bluuebunny/crossref_metadata_2025_split huggingface dataset:
A novel isothermal whole genome sequencing approach for Monkeypox Virus
Authors: Licheri Matthias , Licheri Manon Flore , Probst Lukas , Sägesser Cora , Bittel Pascal , Suter-Riniker Franziska , Dijkman Ronald 
Published: March 2024

Abstract

Monkeypox virus (MPXV) is the zoonotic agent responsible for mpox, an often-self-limiting pox-like disease. Since May 2022, an outbreak characterized by increased human-to-human transmission was detected outside the endemic regions. Whole genome sequencing (WGS) has been successfully used to keep track of viral evolution during outbreaks or for surveillance of multiple pathogens of public health significance. Current WGS protocols for MPXV are either based on metagenomic sequencing or tiled-PCR amplification. The latter allows multiplexing due to the efficient enrichment of the viral DNA, however, mutations or the presence of different clades can negatively influence genome coverage yield. Here, we present the establishment of a novel isothermal WGS method for MPXV based on Phi29 DNA polymerase-based multiple displacement amplification (MDA) properties making use of only 6 primers. This approach yielded from 88% up to 100% genome coverage using either alkaline denatured extracted DNA or clinical material as starting material, with the highest coverage generated by clinical material. We demonstrate that this novel isothermal WGS protocol is suitable for monitoring viral evolution during MPXV outbreaks and surveillance in any conventional laboratory setting.
Beyond the Diagnosis: Exploring the Psychosocial Impact of Drug-Resistant Tuberculosis on Patients in Norway
Authors: Storvig Eline , Harstad Ingunn , Ehrnström Birgitta , Iversen Valentina C. 
Published: March 2024

Abstract
Background: This study aims to explore the varied experiences of patients with resistant tuberculosis in Norway, particularly among immigrants. The study emphasizes challenges and implications of being diagnosed with resistant tuberculosis, including the impact of psychosocial health during the disease, treatment, isolation and recovery phases.
Norway is a low endemic country of tuberculosis. Most patients are immigrants and some have recently arrived in the country. Patients undergoing treatment for drug-resistant tuberculosis endure prolonged and demanding treatment that could affects their psychosocial health.
Methods: This qualitative research approach conducted 16 in-depth interviews with individuals diagnosed and completed treatment for resistant tuberculosis, aged 18 and above, mean age of 33.6. The majority of the participants were immigrants, and eight of them had resided in Norway for less than four years before diagnosis. Data analysis followed the six-phase reflexive thematic analysis framework outlined by Braun and Clarke
Results: The narratives of the participants highlighted the complexities of navigating the TB diagnosis, treatment, side effects and life after treatment. Immigrants encountered additional challenges, including language barriers and adapting to new social environments. All participants reported experiencing physical health issues which additionally affected their mental health and social activity. Many participants had persistent problems at the time of the interviews. Several participants expressed social isolation, and those with confirmed contagious pulmonary tuberculosis experienced hospital isolation up to six months. Three main themes emerged from the analysis: Delayed diagnosis despite seeking health care; Hospital isolation and social isolation; The life after tuberculosis. “They just think that I am healthy”.
Conclusion: This study highlights the enduring impact of DR-TB on patients, the significance of timely diagnosis, the challenges within healthcare services and the importance of psychosocial support. The participants universally faced serious implications of the disease, including stigma and isolation, alongside reflections on missed early intervention opportunities. The need for enhanced healthcare awareness, improved communication and post-treatment follow-up is underscored. Further research conducted in low endemic countries should evaluate the recommendations on psychosocial follow-up after introducing short-oral treatment.
Exploring the link between heart failure and cancer: insights into immune mechanisms and therapeutic targets for CD8 + T-cells
Authors: Zhou Ting , Pan Jing , Na Kun , Yuan Jing , Song Haixu , Han Yaling , Xu Kai 
Published: March 2024

Abstract

Background
Heart failure (HF) is a terminal condition of multiple cardiovascular disorders. Cancer is a highly prevalent and deadly disease worldwide. However, the relationship between HF and cancer remains poorly understood. Therefore, there is a critical need to explore the potential mechanisms and therapeutic targets shared between HF and cancer.
Method
The Gene Expression Omnibus (GEO) database was used to download the RNA sequencing (RNA-seq) data of 356 patients, including individuals with HF and those without HF, to establish a co-expression network using the weighted correlation network analysis (WGCNA) algorithm, to calculate the compositions of immune infiltrating cells in the CIBERSORT algorithm, and to identify candidate hub genes within the modules of individuals with HF. Pearson Correlation Analysis was employed to identify the correlation between hub genes and CD8+T-cells in HF, as well as between hub genes and both tumor mutation burden (TMB) and microsatellite instability (MSI) across cancers. Molecular biology experiments were conducted to confirm the correlation between the hub genes and HF. Finally, the NetworkAnalyst database and the CellMiner database were utilized to predict the transcription factors (TFs) and potential therapeutic drugs of hub genes, respectively.
Results
HF was significantly linked to immune response pathway by the analysis of Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG). The brown and blue modules, identified by WGCNA, were the primary modules related to CD8+T-cells. Concomitantly, we observed a positive correlation between the expression levels of the four hub genes and the infiltration of CD8+T-cells in pan-cancer. Additionally, western blotting and real-time polymerase chain reaction (RT-PCR) validated the high expression of three hub genes (GZMM, NKG7, and ZAP70) in both mice and patients with HF compared to those in the control group. Finally, the hub gene-associated TF-gene networks and 11 agents targeting the hub genes were successfully predicted.
Conclusion
Our study highlights the shared pathogenesis of HF and cancer and provides valuable insights for developing novel therapeutic strategies that target shared pathways, offering new opportunities for improving the management and treatment outcomes of both HF and cancer.
Investigation of molten pool geometry and flow field based on powder scale modeling in laser directed energy deposition
Authors: Liu Weiwei , Liu Huanqiang , Li Wanyang , Liu Bingjun , Ma Zongyu , Song Jianrong , Wang Tandong , Hu Guangda , Lyu Zhenxin , Zhang Yingzhong , Wang Fengtao , Zhang Hongchao 
Published: March 2024

Abstract

Laser directed energy deposition (LDED) technology is currently facing challenges in controlling geometry accuracy of metal components. There is an urgent need to develop a numerical model that is more efficient and accurate compared to existing models and to analyze the dynamic behavior of the melt pool under the interaction of process parameters during LDED process to optimize parameters with fewer experimental studies to reduce costs. Therefore, a 3D powder scale multi-physics model is proposed during the single track LDED process in this study. The powder particles are added by a Lagrangian particle model in this model without the need for assuming that the powder particles entering the molten pool are added by the mass source term, which improves model accuracy and efficiency. The effect of Energy per Unit Mass (EUM, J/g), Mass per Unit Length (MUL, g/mm) and standoff distance (SD, mm) intensities on transient molten pool motion and flow field are comprehensively investigated. It is discovered that the proposed model is able to predict the single track height, width, depth and dilution rate, or less than 9% relative error from experimentation, providing a useful tool for track geometry to predict. Further, the flow velocity, width and depth of melt pool also gradually are improved with higher EUM, MUL and SD intensity and fluctuates within a small range. However, the height is improved and then decreases with higher SD intensity, and is improved with higher EUM or MUL. Overall, this study contributes to developing an optimizing process approach to improve formation accuracy for LDED manufacturing.
Investigation of lemon as an admixture for Concrete work
Authors: Haile Natnael Alem , Ojha Laxmi Narayan , Khshen Zenagebriel Gebremedhn 
Published: March 2024

Abstract
The environmental impact of chemical admixtures on cement and concrete production and carbon emissions has gained attention. Hence, a study was conducted to assess the impact of locally available lemon juice on concrete workability, setting time, and compressive strength by comparing it to concrete with a commercial water-reducing and retarding admixture to improvecement properties, eliminate pollution, and reduce carbon emissions in cement concrete production. The tests were conducted with and without a lemon juice replacement. The experimental results revealed that the workability of the concrete increased in parallel with an increase in the percentage of lemon juice, up to 5%. The setting time results confirm that lemon juice acts as a retardant. The setting time was delayed by an increase in lemon juice of up to 5%. The dosage of 1.5% lemon juice resulted in a 5.2% increase in the compressive strength of the concrete. With the addition of lemon juice, the of the concrete decreased with an increase in the percentage of juice up to 5%. The cost comparison results showed that lemon juice has a lower cost than commercial admixtures. With lemon juices as admixtures, it was confirmed for the first time that they can be used for water-reducing and retarding admixtures at a reasonable cost at lower dosages; however, further research is needed to optimize the lemon juice dose to advance this approach on a pilot scale.
Single-cell Transcriptome Analysis Identifies Senescent Osteocytes as Contributors to Bone Destruction in Breast Cancer Metastasis
Authors: Delgado-Calle Jesus , Adhikari Manish , Kaur Japneet , Sabol Hayley , Anloague Aric , Khan Sharmin , Kurihara Noriyoshi , Diaz-delCastillo Marta , Andreasen Christina , Barnes C. Lowry , Stambough Jeffrey , Palmieri Michela , Reyes-Castro Olivia , Ambrogini Elena , Almeida Maria , O'Brien Charles , Nookaew Intawat 
Published: March 2024

Abstract
Breast cancer bone metastases increase fracture risk and are a major cause of morbidity and mortality among women. Upon colonization by tumor cells, the bone microenvironment undergoes profound reprogramming to support cancer progression that disrupts the balance between osteoclasts and osteoblasts, leading to bone lesions. Whether such reprogramming affects matrix-embedded osteocytes remains poorly understood. Here, we demonstrate that osteocytes in breast cancer bone metastasis develop premature senescence and a distinctive senescence-associated secretory phenotype (SASP) that favors bone destruction. Single-cell RNA sequencing identified osteocytes from mice with breast cancer bone metastasis enriched in senescence and SASP markers and pro-osteoclastogenic genes. Using multiplex in situ hybridization and AI-assisted analysis, we detected osteocytes with senescence-associated distension of satellites, telomere dysfunction, and p16Ink4a expression in mice and patients with breast cancer bone metastasis. In vitro and ex vivo organ cultures showed that breast cancer cells promote osteocyte senescence and enhance their osteoclastogenic potential. Clearance of senescent cells with senolytics suppressed bone resorption and preserved bone mass in mice with breast cancer bone metastasis. These results demonstrate that osteocytes undergo pathological reprogramming by breast cancer cells and identify osteocyte senescence as an initiating event triggering bone destruction in breast cancer metastases.
Cerebral venous thrombosis and deep medullary vein thrombosis: Padua experience over the last two decades
Authors: Cavicchiolo Maria Elena , Brigiari Gloria , Nosadini Margherita , Pin Jacopo Norberto , Vincenti Arianna , Toldo Irene , Ancona Claudio , Simioni Paolo , D'Errico Ignazio , Baraldi Eugenio , Sartori Stefano 
Published: March 2024

Abstract

Background: Cerebral venous thrombosis (CVT) is a cerebrovascular disorder that constitutes 20% of perinatal strokes. The incidence of CVT ranges from 0.67 to 1.12 per 100,000 newborns, while the incidence of "deep medullary vein thrombosis" (DMVT), a subtype of CVT, cannot be accurately estimated. This study aims to analyze the case history of CVT in the neonatal period, with a specific focus on DMVT.
Materials and Methods: Newborns diagnosed with CVT, with or without DMVT, between January 2002 and April 2023, were collected using the Italian Registry of Infantile Thrombosis (RITI), a national thrombosis registry. Cerebral MRIs were reviewed by an expert neuroradiologist following a standardized protocol.
Results: Forty-two newborns with CVT were identified, of which 27/42 (64%) had CVT without DMVT, and the remaining 15/42 (36%) had DMVT (isolated DMVT in 9/15, DMVT associated with CVT in another localization in 6/15). Symptom onset occurred in the first week of life (median 8 days, IQR 4-14) with a male prevalence of 59%. The most common risk factors were complicated delivery in 38% of cases, prematurity in 40% of all patients, congenital heart diseases (48%), and infections (40% of newborns). Seizures were the predominant presenting symptom in 52% of all cases. Hemorrhagic infarction was higher in cases with isolated DMVT compared to patients with CVT without DMVT (78% vs. 11%, p=0.013). Antithrombotic treatment was initiated in 30% of the total, and admission to the NICU was required in 87% of patients with isolated DMVT. Neurological impairment was observed in 48% of cases at discharge.
Conclusions: Our study investigates a CVT, a rare subtype of perinatal stroke, showing that DMVT occurs in over a third of neonates with CVT. Multicentric studies are essential to establish standardized protocols for therapy, neuroimaging, and follow-up in these patients.
No difference in 6-month functional outcome between early and late decompressive craniectomies following acute ischaemic stroke in a national neurosurgical centre: A single centre retrospective case-cohort study
Authors: Nesa Adina S , Gormley Conor , Read Christopher , Power Sarah , O’Brien Donncha , Herlihy Darragh , Boyle Karl , Larkin Caroline M 
Published: March 2024

Abstract
Background
Decompressive craniectomies (DCs) are recommended for the treatment of refractory raised intracranial pressure following acute ischaemic stroke. Some studies have demonstrated improved survival and functional outcomes post early decompressive craniectomy (<48 hours from ictus) in patients who developed malignant cerebral oedema post middle cerebral artery infarction. Limited data is available on the role of suboccipital decompressive craniectomy following cerebellar infarction.
Objective
Our primary objective was to determine whether timing of decompressive craniectomy (DC) influenced functional outcome at 6 months. Our secondary objectives were to analyse whether age, gender, the territory of stroke or preceding thrombectomy impacts functional outcome post DC.
Methods
We conducted a retrospective study of patients admitted between January 2014 and December 2020 who had DCs post acute ischaemic stroke. Data was collected from the ICU electronic records, individual patient medical charts and the stroke database. DCs occurring within 48 hours of stroke were classified as “early”, and after 48 hours, were classified as “late”.
Results
Twenty-six patients had early DC (19 anterior/7 posterior) and 21 patients had late DC (17 anterior/4 posterior). There were no statistically significant differences in age, sex, territory of stroke and NIHSS score between the two groups. There was no difference in the mRS score of the two groups at 90 (p=0.318) and 180 (p=0.333) days post early vs late DC. Overall outcomes were poor, with 5 out of 46 patients (10.9%) having a mRS score £ 3 at six months. There was no difference in mRS scores between the patients that had hemicraniectomies for anterior circulation stroke (n=35) and those that had suboccipital DC for posterior circulation stroke (n=11) (p=.594).
Conclusion
In this single centre retrospective study, functional outcomes at six months were poor among patients with DC post ischaemic stroke. There was no significant difference in functional outcomes between patients with early versus late DC after stroke.
Quality of Life in Children at Different Stages of Chronic Kidney Disease in a Developing Country
Authors: Chaichana Urapee , Jantongsree Maturin , Chantaratin Sasitorn , Sumboonnanonda Achra , Pattaragarn Anirut , Supavekin Suroj , Piyaphanee Nuntawan , Lomjansook Kraisoon , Thunsiribuddhichai Yarnarin , Tinnabut Intraparch , Chaiyapak Thanaporn 
Published: March 2024

Abstract

Background: Children with chronic kidney disease (CKD) require comprehensive assessments, including medical and quality of life (QoL) evaluations. Few studies have been conducted in developing countries.
Methods: This cross-sectional study included 2–18-year-old patients who were categorized into 4 groups: the CKD stage 2–3, stage 4–5, stage 5 with dialysis (D), and kidney transplantation (KT) groups. QoL was measured using the Pediatric Quality of Life InventoryTM (PedsQLTM) version 4.0; relationships between different factors and QoL were determined using multivariable linear regression analysis.
Results: Eighty-seven patients (mean age: 13.3 (4.1) years) were included. The self-reported total scores were 77.5 (12.5), 78.9 (11.2), 77.4 (16.2), and 76.1 (10.9) in the stage 2-3, stage 4-5, stage 5D and KT groups, respectively. Parent-reported scores showed a weak-to-moderate correlation with self-reported scores (r=0.12-0.42), with total scores of 71.8 (12.7), 69.5 (14.9), 63.4 (14.8), and 70.8 (18.1) in the stage 2-3, 4-5, 5D and KT groups, respectively. Multivariable linear regression revealed that the parent-reported score in the stage 5D group was 15.92 points lower than that in the early CKD stage group (p=0.02); the score in the low maternal education group was 10.13 points lower than that in the high maternal education group (p=0.04).
Conclusions: Parent-reported scores showed weak-to-moderate correlation with self-reported scores. CKD stage 5D patients and patients with low maternal education had lower QoL. Regular QoL assessment is recommended for advanced CKD patients and patients with socioeconomic vulnerabilities.
Validity and Reliability of Persian Version of Low Physical Activity Questionnaire (LoPAQ)
Authors: Tabibi Mohammad Ali , Samouei Rahele , Salimian Nasrin , Shahidi Shahrzad , Atapour Abdolamir , Nazemi Farzad , Ghenaat Mahsa , Nikbakht Saghar , Sarbazi Mahboobeh Hoseini , Soleymany Mahsa , Roshanaeian Zahra , Khajeheian Behnaz , Khaki Zahra , Sokani Ali Sadeghi , Ebrahimi Reyhane , Ahmadi Saghar 
Published: March 2024

Abstract
Background
The Low Physical Activity Questionnaire (LoPAQ) was specifically developed to measure the low activity level observed in extremely inactive hemodialysis (HD) patients. This study aims to evaluate reliability and validity of Persian version of the LoPAQ.
Methods
This study was a cross sectional study, conducted in three HD centers in Iran. The LoPAQ was translated into Persian. After cultural adaptions, it was filled out by 120 HD patiens. Convergent validity, was evaluated by calculating the correlations among the Persian version of the LoPAQ and Persian version of the Community Healthy Adults Model Program for Seniors (CHAMPS) questionnaire, physical function scale of the SF-36 and physical function (Short Physical Performance Battery (SPPB) test) using Spearman's correlation coefficients. The test-retest
reliability was analyzed using the intraclass correlation coefficient (ICC).
Results
In total, 109 patients completed all of the questionnaires, took part in physical performance tests and had valid data. Their mean age was 64 ± 11 years, with a dialysis history of 31 ± 10 months. For total calories, there was a strong correlation between the Persian version of the LoPAQ and CHAMPS-measured physical activity (rho = 0.85, p < 0.001). In addition, the higher physical activity level reported by Persian version of the LoPAQ was also correlated with better self-reported physical function (rho = 0.7, p < 0.001) and better physical performance (rho = 0.67, p < 0.001). The ICC ranged from 0.65 to 0.78, indicating strong reliability.
Conclusion
The assessment of the validity and reliability of the Persian version of the questionnaire confirmed its suitability for evaluating the level of physical activity.
Trial registration
ClinicalTrials.gov Identifier: NCT05930964, Registered on 05/07/2023. Registered trial name: Validity and Reliability of Persian Version of Low Physical Activity Questionnaire (LoPAQ)
Modeling Deficit Irrigation Water Demand of Maize and Potato in Eastern Germany using ERA5-Land Reanalysis Climate Time Series
Authors: Ogunsola Olawale Q. , Bankole Abayomi O. , Soboyejo Lukman A. , Adejuwon Joseph O. , Makinde Akeem A. 
Published: March 2024

Abstract
ERA5-Land reanalysis (ELR) climate time series has proven useful in (hydro)meteorological studies, however, its adoption for local studies is limited due to accuracies constraints. Meanwhile, local agricultural use of ELR could help data-scarce countries by addressing gaps in (hydro)meteorological variables. This study aimed to evaluate the first applicability of the ELR climate time series for modeling maize and potato irrigation water demand (IWD) at field scale and examined the performance of ELR precipitation with bias correction (DBC) and without bias correction (WBC). Yield, actual evapotranspiration (ETa), irrigation, water balance, and crop water productivity (CWP) were evaluated using the deficit irrigation toolbox. The study found that maize (13.98–14.49 ton/ha) and potato (6.84–8.20 tons/ha) had similar mean seasonal yield under different irrigation management strategies (IMS). The Global Evolutionary Technique for OPTimal Irrigation Scheduling (GET-OPTIS_WS) IMS had the highest mean seasonal yields under DBC and WBC, while rainfall and constant IMS had the most crop failures. DBC had a higher mean seasonal ETa than WBC, except for the potato FIT and rainfall IMS. Global Evolutionary Technique for OPTimal Irrigation Scheduling: one common schedule per crop season (GET-OPTIS_OS) and GET-OPTIS_WS IMS outperformed conventional IMS in IWD by 44%. Overall, GET-OPTIS_OS and GET-OPTIS_WS performed best for maize and potato CWP in terms of IWD, scheduling, and timing. Therefore, adoption of ELR climate time series and advanced irrigation optimization strategies such as GET-OPTIS_OS and GET-OPTIS_WS can be beneficial for effective and efficient management of limited water resources, where agricultural water allocation/resource is limited.