bluuebunny/crossref_metadata_2025 huggingface dataset:
Enriching expertise with Artificial Intelligence - An ethical inquiry in image-driven medicine
Authors:   , Drogt Jojanneke Marion Theresa Maria
Published: December 2024

In 2016, advancements in AI technology generated much excitement, and it was
recognized that AI systems carry significant potential for medical, image-driven fields
such as radiology and pathology. The promise of AI for these medical domains seemed
so great that some academics and computer scientists started to voice the expectation of
replacing healthcare professionals with advanced AI. Geoffrey Hinton even claimed that
radiologists should not be trained anymore, believing that AI would become better at
reading X-rays, CT scans, and MRIs than radiologists in five years and would make human
experts obsolete.

Nevertheless, radiologists and pathologists themselves seemed generally less prone
to participate in the hype and more cautiously optimistic about AI’s promise. Their caution
seemed justified, as, in 2020, four years after Hinton’s prediction and when this PhD
research started, there was still little AI involvement within diagnostic practice, and more
attention was being paid to the safety and desirability of AI technologies. AI faced several
technical challenges, such as application scalability and dataset bias. More fundamentally,
it became clear that social and ethical concerns also challenged the use of AI in medicine.
For instance, medical practitioners’ caution towards AI’s potential effects pointed
to the necessity of determining how AI can and should impact medical expertise in image-
driven medicine. In their interaction with AI, medical professionals must renegotiate
their position and consider what expertise they are willing to outsource to AI systems in
decision-making processes and which (new) competencies and tasks should depend on
human expertise alone. The outcome of these negotiations will likely define the roles and
responsibilities AI may take up in image-driven medicine, requiring proactive scrutiny and
reflection.

This PhD thesis responds to the ethical unclarity about AI’s potential and desired impact
on medical expertise in image-driven medicine and aims to address it. The central aim
of this PhD thesis is twofold: to identify how AI relates to human expertise in image-driven
medicine and to ethically evaluate how a desirable impact on human expertise can be
achieved. The main aim is divided into four research questions: (I) What insights can be
gained from analyzing medical expertise, especially in image-driven medicine, that are
relevant to the implementation of AI? (II) What are the expectations of and experiences
with AI in image-driven medicine? (III) How can the desirability of AI’s impact on expertise
in image-driven medicine be evaluated? (IV) What methodology should ground (future)
ethical reflection on using AI in image-driven medicine? These four questions correspond
with the four parts of this thesis.
Foreign Aid In Türkiye-Africa Relations: Past, Present And Future
Authors: Turhan Yunus
Published: December 2024

Türkiye's relationship with African countries come to realize exigency of ameliorating relation over last two decades which has inevitable corollary of Türkiye’s belated efforts to expand into Africa. Türkiye’s efforts in Africa, slowly but surely, come to fruition, involving from an opening policy to a strategic partnership which eventually has brought a new dynamic to both Turkish orthodox foreign policy and Africa's relations with the outside world. Contrary to most analysts whom interpreted such pace as a temporary enthusiasm just blended with economic consideration, this relationship in fact represent rapprochement after 2008. This article chronologically examines Türkiye's retrospective to strategic partnership with African states in the context of "foreign aid", one of the elements of soft power, and analyses the historical turning points in it’s Africa outreach. Moving on to the concrete outputs of Türkiye's increasing aid to the continent, the article compares Türkiye’s foreign aid with Russia, China and the United States, while emphasizing the importance of Turkish foreign aid to Africa in the construction of a "benevolence power" policy, which is the most concrete practice of Türkiye's "Entrepreneurial and Humanitarian Foreign Policy" paradigm. In the final analysis, a forecast of Türkiye-Africa relations in the context of foreign aid is discussed.
Muhammed et-Trabzonî’nin (ö. 1200/1786) Risâle fî Şerâiti Sıhhati’n-Nezr Adlı Risâlesi: İnceleme ve Tahkik
Authors: Saylan Şenol
Published: December 2024

Fıkıh terimi olarak “dinen mükellef olmadığı halde, kişinin farz veya vâcip türünden bir ibadeti yapacağına dair Allah’a söz vermesi” şeklinde tarif edilen nezir kelimesi Türkçede “adak” olarak ifade edilir. Adak ile ilgili konular bazı fıkıh kitaplarında nezir ve yemin bölümlerinde veya nezredilebilen namaz, oruç hac gibi her bir ibadet işlenirken bahis konusu yapılmıştır. Nadir de olsa nezir ahkâmı ile ilgili bazı konulara temas eden müstakil eserler de kaleme alınmıştır. Konuyla ilgili müstakil bir risâle kaleme alan âlimlerden biri de Muhammed et-Trabzonî el-Medenî’dir (ö. 1200/1786). 18. yüzyıl Osmanlı âlimlerinden olan Muhammed et-Trabzonî, ilk eğitimini Trabzon’da tamamladıktan sonra tahsilini ilerletmek üzere İstanbul’a gitmiştir. Trabzonî, ilerleyen süreçte çeşitli tarihlerde İslam coğrafyasının Halep, Şam, Kudüs, Mısır, Mekke ve Medine gibi bölgelerine seyahatlerde bulunmuştur. Buralarda birçok eseri istinsah ve mukabele etmiş, çeşitli ilimlerde icazetler almıştır. 1753 yılında İstanbul’a döndükten sonra Süleymaniye Medresesi’nde hâfız-ı kütüb ve müderris olarak görev yapmıştır. Kâdîrî tarikatına mensup bir sufî olan Trabzonî, fıkıh, hadis, tefsir gibi çeşitli ilim dallarında birçok eser kaleme almıştır. Telif ettiği bu eserlerden biri de Risâle fî şerâiti sıhhati’n-nezr adlı adak konulu risâlesidir. Söz konusu risâlede adak konusuyla ilgili şartları ele alan Trabzonî, Hanefî fürû fıkıh literatüründe çeşitli konularda zikredilen bu şartları, genel ilkeler (davâbıt) olarak yedi başlık altında bir araya getirmeye çalışmıştır. Sadece ilk kâideye değinirken mezhepte yer alan konuyla ilgili farklı görüşlere yer veren Trabzonî diğer kâideleri kısaca zikretmekle yetinmiştir. Bu makalede Muhammed et-Trabzonî’nin adak konusuyla ilgili şartları ihtiva eden risâlesini inceleyerek risâlenin tahkikli metnine yer verdik.
Vehhâbîlik Reddiyeleri Bağlamında Muhammed et-Trabzonî el-Medenî’nin Görüşleri
Authors: Koçak Ebru
Published: December 2024

XVIII. ve XIX. asırlar Osmanlı toplumu için pek çok fikrî ve siyasî buhranın yaşandığı çalkantılı bir dönemdir. Hiç kuşkusuz bunların en önemlilerinden biri Vehhâbî hareketin ortaya çıkmasıdır. Vehhâbîlik ortaya çıktığı andan günümüze kadar İslam dünyasında önemli yankılar uyandırmış bir harekettir. Tevhidi bütün yönleriyle hâkim kılma söylemi ile yola çıkan bir topluluğun Müslümanlar için kutsal kabul edilen değerleri ve mekanları hedef alması İslam ulemasının tepkisini beraberinde getirmiştir. Kolektif bir bilincin ürünü olan bu tepkiler sonucunda Vehhâbîlik Reddiyeleri olarak ifade edebileceğimiz hatırı sayılır bir literatür ortaya çıkmıştır. Vehhâbîlik Reddiyeleri Muhammed b. Abdülvehhâb’ın görüşlerini ortaya koyduğu ilk andan günümüze dek yazılmaya devam etmiştir. Mezhep aidiyetlerinden bağımsız olarak Vehhâbî görüşleri eleştiren/reddeden pek çok âlim tarafından kimisi küçük bir risale, kimisi de hacimli bir eser hüviyetinde pek çok reddiye kaleme alınmıştır. Reddiye yazan âlimlerin öncelikli hedefleri dinî ve kültürel değerlerin korunması ile halkın bilinçlendirilmesi olmuştur. Hanefî-muhaddis kimliği ile bilinen Muhammed et-Trabzonî el-Medenî’nin (ö. 1200-1786) Sârimü’l-Vâridât fî’r-Reddi alâ Ehli Hevâ adlı risalesi de Muhammed b. Abdülvehhâb’ın görüşlerine karşı Hanefî bir âlim tarafından erken dönemde yazılmış reddiyelerden bir tanesidir. Muhammed et-Trabzonî el-Medenî’nin eseri dönemin toplumsal hafızasına ışık tutması ve gerek halkın gerekse ulemanın zihinlerini meşgul eden tartışma konularını ortaya koyması bakımından önem arz etmektedir. Zira bu konular Muhammed et-Trabzonî’nin yaşadığı yüzyılın bir öncesinde ve bir sonrasında İslam dünyasında tartışılagelip toplumsal kutuplaşmanın ana ekseninde yer almıştır. Öyle ki söz konusu edilen mevzular XVI ve XVII. yüzyıl Osmanlı toplumunda Kadızadelî-Sivasî çekişmesinin parçası XVIII ve XIX. yüzyıllarda ise Vehhâbîler ile Ehl-i Sünnet uleması arasındaki tartışmaların içeriğini oluşturmuştur. Bu itibarla makalede Muhammed et-Trabzonî el-Medenî’nin reddiyesinin metinsel analizi yapılarak, Vehhâbîlik Reddiyeleri arasındaki konumu ve önemi irdelenmiştir. Reddiye mecmuasının içerisinde yer alan konuyla ilgili diğer risalelerin de analizi yapılmış, makale söz konusu çalışmalarla sınırlandırılmıştır. Bununla beraber makalede metinler ve şahıslar üzerinde derinleşme yöntemi kullanılarak Muhammed et-Trabzonî’nin Vehhâbilik ile ilgili yaklaşımlarına ve reddiye verdiği konulara ulaşılmıştır. Diğer yandan söz konusu reddiye mecmuasının Kadızâdeli ulemaya hitaben yazılmadığının, Vehhâbîliği doğrudan hedef aldığının tespit edilmesi ise makalenin diğer kazanımı olmuştur.
Incorporation of charge discreteness and ion correlations into lattice models of ionic liquids
Authors: Bossa Guilherme Volpe , May Sylvio
Published: December 2024

Lattice-based mean-field models of ionic liquids neglect charge discreteness and ion correlations. To address these limitations, we propose separating the short-range and long-range parts of the electrostatic interaction by truncating the Coulomb potential below a fixed distance that is equal to or slightly larger than that between neighboring ions. Interactions and correlations between adjacent ions can then be modeled explicitly, whereas longer-ranged electrostatic interactions are captured on the mean-field level. We implement this approximation into the framework of modeling a compact, solvent-free ionic liquid by, first, considering terms up to the fourth order of the operator that represents the truncated Coulomb potential and, second, by accounting for electrostatic correlations between pairs of neighboring ions on the level of the quasi-chemical approach. A set of boundary conditions for the resulting self-consistent fourth-order differential equation follows from functional minimization of the free energy. The differential capacitance of an ionic liquid in contact with a planar electrode is calculated analytically up to quadratic order in the electrode’s surface charge density by solving the linearized model and applying a perturbation approach valid beyond the linear regime. We demonstrate that charge discreteness enhances the differential capacitance, whereas electrostatic correlations between ion–ion pairs drive the transition from a bell-shaped to a camel-shaped profile of differential capacitance. Our approach offers a systematic way to further improve the treatment of charge discreteness, account for short-range electrostatic and non-electrostatic interactions, and include higher-order ion–ion correlations.
Nonhuman primate models of pediatric viral diseases
Authors: Vijayan K. K. Vidya , De Paris Kristina
Published: December 2024

Infectious diseases are the leading cause of death in infants and children under 5 years of age. In utero exposure to viruses can lead to spontaneous abortion, preterm birth, congenital abnormalities or other developmental defects, often resulting in lifelong health sequalae. The underlying biological mechanisms are difficult to study in humans due to ethical concerns and limited sample access. Nonhuman primates (NHP) are closely related to humans, and pregnancy and immune ontogeny in infants are very similar to humans. Therefore, NHP are a highly relevant model for understanding fetal and postnatal virus-host interactions and to define immune mechanisms associated with increased morbidity and mortality in infants. We will discuss NHP models of viruses causing congenital infections, respiratory diseases in early life, and HIV. Cytomegalovirus (CMV) remains the most common cause of congenital defects worldwide. Measles is a vaccine-preventable disease, yet measles cases are resurging. Zika is an example of an emerging arbovirus with devastating consequences for the developing fetus and the surviving infant. Among the respiratory viruses, we will discuss influenza and Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). We will finish with HIV as an example of a lifelong infection without a cure or vaccine. The review will highlight (i) the impact of viral infections on fetal and infant immune development, (ii) how differences in infant and adult immune responses to infection alter disease outcome, and emphasize the invaluable contribution of pediatric NHP infection models to the design of effective treatment and prevention strategies, including vaccines, for human infants.
Development and evaluation of a machine learning model for post-surgical acute kidney injury in active infective endocarditis
Authors: Liu XinPei , Ai SanXi , Yu RuiMing , Zhang ChaoJi , Miao Qi
Published: December 2024

Introduction

Acute kidney injury (AKI) is notably prevalent after cardiac surgery for patients with active infective endocarditis. This study aims to create a machine learning model to predict AKI in this high-risk group, improving upon existing models by focusing specifically on endocarditis-related surgeries.

Methods

We analyzed medical records from 527 patients who underwent cardiac surgery for active infective endocarditis from January 2012 to December 2023. Feature selection was performed using LASSO regression. These features informed the development of machine learning models, including logistic regression, linear and radial basis function support vector machines, XGBoost, decision trees, and random forests. The optimal model was selected based on ROC curve AUC. Model performance was assessed through discrimination, calibration, and clinical utility, with explanations provided by SHAP values.

Results

Post-surgical AKI was observed in 261 patients (49.53%). LASSO regression identified 25 significant features for the models. Among the six algorithms tested, the radial basis function support vector machine (RBF-SVM) had the highest AUC at 0.771. The 15 most critical features were valve replacement, pre-operative hypertension, large vegetations, NYHA class, alcoholism, age, post-operative low cardiac output syndrome, TyG index, pre-operative creatinine clearance, cardiopulmonary bypass duration, intra-operative red blood cell transfusion, intra-operative urine output, pre-operative hemoglobin levels, and timing of surgery.

Conclusion

Compared to standard cardiac surgery, AKI occurs more frequently and with a more complex etiology in surgeries for active infective endocarditis. Machine learning models enable early prediction of post-surgical AKI, facilitating targeted perioperative optimization and risk stratification in this distinct patient group.
Leading sustainable school improvement: a meta-synthesis of qualitative research on problems and challenges faced by school leaders
Authors: Karakose Turgut , Ozdogru Mehmet , Malkoc Nedim
Published: December 2024

Introduction

Developing broader insights into the problems or challenges faced by school leaders resulting from various factors both within and out of school is a crucial attempt to provide solutions on scientific grounds and to ensure the sustainability of schools.

Methods

This study aims to contribute to both the theory and practice of sustainable school administration through conducting the meta-synthesis of prior qualitative studies on the problems and challenges faced by school leaders. Data were collected from several databases indexing educational research, and the analysis was conducted using data from 24 studies presenting the perspectives of a total of 614 participants.

Results

The results showed that school leaders had significant problems particularly with insufficient funds and budgets, shortage of school staff, insufficient or unwilling teachers, an abundance of responsibilities with limited authority, maintenance of school buildings, and tackling excessive and fast-changing legislations. Lack of inspectors’ expertise and their being closed to novel ideas, principal assignments not based on merit, insufficient communication and collaboration among teachers, and pressures from the superiors or unions were also listed among the other serious problems and challenges.

Discussion

These findings suggest putting more effort into improving human resources, school budgets, curriculum and instruction, parental involvement, mechanisms to tackle student problematic behavior, ensuring the professional quality of teachers, school leaders, and inspectors as well as providing school leaders with the necessary support while expecting them to realize an abundance of responsibilities. The challenges caused by bureaucratic pressures, political press, and union discord should also be crucially considered by the higher authorities if school leaders are expected to contribute to the sustainable improvement of schools.
Climate change injustice and school attendance and absenteeism: proximal and distal ecological links
Authors: Kearney Christopher A. , Ellis Kinsey , Arcaina V. Jefferson
Published: December 2024

Climate change has been linked to a myriad of problems related to human functioning, with a particular scientific emphasis on economic, physical damage, and health sectors. Less attention, however, has been given to the links between climate change and problems in the educational sector, such as school attendance problems, which represent practical and everyday manifestations of the effects of climate change. This is unfortunate given that children, and particularly those in Black and Brown communities and in the majority world, are expected to bear the greatest burden from climate change now and in the future. One fundamental right of children is the right to an education and to attend school, and this right is threatened particularly for vulnerable populations in different ways by climate change. Narrative synthesis of key terms (e.g., climate change, school absenteeism) for literature review was conducted to identify key patterns that produced the primary themes represented in this article: physical health, mental health, violence, school environment, school displacement and migration, and economic challenges. These themes were organized along a general proximal-to-distal spectrum. The descriptions of each theme also illustrate mechanisms connecting these issues that may help inform future mitigation efforts.
Associations of serum folate and vitamin B12 levels with all-cause mortality among patients with metabolic dysfunction associated steatotic liver disease: a prospective cohort study
Authors: Zhu Jiaxin , Liao Xinyi , Du Lei , Lv Pengju , Deng Jian
Published: December 2024

Introduction

Serum folate and vitamin B12 levels correlate with the prevalence of fatty liver disease, but it is not clear how they affect mortality. Therefore, this study aimed to investigate the association of serum folate and vitamin B12 concentrations with all-cause mortality in individuals with metabolic dysfunction-associated steatotic liver disease (MASLD).

Methods

MASLD subjects were from the Third National Health and Nutrition Examination Survey (NHANES III) in the United States, and mortality follow-up data were obtained by linkage to death records from the National Death Index. Multivariable Cox proportional regression models and restricted cubic spline (RCS) models were used to evaluate the association of serum folate/vitamin B12 with all-cause mortality in the MASLD population.

Results

3,636 and 2,125 MASLD individuals were included in the analyses related to serum folate and vitamin B12, respectively. During a follow-up period of more than 20 years, the RCS models demonstrated significant nonlinear associations of both serum folate (P <0.001) and vitamin B12 (P =0.016) with all-cause mortality in MASLD. When their serum concentrations were below the median level, the risk of all-cause mortality decreased with increasing concentration, reaching a lowest risk around the median level, and then leveled off. In the multivariable cox regression model, for vitamin B12, the risk of all-cause mortality was reduced by 42% and 28% in the third and fourth quartile groups, respectively, compared with the lowest quartile group (hazard ratio [HR]=0.58, 95% CI: 0.39-0.86, P =0.008; HR =0.72, 95% CI: 0.54-0.96, P=0.026, respectively). For folate, the risk of all-cause mortality was reduced by 28% in the third quartile compared with the lowest quartile (HR =0.72, 95% CI: 0.57-0.91, P =0.005).

Conclusion

This longitudinal cohort study suggests that low serum folate and vitamin B12 levels in patients with MASLD are significantly associated with an elevated risk of all-cause mortality.
Ocular surface disease index in Graves’ orbitopathy: a cross-sectional study
Authors: Maglionico Maria Novella , Lanzolla Giulia , Figus Michele , Cosentino Giada , Comi Simone , Marinò Michele , Santini Ferruccio , Posarelli Chiara
Published: December 2024

Introduction

Graves' Orbitopathy (GO) is an autoimmune disorder characterized by inflammation of orbital tissues, leading to various ocular manifestations, including ocular surface disease. This cross-sectional study aimed to assess the presence of ocular surface disease using the Ocular Surface Disease Index (OSDI) in patients with Graves' disease (GD) and moderate-to-severe active GO compared to those with GD and mild non-active GO. Additionally, we aimed to investigate the correlation between ocular surface disease and the eye features of GO.

Methods

Consecutive GD patients with GO referred to the Ophthalmology and Endocrinology Units of the University Hospital of Pisa between June 2022 and February 2023 were enrolled. OSDI scores were obtained from 79 GD patients, categorized into moderate-to-severe active GO and mild non-active GO groups.

Results

OSDI scores were significantly higher in patients with moderate-to-severe active GO compared to those with mild non-active GO (P=0.0006). A cutoff value of 33 for positive tests revealed a higher frequency of pathological OSDI in moderate-to-severe active GO patients compared to mild non-active GO patients (P=0.0221; OR 3.673, CI 1.277-9.531). Within the moderate-to-severe active GO group, a significant positive correlation was found between OSDI and Clinical Activity Score (CAS) (R= 0.3867, 95% CI from 0.1403 to 0.5880; P=0.0030). Using a cutoff value of 55 (the 75th percentile of the study population), patients with CAS ≥ 3 had a significantly higher proportion of pathological OSDI compared to those with CAS <3 (P=0.0039; OR 4.075, CI 1.619-10.39). Proptosis values ≥ 22 mm and the presence of lagophthalmos were identified as significant risk factors for ocular surface disease development (P=0.0406 and P=0.0493, respectively).

Discussion

Our study highlights a significantly higher prevalence of ocular surface disease, as measured by OSDI, in patients with moderate-to-severe active GO compared to those with mild non-active disease. The degree of GO activity positively correlates with ocular surface involvement, and proptosis and lagophthalmos increase the risk of its occurrence. These findings emphasise the importance of assessing and managing ocular surface health in GO patients. Early identification and appropriate treatment of ocular surface disease need to be pursued to improve patient management.
Macroevolutionary processes in turtles (Testudines): a view from biomic specialization and historical climatic changes
Authors: Thomas Juan S. , Gamboa Sara , Hernández Fernández Manuel , Murillo Oscar , Pelegrin Jonathan S.
Published: December 2024

The resource-use hypothesis proposed by Elisabeth S. Vrba suggests that lineages display varying tendencies toward generalism or specialization in biome occupancy, with a tendency towards the accumulation of specialists due to their higher rate of speciation through vicariance. It also posits differences in biome occupancy patterns driven by the environmental characteristics of biomes, with a higher presence of biome specialist species in biomes that are placed in the extremes of the global climatic gradients. Here, we tested this hypothesis in turtles, a very ancient and morphologically stable lineage, representing a remarkable diversity with 357 species, many of which are threatened with extinction. We analyzed the resource-use hypothesis in a phylogenetic context within the Testudines lineage. For this purpose, a presence/absence matrix was compiled for all species across all 10 terrestrial biomes. Their distribution across biomes was contrasted with 10,000 Monte Carlo simulations. The relationship between diversification rates and both the biomic specialization index and the biomes occupied by specialists species was evaluated. The results demonstrate strong consistency with Vrba`s hypothesis, revealing a higher number of biome specialist species than expected by chance, with a significant accumulation of species in tropical ecosystems. These trends also were observed for ecological groups (terrestrial and freshwater species). In addition, higher diversification rates were observed for biome specialist species, although the particular biome occupied did not significantly influence their diversification rates.
Microbiome in urologic neoplasms: focusing on tumor immunity
Authors: Zou Jun , Xu Baisheng , Gao Hongbing , Luo Peiyue , Chen Tao , Duan Huanglin
Published: December 2024

Urological tumors are an important disease affecting global human health, and their pathogenesis and treatment have been the focus of medical research. With the in - depth study of microbiomics, the role of the microbiome in urological tumors has gradually attracted attention. However, the current research on tumor - associated microorganisms mostly focuses on one type or one site, and currently, there is a lack of attention to the microbiome in the immunity and immunotherapy of urological tumors. Therefore, in this paper, we systematically review the distribution characteristics of the microbiome (including microorganisms in the gut, urine, and tumor tissues) in urologic tumors, the relationship with disease prognosis, and the potential mechanisms of microbial roles in immunotherapy. In particular, we focus on the molecular mechanisms by which the microbiome at different sites influences tumor immunity through multiple “messengers” and pathways. We aim to further deepen the understanding of microbiome mechanisms in urologic tumors, and also point out the direction for the future development of immunotherapy for urologic tumors.
Immune-related diagnostic markers for benign prostatic hyperplasia and their potential as drug targets
Authors: Wang YaXuan , Wang Jing , Liu Jibin , Zhu HaiXia
Published: December 2024

Background

Benign prostatic hyperplasia (BPH) is a common issue among older men. Diagnosis of BPH currently relies on imaging tests and assessment of urinary flow rate due to the absence of definitive diagnostic markers. Developing more accurate markers is crucial to improve BPH diagnosis.

Method

The BPH dataset utilized in this study was sourced from the Gene Expression Omnibus (GEO). Initially, differential expression and functional analyses were conducted, followed by the application of multiple machine learning techniques to identify key diagnostic markers. Subsequent investigations have focused on elucidating the functions and mechanisms associated with these markers. The ssGSEA method was employed to evaluate immune cell scores in BPH samples, facilitating the exploration of the relationship between key diagnostic markers and immune cells. Additionally, molecular docking was performed to assess the binding affinity of these key markers to therapeutic drugs for BPH. Tissue samples from BPH patients were collected for experimental validation of the expression differences of the aforementioned genes.

Result

A total of 185 differential genes were identified, comprising 67 up-regulated and 118 down-regulated genes. These genes are implicated in pathways that regulate extracellular matrix tissue composition and cellular responses to transforming growth factor beta stimulation, as well as critical signaling pathways such as AMPK and mTOR. Through the application of various machine learning techniques, DACH1, CACNA1D, STARD13, and RUNDC3B were identified as key diagnostic markers. The ssGSEA algorithm further corroborated the association of these diagnostic genes with diverse immune cells. Moreover, molecular docking analysis revealed strong binding affinities of these markers to tamsulosin and finasteride, suggesting their potential as drug targets. Finally, experimental validation confirmed the expression differences of DACH1, CACNA1D, STARD13, and RUNDC3B in BPH tissues.

Conclusion

This study introduces novel immune-related diagnostic markers for BPH and highlights their promise as new drug targets, providing a valuable approach for predictive diagnosis and targeted therapy of BPH.
Importance of the water-sediment bed interactions in simulating microplastic particles in an estuarine system
Authors: Summers Emily , Du Jiabi , Park Kyeong , Wharton Marcus , Kaiser Karl
Published: December 2024

Retention of plastics in estuaries and storage in sediments likely contributes to the mass imbalance between the amount of ocean plastic debris and input from land. A sediment transport model, coupled with a hydrodynamic and wave model, was employed to analyze how microplastics of varying settling velocities behave under non-storm conditions and during extreme storm events in Galveston Bay, USA. The model was informed by measured concentrations of microplastics in a main tributary (Buffalo Bayou), which flows through the highly populated Houston-metro area. Under non-storm conditions, concentrations of neutrally buoyant particles are highest near the source location. In contrast, negatively buoyant particles are highest near the bay mouth where bed shear stress, and thus the potential for erosion/resuspension, is highest. Simulation of Hurricane Harvey, an unpreceded 1000-year flood event, shows a drastic increase of overall microplastic levels in Galveston Bay, approximately 5x that of non-storm conditions, and an increase in corresponding flux of microplastics to the Gulf of Mexico. The differences are attributed both to increases in microplastic loading and erosion of microplastics from bed sediments during Harvey. Differences in concentration between storm and non-storm conditions are most clear in the upper bay, where shear stress is low under normal conditions but shows a significant increase during storms due to wave-enhanced stress. Following Harvey, negatively buoyant particles levels return to normal in less than a week, but neutrally buoyant particle concentrations remain elevated over several months. Use of a sediment transport model that simulates erosion/resuspension to understand particle behavior lends further understanding of processes of microplastics not explored through previous use of particle tracking models that do not account for erosion/resuspension. This is of upmost importance for simulation of negatively buoyant particles, which have more potential to interact with the sediment bed layer. Variation of critical shear stress for erosion, erosion rate, and use of a wave model, all show significant impacts on particle behavior. Future parameterization of microplastic behavior in sediments will enhance our understanding of estuarine retention and export ability.
Single-cell transcriptome analysis reveals status changes of immune cells in chronic kidney disease
Authors: Fan Xinhuan , Zhu Yuxin , Kan Hao , Mao Aiqin , Geng Li , Li Changzhu , Zhang Ka
Published: December 2024

Background and aims

The immune system plays a crucial role in the development of kidney diseases. Chronic kidney disease (CKD) can lead to various complications, potentially affecting multiple systems throughout the body. Currently, the description of the immune system in human CKD is not comprehensive enough. Constructing a CKD kidney atlas using single-cell RNA sequencing (scRNA-seq) can provide deeper insights into the composition and functional changes of immune cells in CKD, facilitating the discovery of new therapeutic targets.

Methods

We processed and integrated scRNA-seq datasets from healthy and CKD kidneys from three independent cohorts using the same approach (including 42 normal samples and 23 chronic kidney disease samples). Subsequently, we conducted gene enrichment and intercellular communication analysis to construct an immune cell atlas of the kidneys in CKD patients.

Results

We identified nine major kidney cell clusters. Further clustering analysis of different immune cell clusters revealed that, compared to normal kidneys, CKD patients’ kidneys had decreased CD16+ NK cells while CD4+ naive helper T cells and CCR7+ DC increased. Partial activation of the WNT signaling pathway was observed in T cells and NK cells of CKD patients, while some metabolism-related genes were inhibited. Myeloid cell subgroups also exhibited abnormal signaling pathway alterations. Additionally, we discovered a unique population of SPP1 macrophages in CKD, which are recruited by chemokines released from aPT and aTAL cell subpopulations. These SPP1 macrophages may promote cellular fibrosis through the signaling of SPP1, FN1, and various receptors.

Conclusion

We established a human CKD kidney immune cell atlas and identified SPP1 macrophages as a unique cell type in CKD. The interaction between SPP1 macrophages and damaged cells may serve as a potential therapeutic target for treating CKD in the future.
Optimization of convolutional neural network and visual geometry group-16 using genetic algorithms for pneumonia detection
Authors: Chihaoui Mejda , Dhibi Naziha , Ferchichi Ahlem
Published: December 2024

Pneumonia is still a major global health issue, so effective diagnostic methods are needed. This research proposes a new methodology for improving convolutional neural networks (CNNs) and the Visual Geometry Group-16 (VGG16) model by incorporating genetic algorithms (GAs) to detect pneumonia. The work uses a dataset of 5,856 frontal chest radiography images critical in training and testing machine learning algorithms. The issue relates to challenges of medical image classification, the complexity of which can be significantly addressed by properly optimizing CNN. Moreover, our proposed methodology used GAs to determine the hyperparameters for CNNs and VGG16 and fine-tune the architecture to improve the existing performance measures. The evaluation of the optimized models showed some good performances with purely convolutional neural network archetyping, averaging 97% in terms of training accuracy and 94% based on the testing process. At the same time, it has a low error rate of 0.072. Although adding this layer affected the training and testing time, it created a new impression on the test accuracy and training accuracy of the VGG16 model, with 90.90% training accuracy, 90.90%, and a loss of 0.11. Future work will involve contributing more examples so that a richer database of radiographic images is attained, optimizing the GA parameters even more, and pursuing the use of ensemble applications so that the diagnosis capability is heightened. Apart from emphasizing the contribution of GAs in improving the CNN architecture, this study also seeks to contribute to the early detection of pneumonia to minimize the complications faced by patients, especially children.
Morphological and molecular identification of Schizophyllum commune causing storage bulb rot disease of Lanzhou edible lily in China and its biological characteristics
Authors: Liang Qiaolan , Wei Liexin , Chen Ying’e , Xu Bingliang , Zhang Na
Published: December 2024

Lily bulb rot disease has harmed edible lily in recent years, resulting in yield losses in China. As a results, both morphological and molecular techniques must be used to confirm the etiology of storage bulb rot disease on lily bulbs. Lily bulbs with indications of rot symptoms during storage were gathered in Lanzhou, Gansu Province, China. A strain was isolated and its morphologically characterized as a Schizophyllum commune specie. Pathogenicity tests further confirmed that the strain caused apparent S. commune symptoms on lily bulbs which were consistent with those seen in the field. The pathogenicity of S. commune to lily bulb was 100%, and morphological identification showed that the mycelia of the pathogen were white and villous, with septate, branched, and acicular bodies and obvious lock-shaped joints. The mycelia had uneven thickness, ranging from 1.03 to 3.06 μm, and turned gray-white at the later growth stage. Moreover, the pathogen formed a mycelial column on potato dextrose agar (PDA) medium, which formed a coral-like fruiting body primordium, which split, forming pileus for spore production. The spores were colorless and cylindrical, with an oblique tip and a size of 4.6–7.2 μm × 2.2–2.7 μm. The isolate was deduced as based on phylogenetic analysis with 2 genes (ribosomal DNA-ITS and LSU) as well as morphological characteristics and cultural features, the isolate was identified S. commune. Soluble starch, yeast extract, temperature of 30°C, pH 7, relative humidity of 100%, and complete dark were shown to be the optimum culture conditions for surface mycelium growth. In conclusion, this is the first report of S. commune causing bulb rot of edible lilies in China. The study provides a basis for more effective control strategies for lily bulb rot disease.
Enhancing D-lactic acid production from non-detoxified corn stover hydrolysate via innovative F127-IEA hydrogel-mediated immobilization of Lactobacillus bulgaricus T15
Authors: Zheng Yuhan , Sun Feiyang , Liu Siyi , Wang Gang , Chen Huan , Guo Yongxin , Wang Xiufeng , Escobar Bonora Maia Lia , Zhang Sitong , Li Yanli , Chen Guang
Published: December 2024

Background

The production of D-lactic acid (D-LA) from non-detoxified corn stover hydrolysate is hindered by substrate-mediated inhibition and low cell utilization times. In this study, we developed a novel temperature-sensitive hydrogel, F127-IEA, for efficient D-LA production using a cell-recycle batch fermentation process.

Results

F127-IEA exhibited a porous structure with an average pore size of approximately 1 μm, facilitating the formation of stable Lactobacillus bulgaricus clusters within the gel matrix. It also maintains excellent mechanical properties. It also maintains excellent mechanical properties. F127-IEA immobilized Lactobacillus bulgaricus T15 (F127-IEA-T15) can be used in cell-recycle fermentation for over 150 days from glucose and 50 days from corn stover hydrolysate, achieving high production rates of D-LA from glucose (2.71 ± 0.85 g/L h) and corn stover hydrolysate (1.29 ± 0.39 g/L h). F127-IEA-T15 enhanced D-LA production by adsorbing and blocking toxic substances present in corn stover hydrolysate that are detrimental to cellular activity.

Conclusions

The newly developed hydrogels in this study provide a robust platform for large-scale extraction of D-LA from non-detoxified corn stover.
The neural basis of neuropsychiatric symptoms in Alzheimer’s disease
Authors: Zhang Nicole K. , Zhang Selena K. , Zhang Li I. , Tao Huizhong W. , Zhang Guang-Wei
Published: December 2024

Neuropsychiatric symptoms (NPS) such as depression, anxiety, apathy and aggression affect up to 90% of Alzheimer’s disease (AD) patients. These symptoms significantly increase caregiver stress and institutionalization rates, and more importantly they are correlated with faster cognitive decline. However, the neuronal basis of NPS in AD remains largely unknown. Here, we review current understanding of NPS and related pathology in studies of AD patients and AD mouse models. Clinical studies indicate that NPS prevalence and severity vary across different AD stages and types. Neuroimaging and postmortem studies have suggested that pathological changes in the anterior cingulate cortex, hippocampus, prefrontal cortex, and amygdala are linked to NPS, although the precise mechanisms remain unclear. Studies of AD mouse models have indicated that amyloid-beta and tau-related neurodegeneration in the hippocampus, prefrontal cortex, and anterior cingulate cortex are correlated with NPS-like behavioral deficits. A better understanding of the NPS phenotypes and related pathological changes will pave the way for developing a better management strategy for NPS in AD patients.
Case report: Ectopic production of intact parathyroid hormone (iPTH) by malignoma mimicking primary hyperparathyroidism
Authors: Wendt Ralph , Heller Marie , Härtwig Daniel , Ullmann Sven Oliver , Bisanz Heike , Geister Daniela , Mantovani Luisa , Hoffmann Ulrike
Published: December 2024

Background

Malignant hypercalcemia is usually caused by osteolytic processes of metastases, production of parathormone-related peptide, or secretion of 1,25-dihydroxyvitamin D. Ectopic PTH (parathyroid hormone) production by malignancy is very unusual.

Methods

Case report and review of the literature.

Results

We present a case of a malignant hypercalcemia with a presentation that mimicked primary hyperparathyroidism in a patient with endometrial carcinoma. Finally, ectopic production of PTH by a rapidly progressive neuroendocrine tumor was proven. Systematic literature review revealed ectopic PTH production by malignancies as an extremely rare cause of hypercalcemia and that most cases were initially misdiagnosed as primary hyperparathyroidism and underwent unnecessary surgical neck exploration in almost all cases.

Conclusion

In patients even with a suggestive constellation of primary hyperparathyroidism, an ectopic paraneoplastic PTH source should be considered if the localization diagnostics are without abnormalities or if the PTH values are unusually high. Concomitant elevated LDH levels should also raise concern about an ectopic malignant source.
ARMH1 is a novel marker associated with poor pediatric AML outcomes that affect the fatty acid synthesis and cell cycle pathways
Authors: Bakhtiari Mojtaba , Jordan Sean C. , Mumme Hope L. , Sharma Richa , Shanmugam Mala , Bhasin Swati S. , Bhasin Manoj
Published: December 2024

Introduction

Despite remarkable progress in Pediatric Acute Myeloid Leukemia (pAML) treatments, the relapsed disease remains difficult to treat, making it pertinent to identify novel biomarkers of prognostic/therapeutic significance.

Material and methods

Bone marrow samples from 21 pAML patients were analyzed using single cell RNA sequencing, functional assays with ARMH1 knockdown and overexpression were performed in leukemia cell lines to evaluate impact on proliferation and migration, and chemotherapy sensitivity. Mitochondrial function was assessed via Seahorse assay, ARMH1 interacting proteins were studied using co-immunoprecipitation. Bulk RNA-seq was performed on ARMH1knockdown and over expressing cell lines to evaluate the pathways and networks impacted by ARMH1.

Results

Our data shows that ARMH1, a novel cancer-associated gene, is highly expressed in the malignant blast cells of multiple pediatric hematologic malignancies, including AML, T/B-ALL, and T/B-MPAL. Notably, ARMH1 expression is significantly elevated in blast cells of patients who relapsed or have a high-risk cytogenetic profile (MLL) compared to standard-risk (RUNX1, inv (16)). ARMH1 expression is also significantly correlated with the pediatric leukemia stem cell score of 6 genes (LSC6) associated with poor outcomes. Perturbation of ARMH1 (knockdown and overexpression) in leukemia cell lines significantly impacted cell proliferation and migration. The RNA-sequencing analysis on multiple ARMH1 knockdown and overexpressing cell lines established an association with mitochondrial fatty acid synthesis and cell cycle pathways.The investigation of the mitochondrial matrix shows that pharmacological inhibition of a key enzyme in fatty acid synthesis regulation, CPT1A, resulted in ARMH1 downregulation. ARMH1 knockdown also led to a significant reduction in CPT1A and ATP production as well as Oxygen Consumption Rate. Our data indicates that downregulating ARMH1 impacts cell proliferation by reducing key cell cycle regulators such as CDCA7 and EZH2. Further, we also established that ARMH1 is a key physical interactant of EZH2, associated with multiple cancers.

Conclusion

Our findings underscore further evaluation of ARMH1 as a potential candidate for targeted therapies and stratification of aggressive pAML to improve outcomes.
Case report: Paraganglioma masquerading as angiosarcoma: diagnostic‐dilemma in vascular tumors
Authors: Rajoo Ahilan Raj , Kannairan Saravanan , Habeebullah Khan Hisham Arshad , Md Idris Mohamad Azim , Tan Geok Chin , Chandra Sakaran Kishen Raj , Safri Lenny Suryani
Published: December 2024

Paragangliomas originating from blood vessels are exceptionally rare, presenting diagnostic challenges due to their histological resemblance to other vascular neoplasms. We present a case study of a 60-year-old woman with underlying hypertension and dyslipidemia with obesity, initially diagnosed with angiosarcoma based on imaging and histological characteristics viewed via CT-guided biopsy. Intraoperative exploration revealed a lobulated tumor located between the inferior vena cava (IVC) and aorta measuring 7 cm × 8 cm, during which the patient developed transient hemodynamic instabilities. Histopathological examination and immunohistochemical staining using neuroendocrine markers (chromogranin, synaptophysin, S-100 protein, and CD-56) later confirmed the tumor as a retroperitoneal paraganglioma. Retroperitoneal paraganglioma was initially misdiagnosed as angiosarcoma due to the overlapping imaging characteristics between the two tumors. This highlights the importance of raising suspicion on the possibility of retroperitoneal paraganglioma when imaging examination indicates angiosarcoma and to incorporate histopathological examination and immunohistochemistry in the diagnosis to avoid misdiagnosis.