities associated with healthy Penaeus stylirostris larvae and their rearing water
Authors: Giraud Carolane , Wabete Nelly , Lemeu Célia , Selmaoui-Folcher Nazha , Pham Dominique , Boulo Viviane , Callac Nolwenn 
Published: November 2024

Abstract
Microbial dysbiosis is hypothesized to cause larval mass mortalities in New Caledonian shrimp hatcheries. In order to confirm this hypothesis and allow further microbial comparisons, we studied the active prokaryotic communities of healthy Penaeus stylirostris larvae and their surrounding environment during the first 10 days of larval rearing. Using daily nutrient concentration quantitative analyses and spectrophotometric organic matter analyses, we highlighted a global eutrophication of the rearing environment. We also evidenced drastic bacterial community modifications in the water and the larvae samples using Illumina HiSeq sequencing of the V4 region of the 16S rRNA gene. We confirmed that Alteromonadales, Rhodobacterales, Flavobacteriales, Oceanospirillales, and Vibrionales members formed the core bacteriota of shrimp larvae. We also identified, in the water and the larvae samples, several potential probiotic bacterial strains that could lead to rethink probiotic use in aquaculture (AEGEAN 169 marine group, OM27 clade, Ruegeria, Leisingera, Pseudoalteromonas, and Roseobacter). Finally, investigating the existing correlations between the environmental factors and the major bacterial taxa of the water and the larvae samples, we suggested that deterministic and stochastic processes were involved in the assembly of prokaryotic communities during the larval rearing of P. stylirostris. Overall, our results showed that drastic changes mostly occurred during the zoea stages suggesting that this larval phase is crucial during shrimp larval development.
GenoTools: an open-source Python package for efficient genotype data quality control and analysis
Authors: Vitale Dan , Koretsky Mathew J , Kuznetsov Nicole , Hong Samantha , Martin Jessica , James Mikayla , Makarious Mary B , Leonard Hampton , Iwaki Hirotaka , Faghri Faraz , Blauwendraat Cornelis , Singleton Andrew B , Song Yeajin , Levine Kristin , Kumar-Sreelatha Ashwin Ashok , Fang Zih-Hua , Nalls Mike 
Published: November 2024

Abstract
GenoTools, a Python package, streamlines population genetics research by integrating ancestry estimation, quality control, and genome-wide association studies capabilities into efficient pipelines. By tracking samples, variants, and quality-specific measures throughout fully customizable pipelines, users can easily manage genetics data for large and small studies. GenoTools' “Ancestry” module renders highly accurate predictions, allowing for high-quality ancestry-specific studies, and enables custom ancestry model training and serialization specified to the user's genotyping or sequencing platform. As the genotype processing engine that powers several large initiatives, including the NIH's Center for Alzheimer's and Related Dementias and the Global Parkinson's Genetics Program, GenoTools was used to process and analyze the UK Biobank and major Alzheimer's disease and Parkinson's disease datasets with over 400,000 genotypes from arrays and 5,000 whole genome sequencing samples and has led to novel discoveries in diverse populations. It has provided replicable ancestry predictions, implemented rigorous quality control, and conducted genetic ancestry-specific genome-wide association studies to identify systematic errors or biases through a single command. GenoTools is a customizable tool that enables users to efficiently analyze and scale genotyping and sequencing (whole genome sequencing and exome) data with reproducible and scalable ancestry, quality control, and genome-wide association studies pipelines.
Optimizing neurosurgery clinic operations: a comparative study of interventions in Finland’s public healthcare system
Authors: Huttunen Jukka , Koivisto Timo 
Published: November 2024

Abstract

Background
The Finnish public healthcare system aims to ensure equal access to health services for all but faces challenges in meeting the demand for specialized care, such as neurosurgery, due to resource constraints. This study investigates interventions to increase resources at a neurosurgery outpatient clinic to improve patient care without compromising waiting times for diagnoses and treatments, leveraging Finland’s unique healthcare landscape.

Methods
The study was conducted at Kuopio University Hospital’s Department of Neurosurgery, the sole provider of neurosurgical care in Eastern Finland. Two interventions were designed to optimize clinic operations: one focusing on dynamic resource allocation through continuous monitoring and the other on establishing a fixed additional neurosurgeon slot. Process capability and regression analysis were employed to evaluate the effects of these interventions on the number of outpatient visits and the variability in daily patient numbers.

Results
The preliminary analysis showed an average of 9.3 outpatient visits per day (SD 5.2). The introduction of an additional neurosurgeon led to an increase of 5.014 visits per day, according to the regression analysis performed before the interventions. Following the interventions, the clinic observed an increase in the average number of daily outpatient visits to 9.8 after the first intervention and 11.6 after the second, with corresponding improvements in the number of neurosurgeons present. The second intervention, which established a predictable additional resource, resulted in a more significant improvement in process efficiency and stability. After the interventions, the number of new neurosurgical first patient visits increased by 7% (97 patients).

Conclusion
This study demonstrates the importance of structured and predictable resource allocation in enhancing the efficiency of specialized healthcare services, particularly in neurosurgery. It also underscores the potential of planned interventions to manage and improve patient care in a publicly funded healthcare system, despite the challenges posed by limited resources and the need for prioritization. Moreover, the findings highlight the necessity of ongoing measurement and analysis of development projects to ensure sustained improvement and avoid regression in process quality.
Proof of Concept: Autonomous Machine Vision Software for Botanical Identification
Authors: Stern Nathan , Leidig Jonathan , Wolffe Gregory 
Published: November 2024

Abstract

Background
High-performance thin-layer chromatography (HPTLC) is a widely used and accepted technique for identification of botanicals. Current best practices involve subjective comparison of HPTLC-generated images between test samples and certified botanical reference materials based on specific bands.

Objective
This research was designed to evaluate the potential of cutting-edge machine vision-based machine learning techniques to automate identification of botanicals using native HPTLC image data.

Method
HPTLC images from ginger and its closely related species and common adulterants were used to create large, synthetic datasets using a deep conditional generative adversarial network. This synthetic dataset was used to train and validate a deep convolutional neural network capable of automatically identifying new HPTLC image data. Performance of both neural networks was evaluated over time using appropriate loss functions as an indicator of their progress during learning. Validation of the overall system was measured via the accuracy of the learned model when applied to real HPTLC data.

Results
The machine vision system was able to generate realistic synthetic HPTLC images that were successfully used to train a deep convolutional neural network. The resulting learned model achieved high-accuracy identification from HPTLC images corresponding to ginger and six other related species.

Conclusions
A proof-of-concept HPTLC image-based machine vision system for the identification of botanicals was proven to be feasible, and a fully working prototype was validated for several species related to ginger.

Highlights
This use of an autonomous machine-vision system for botanical identification removed the subjectivity inherent to human-based evaluation. The learned model also accurately evaluated botanical HPTLC images significantly faster than its human counterpart, which could save both time and resources.
FraMiTrACR: A Sustainable and Economical Technology for Analytical Sample Preparation
Authors: Steils Jan-Michael , Kaluza Alexander , Schöne Klaus , Cashman John , Baumgartner Christian , Lang Maren , Kraus Melina 
Published: November 2024

Abstract

Background
There are several globally recognized methods for preparing laboratory samples. Of these, the Quick, Easy, Cheap, Effective, Rugged and Safe (QuEChERS) and Quick Polar Pesticides (QuPPe) methods are commonly used for food laboratory sample preparation. As an alternative, we developed a fractionation method using Fractionation of Milk for Trace Analysis of Contaminats and Residues (FraMiTrACR).

Objective
We present a life-cycle assessment for the QuEChERS, QuPPe, and FraMiTrACR methods. Our objective was to collect data to evaluate the carbon footprint of each method. However, as the ecological factors alone do not inform suitability of any given method, we also evaluated economic factors.

Methods
Our life cycle assessments (LCAs) followed ISO 14040/44 to determine the carbon footprint of each method. Also, we have analyzed existing data to support our comparison of all three methods.

Results
The mass of consumables and packaging for our FraMiTrACR method was observed to decrease by 45 and 34% from those required for the QuPPe and QuEChERS methods, respectively. Furthermore, we calculated a 43% reduction in carbon footprint when using FraMiTrACR compared to QuPPe and a 31% reduction compared to QuEChERS. In addition, we determined that our method offers time savings &gt;87 and &gt;71% compared to QuEChERS and QuPPe, respectively. The main economic benefit of FraMiTrACR comes from 84 and 70% labor cost savings compared to QuEChERS and QuPPe, respectively. The laboratory using the fractionation method can process 320 samples with FraMiTrACR within 8 h, an 87% increase in potential compared to QuEChERS and a 71% increase compared to QuPPe.

Conclusion
Fractionation using FraMiTrACR is a more sustainable method for analytical sample preparation, offering the same quality of results and far-reaching economic advantages.

Highlights
In comparison, FraMiTrACR uses up to 45% less consumables and packaging by weight and a reduction in kg CO2eq of up to 43%. In addition, the fractionation method offers up to 85% time-saving and up to an 84% reduction in labor cost per sample.