bluuebunny/crossref_metadata_2025_split huggingface dataset:
Uncovering the transcriptional landscape of Fomes fomentarius during fungal-based material production through gene co-expression network analysis
Authors: Cairns Timothy , Freidank-Pohl Carsten , Birke Anna Sofia , Regner Carmen , Jung Sascha , Meyer Vera 
Published: February 2025

Abstract

Background
Fungal-based composites have emerged as renewable, high-performance biomaterials that are produced on lignocellulosic residual streams from forestry and agriculture. Production at an industrial scale promises to revolutionize the world humans inhabit by generating sustainable, low emission, non-toxic and biodegradable construction, packaging, textile, and other materials. The polypore Fomes fomentarius is one of the basidiomycete species used for biomaterial production, yet nothing is known about the transcriptional basis of substrate decomposition, nutrient uptake, or fungal growth during composite formation. Co-expression network analysis based on RNA-Seq profiling has enabled remarkable insights into a range of fungi, and we thus aimed to develop such resources for F. fomentarius.

Results
We analysed gene expression from a wide range of laboratory cultures (n = 9) or biomaterial formation (n = 18) to determine the transcriptional landscape of F. fomentarius during substrate decomposition and to identify genes important for (i) the enzymatic degradation of lignocellulose and other plant-based substrates, (ii) the uptake of their carbon monomers, and (iii) genes guiding mycelium formation through hyphal growth and cell wall biosynthesis. Simple scripts for co-expression network construction were generated and tested, and harnessed to identify a fungal-specific transcription factor named CacA strongly co-expressed with multiple chitin and glucan biosynthetic genes or Rho GTPase encoding genes, suggesting this protein is a high-priority target for engineering adhesion and branching during composite growth. We then updated carbohydrate activated enzymes (CAZymes) encoding gene annotation, used phylogenetics to assign putative uptake systems, and applied network analysis to predict repressing/activating transcription factors for lignocellulose degradation. Finally, we identified entirely new types of co-expressed contiguous clusters not previously described in fungi, including genes predicted to encode CAZymes, hydrophobins, kinases, lipases, F-box domains, chitin synthases, amongst others.

Conclusion
The systems biology data generated in this study will enable us to understand the genetic basis of F. fomentarius biomaterial formation in unprecedented detail. We provided proof-of-principle for accurate network-derived predictions of gene function in F. fomentarius and generated the necessary data and scripts for analysis by any end user. Entirely new classes of contiguous co-expressed gene clusters were discovered, and multiple transcription factor encoding genes which are high-priority targets for genetic engineering were identified.
Serum magnesium level in a sample of Egyptian patients with major depressive disorder: cross-sectional study
Authors: Okasha Tarek Ahmed , Elserafi Doha Mostafa , Naguib Rehab Mohamed , Abdelhadi Mariam Abdelhamid , Dessouki Nahla Abdel Rahim 
Published: February 2025

Abstract

Background
Major depressive disorder (MDD) is a prevalent mental health condition that manifests as profound emotional disturbances and considerable functional deficits. Magnesium (Mg), a vital mineral, plays a recognized role in numerous neuropsychiatric conditions, including depressive disorders. Nonetheless, the association between circulating Mg concentrations and MDD within the Egyptian demographic has yet to be definitively elucidated. This study aimed to evaluate serum Mg levels in MDD patients, assess their correlation with depression severity, and explore the diagnostic utility of serum Mg.

Results
The study included 30 newly diagnosed MDD patients and 30 healthy controls. Serum Mg levels were significantly lower in MDD patients (1.880 ± 0.190 mg/dL) compared to controls (1.996 ± 0.169 mg/dL, p = 0.015). An inverse relationship of notable strength was identified between serum magnesium concentrations and the severity of depressive symptoms, quantified using the Hamilton Depression Rating Scale (Ham-D17) (r = − 0.592, p = 0.001). ROC curve analysis determined a serum Mg threshold of ≤ 1.8 mg/dL, yielding sensitivity and specificity rates of 46.7% and 80.0%, respectively, with an overall diagnostic accuracy of 67%.

Conclusions
A notable reduction in serum Mg levels was identified in individuals with MDD relative to healthy controls, and these levels correlated inversely with depression severity. Serum Mg may serve as a potential biomarker for MDD and its severity.
The Zweymüller primary stem is a reliable, effective, and less invasive implant in revision hip arthroplasty for Paprosky type I and II defects
Authors: Battaglia Antonino G. , D'Apolito Rocco , Ding Benjamin T. K. , Tonolini Stefano , Ramazzotti Joil , Zagra Luigi 
Published: February 2025

AimsRevision hip arthroplasty for femoral stem loosening remains challenging due to significant bone loss and deformities requiring specialized revision stems. The aim of this study was to evaluate the clinical and radiological outcomes, and survival, of a consecutive series of femoral revisions performed using a primary cementless stem with tapered geometry and rectangular cross-section at medium-term follow-up.MethodsWe retrospectively evaluated 113 patients (115 hips) with intraoperative Paprosky type I (n = 86) or II (n = 29) defects, who underwent femoral revision with Alloclassic Zweymüller SL stem for one-stage aseptic revision or two-stage septic revision from January 2011 to December 2020. The mean follow-up was 77.9 months (SD 33.8). Nine patients were lost to follow-up (deceased or not available), leaving 104 patients (106 hips) for the clinical and radiological analysis. Clinical assessment was performed with Harris Hip Score (HHS) and visual analogue scale (VAS) before surgery and at final follow-up.ResultsThere were 60 males and 53 females with a mean age at time of surgery of 71.2 years (SD 12.6). The mean HHS and VAS significantly improved at final follow-up, from 33.7 (SD 13.0) and 5.8 (SD 1.8) preoperatively to 66.4 (SD 16.8) and 2.1 (SD 1.8) postoperatively, respectively (p = 0.001 and p = 0.001). Overall, 28 patients (25%) showed non-progressive radiolucent lines at the level of proximal femur without radiological or clinical signs of loosening. One patient had a recurrence of periprosthetic joint infection after a two-stage procedure requiring re-revision surgery. One patient underwent exchange of modular components for recurrent dislocation, and another case of dislocation was treated conservatively. The survival with aseptic loosening as endpoint was 100%, while stem revision for any reason was 99.1% at up to 152 months’ follow-up.ConclusionAlloclassic Zweymüller SL primary stem showed favourable medium-term results and survival for revision total hip arthroplasty in Paprosky type I and II defects.Cite this article: Bone Jt Open 2025;6(2):186–194.
El apego, la comunicación y las finanzas como factores que explican la satisfacción marital
Authors: Cabrera-García Victoria Eugenia , Docal-Millán María del Carmen , Bermúdez-Orjuela Jerson Fabián , Mondragón-Rubiano Leisy , Chica-Guzmán Martha Lucía 
Published: February 2025

Introducción: Las relaciones maritales son fundamentales en la consolidación de la familia y el bienestar de todos sus miembros, la satisfacción marital es la variable que más peso tiene en la explicación de la estabilidad marital.
Objetivos: Analizar las diferencias en la satisfacción marital, los estilos de apego, los estilos de comunicación y el manejo de las finanzas, de acuerdo con el sexo de los cónyuges, el tipo de vínculo y el tiempo de convivencia. Conocer la correlación entre los estilos de apego, los estilos de comunicación y el manejo de las finanzas con la satisfacción marital. Explicar la satisfacción marital desde los estilos de apego, la comunicación y el manejo de las finanzas.Método: Estudio cuantitativo, de tipo transversal, descriptivo, correlacional. De 266 participantes, 82 hombres y 184 mujeres de nacionalidad colombiana. Como batería de instrumentos se utilizó: la Escala de Satisfacción de la Pareja (ESP-10), Experiencias en Relaciones Cercanas (ECR), Escala de Estilos de Comunicación Marital y Escala de comportamiento de gestión financiera (FMBS).
Resultados: Las variables que mejor explican la satisfacción marital en orden de relevancia son: la evitación (inversa), la percepción del estilo de comunicación positivo de la pareja y, el estilo de comunicación violento propio (inversa), es decir, cuando una persona evita estar cerca de su pareja y se comunica de forma violenta, la satisfacción marital tiende a ser baja; en contraste, la satisfacción marital tiende a ser alta cuando la persona percibe un estilo de comunicación positivo, abierto y agradable en su relación.

Conclusión: Es pertinente adelantar acciones de promoción de la satisfacción marital que aborden estilos de comunicación positivos y trabajen en la prevención de estilos de comunicación violentos, donde se evidencien comportamientos de evitación.
Peningkatan Pengetahuan Pasien terkait Pil KB di Poli Kandungan RSUD Ulin Banjarmasin
Authors: Tangkas Hansel Hens , Rizal Ahmad , Hadiastuti Adinda Dwina , Rapi'ah Rizka , Intannia Difa , Yulianti Mawar Dwi 
Published: February 2025

Permasalahan utama kependudukan di Indonesia meliputi persebaran penduduk yang tidak merata dan jumlah penduduk yang besar dengan laju pertumbuhan penduduk yang relatif tinggi. Untuk mengatasi masalah ini, pemerintah mengeluarkan program Keluarga Berencana (KB). Ketidakpatuhan pasien dalam mengonsumsi pil KB akan menyebabkan kegagalan dari program KB tersebut. Oleh sebab itu, tujuan dari kegiatan ini untuk memaksimalkan efektivitas penggunaan pil KB pada pasien di RSUD Ulin. Metode yang digunakan pada promosi kesehatan ini yaitu media cetak berupa leaflet dan penjelasan langsung kepada masyarakat yang sedang menunggu antrean pemeriksaan. Sampel pada kegiatan promosi kesehatan ini adalah pasien Poli Kandungan yang berobat ke RSUD Ulin pada Senin, 1 September 2024. Rata-rata nilai pretest sebesar 91% dan nilai posttest sebesar 100% yang menunjukkan terdapat peningkatan pengetahuan dan pemahaman responden dengan adanya peningkatan persentase rata-rata benar sebesar 9%. Oleh karena itu kegiatan promosi kesehatan yang dilakukan di Poli Kandungan RSUD Ulin meningkatkan pengetahuan responden mengenai Pil KB. Kegiatan promosi kesehatan yang dilakukan diharapkan dapat mengubah perilaku pasien untuk semakin rutin meminum pil KB dan pasien meyakini bahwa pil KB aman untuk dikonsumsi secara rutin. Kata Kunci: Edukasi, Cara Pakai, Keamanan, Kontrasepsi, Promosi Kesehatan The main population problems in Indonesia include uneven population distribution and a large population. To overcome this problem, the government issued a family planning program. Patient's non-compliance in taking birth control pills will lead to the failure of the birth control program. Therefore, the purpose of this activity is to maximize the effectiveness of the use of birth control pills in patients at RSUD Ulin. The methods used in this health promotion are printed media in the form of leaflets and direct explanation to the public. The samples in this health promotion activity were Gynecology Poly patients RSUD Ulin on Monday, September 1, 2024. The average pretest score was 91% and the posttest score was 100% which showed that there was an increase in the knowledge and understanding of respondents with an increase in the average percentage correct by 9%. Therefore, health promotion activities carried out at the RSUD Ulin, Gynecology Clinic increased respondents' knowledge about birth control pills. The health promotion activities carried out are expected to change the patient's behavior to be more routine in taking birth control pills and the patient believes that birth control pills are safe for routine consumption.
A Machine Learning Approach for Early Parkinson's Disease Diagnosis Based on Brain Texture Features from T1-Weighted Imaging
Authors: Xu Yuhua , Feifan Zhou , Gao Qianqian , Ma Yazhou , Chen Xin , Li Dong , Lian Xuegan 
Published: February 2025

Abstract

This study presents an early diagnostic method for Parkinson’s disease using T1-weighted imaging texture features combined with machine learning models. T1-weighted imaging data from the PPMI database were preprocessed to extract texture features from various brain regions,including the thalamus, hippocampus, caudate nucleus, amygdala, globus pallidus and putamen. The Random Forest (RF) model demonstrated excellent performance in distinguishing Parkinson’s patients from healthy controls, achieving an AUC of 0.90, accuracy of 88.9%, precision of 92.3%, sensitivity of 92.3%, specificity of 80.0%, and an F1 score of 92.3%. A simplified RF model also exhibited strong performance with a prediction accuracy of 77.8%. This method effectively leverages brain texture features to assist in the early diagnosis of Parkinson’s disease.
DoseTAIlor: A Web-Based Platform for Personalised Tacrolimus Dose Optimisation Across Multi-Centre Populations Using Interpretable AI
Authors: Abdalla Youssef , Gongas Laura , Castro Brais Muñiz , Cela Luis Ramudo , Suárez Francisco , Orlu Mine , Margusino-Framiñán Luis , Basit Abdul W. , Shorthouse David , Goyanes Alvaro 
Published: February 2025

Abstract

Tacrolimus, commonly used after organ transplantation, has a narrow therapeutic index (NTI) and a high risk of dosing errors, with over 50% of patients suffering serious, potentially life-threatening adverse effects. To address this, we developed an interpretable long short-term memory (LSTM) model trained on 14 years of data from 1,774 patients across Spain and the United States. This LSTM predicts tacrolimus levels using clinical data, with approximately 5% mean absolute error, outperforming state-of-the-art models. Addressing data privacy concerns, we demonstrate that synthetic data can replace real data for training without performance loss. Finally, we launched dosetailor.com, a platform providing personalised tacrolimus dosing recommendations for clinicians. Although focused on tacrolimus, this platform forms a foundation for personalising dosage for high-risk, NTI drugs.
Reevaluating the Association between Type 1 Diabetes and Polycystic Ovary Syndrome: Insights from Two-Sample Mendelian Randomization
Authors: Zhu San , Zhu Manman , Zhang Yaoyao 
Published: February 2025

Abstract

Polycystic ovary syndrome (PCOS) is one of the most common heterogeneous endocrine disorders among women of reproductive age. PCOS and its related traits are frequently observed in women with type 1 diabetes (T1DM), but the exact association between T1DM and PCOS remains unclear. We conducted a two-sample Mendelian randomization (MR) study to explore the causal association between genetically predicted T1DM and PCOS risk in individuals of European ancestry. We selected 31 single nucleotide polymorphisms (SNPs) as instrumental variables (IVs) for T1DM (exposure data) and obtained outcome data from the newest and largest published genome-wide association study (GWAS) of Europeans, which includes 24840 participants to date. Our results demonstrate that strict T1DM (excluding T2DM) might not result in a higher risk of PCOS genetically in Europeans (odds ratio (OR) = 1.024, 95% confidence interval (CI) = 0.975–1.074, p = 0.347). Moreover, we did not observe heterogeneity or pleiotropy in our study. Our results indicate that T1DM itself might not explain the relatively high prevalence of PCOS in women; adequately powered studies are needed to explore the mechanisms behind the frequent association of PCOS with T1DM and its possible effect on the health of patients.
Is Complement C3 a Reliable Indicator of Endometriosis Severity? Insights from a Retrospective Study
Authors: Guo Yuyan , Huang Penghui , Zhang Jinna , Liu Chaobin , Xie Xi , Wang Zhenna , Lin Yan , Lin Guan , Lin Shunhe 
Published: February 2025

Abstract

Objective
This study evaluates the potential of complement C3 as a predictive biomarker for endometriosis severity and examines its correlation with clinical features and biochemical markers.
Methods
In this retrospective analysis, 82 women diagnosed with endometriosis were classified into severe and minimal-to-moderate groups based on revised American Society for Reproductive Medicine (rASRM) scores. Peripheral blood samples were analyzed for complement components (C3, C4), tumor markers (CA125, CA199), and other biochemical indices.
Results
Patients with severe endometriosis exhibited significantly higher frequencies of dysmenorrhea, larger cyst dimensions, and elevated serum levels of complement C3, CA125, and triglycerides compared to those with less severe disease (p < 0.05). Notably, complement C3 and CA125 levels were strongly correlated with disease severity, highlighting their potential role in clinical assessment.
Conclusion
Complement C3 shows promise as a biomarker for assessing the severity of endometriosis. The integration of complement components into diagnostic and prognostic frameworks could facilitate earlier detection and the development of personalized therapeutic approaches for endometriosis.
Lianbinite, (NH4)(C2H3O3)(C2H4O3), a new glycolate mineral, from the Santa Catalina Mountains, Tucson, Arizona, USA
Authors: Yang Hexiong , Gu Xiangping , Lazar Warren , Gibbs Ronald B. , Downs Robert T. 
Published: February 2025

Abstract
A new organic mineral species, lianbinite, ideally (NH4)(C2H3O3)(C2H4O3), was discovered from the western end of Pusch Ridge in the Santa Catalina Mountains, north of Tucson, Arizona, USA. It occurs as bladed or acicular crystals, associated with baryte, fluorite, glecklerite, jarosite, jimkrieghite, quartz, and rasmussenite. Lianbinite is colorless, transparent with a white streak and vitreous luster. It is brittle and has a Mohs hardness of 1-1½; cleavage is perfect on {100}. No parting or twinning was observed. The calculated density is 1.497 g/cm3. The chemical composition of lianbinite was determined with a Thermo Finnigan DELTAplus XL Elemental Combustion System equipped with a mass spectrometer, yielding an empirical formula (N0.98H4.06)(C1.98H3O3)(C1.99H3O3), or N0.98C3.97H11.06O6, on the basis of 6 O apfu.
Lianbinite is the natural counterpart of synthetic (NH4)(C2H3O3)(C2H4O3), which is isostructural with synthetic K(C2H3O3)(C2H4O3) and Rb(C2H3O3)(C2H4O3). It is monoclinic with space group P21/c, and unit-cell parameters a = 3.91305(11), b = 18.7499(4), c = 10.7214(2) Å, β = 107.444(2)°, V = 750.45(3) Å3, and Z = 4. The crystal structure of lianbinite contains two forms of glycolate units: glycolate anions (GAs) and glycolic acid molecules (GMs). These two units are linked together by hydrogen bonds to form a three-dimensional network with two kinds of channels extending along [100]. The large channel is surrounded by O atoms, with (NH4)+ groups situated inside, whereas the small one is enclosed by H atoms. The discovery of lianbinite, together with other glycolate minerals documented thus far, namely domitrovicite, glecklerite, jimkrieghite, lazaraskeite, rasmussenite, and stanevansite, implies that glycolate minerals may be rather widespread in nature, thus serving as a potential reservoir for biologically-fixed carbon.
Growing smarter: a systematic review of the impact and challenges of climate information on farming
Authors: Madhuri  
Published: February 2025

ABSTRACT
Understanding the application and format of climate information services (CIS) can enhance forecast application skills. With the help of the systematic review method of 112 papers, the study assesses the format of forecast delivery to farmers, the anticipated values for farmers, and the integration of CIS integration into adaptation strategies. A significant surge in studies has emerged since 2010 and has been primarily driven by increased climate funding commitments in the developed world since 2009. The study explored adaptation strategies predominately in Africa and developed nations, with Asian nations following suit. While the value of CIS is evident in increasing yields and aiding decision-making, challenges such as the interpretation of forecasts and the adoption of anticipatory adaptation techniques remain. The research underscores the importance of understanding farmers' adaptation strategies and the need for targeted interventions to enhance resilience in agricultural systems facing climate change impacts.
Analyzing and Validating the Role of Genes Related to Glucagon-like Peptide-1 Signaling in the Prognosis of Pancreatic Cancer
Authors: Wang Anbin , Yang Hong , Zhu Yuming 
Published: February 2025

Aims:
We aimed to develop a reliable prognostic tool related to glucagon-like
peptide-1 (GLP-1) for guiding treatment of pancreatic cancer (PC).

Background:
The treatment strategies for PC being greatly advanced the prognosis of
cancer still remains unfavorable.

Objective:
To develop a RiskScore model for evaluating PC prognosis.

Method:
The bulk RNA-seq data of PC patients were obtained from the UCSCXena and
GEO database, and the GSE156405 cohort was used for single-cell RNA-seq (scRNA-
seq) analysis in the “Seurat” package. Firstly, the gene expression and mutation in
the PC samples were analyzed to perform differentially expressed genes (DEGs) analysis
using the “limma” package. The “survival” package was employed to conduct un/-
multivariate Cox regression and Kaplan-Meier (KM) survival analysis. Secondly, a
RiskScore model was developed and assessed using the “glmnet” and “timeROC” packages.
Next, the CIBERSORT algorithm and the ssGSEA method were applied for immune
infiltration analysis and calculation of the immune cell scores, respectively. Finally,
pathway enrichment analysis was conducted using gene set enrichment analysis
(GSEA).

Results:
Most GLP-1 signaling genes were overexpressed in the PC samples with multiple
mutation types. LASSO analysis selected 3 GLP-1 genes for the development of a
RiskScore model with a high classification accuracy (AUC >0.6). Notably, high-risk patients
showed a significantly shorter survival time in both training and validation sets. In
addition, as an independent factor, the RiskScore was further used to establish a nomogram
model for the survival prediction of PC in clinical practice. The tumor microenvironment
(TME) analysis revealed that low-risk patients with more abundant immune
and stroma components had higher levels of anti-tumor immune cell infiltration (such as
activated B and T cells), while the proliferation pathways (E2F targets, G2M checkpoint)
were significantly activated in the high-risk groups. The genes in the RiskScore model
may affect the survival of PC patients through modulating the activities of NK cells and
macrophages.

Conclusion:
We demonstrated that the GLP-1 signaling affected PC development and
developed a reliable RiskSocre model for the prognosis assessment in PC. Our findings
are expected to improve PC diagnosis and treatment in clinical practice.