bluuebunny/crossref_metadata_2025_split huggingface dataset:
Prediction of asthma using a four-locus gene model including IL13, IL4, FCER1B, and ADRB2 in children of Kazak nationality
Authors: Bai Shasha , Lu Jun , Hua Li , Liu Quanhua , Chen Mengxue , Gu Yutong , Zhang Jianhua , Ma Dongjun , Bao Yixiao 
Published: December 2023

Abstract
Background
To study whether the four locus gene model consisting of ADRB2 rs1042713, IL4 rs2243250, FCER1B rs569108 and L13 rs20541 can predict asthma of the Kazak children in Xinjiang, China.

Methods
Four single nucleotide polymorphisms about the 4 genes were genotyped in asthma group and control group of Han children and Kazak children respectively. The frequencies of different genotypes and alleles were compared between the asthma group and the control group in the two nationalities. Different risk genotypes for asthma were evaluated in the two nationalities.

Results
The differences about frequencies of genotypes in ADRB2 rs1042713 and IL4 rs2243250 and IL13 rs20541 between asthma group and control group were statistically significant in Han children, as were the frequencies of alleles in the 3 single nucleotide polymorphisms, but there were no statistical differences in FCER1B rs569108(P > 0.05). For the Kazak children, no differences were existed among all the genotypes and alleles in asthma group and control group. For the Han children, more children were asthma high risk genotype in the asthma group than those in the control group and no difference was found in the Kazak children.

Conclusions
The four locus gene model consisting of ADRB2 rs1042713, IL4 rs2243250, FCER1B rs569108 and L13 rs20541 can predict asthma of Han children but not for the Kazak children in Xinjiang, which illustrating that the difference of asthma prevalence between different races is closely related to the genetic background.
Haplotype-resolved assemblies and variant benchmark of a Chinese Quartet
Authors: Jia Peng , Dong Lianhua , Yang Xiaofei , Wang Bo , Bush Stephen J. , Wang Tingjie , Lin Jiadong , Wang Songbo , Zhao Xixi , Xu Tun , Che Yizhuo , Dang Ningxin , Ren Luyao , Zhang Yujing , Wang Xia , Liang Fan , Wang Yang , Ruan Jue , Xia Han , Zheng Yuanting , Shi Leming , Lv Yi , Wang Jing , Ye Kai 
Published: December 2023

Abstract
Background
Recent state-of-the-art sequencing technologies enable the investigation of challenging regions in the human genome and expand the scope of variant benchmarking datasets. Herein, we sequence a Chinese Quartet, comprising two monozygotic twin daughters and their biological parents, using four short and long sequencing platforms (Illumina, BGI, PacBio, and Oxford Nanopore Technology).

Results
The long reads from the monozygotic twin daughters are phased into paternal and maternal haplotypes using the parent–child genetic map and for each haplotype. We also use long reads to generate haplotype-resolved whole-genome assemblies with completeness and continuity exceeding that of GRCh38. Using this Quartet, we comprehensively catalogue the human variant landscape, generating a dataset of 3,962,453 SNVs, 886,648 indels (< 50 bp), 9726 large deletions (≥ 50 bp), 15,600 large insertions (≥ 50 bp), 40 inversions, 31 complex structural variants, and 68 de novo mutations which are shared between the monozygotic twin daughters. Variants underrepresented in previous benchmarks owing to their complexity—including those located at long repeat regions, complex structural variants, and de novo mutations—are systematically examined in this study.

Conclusions
In summary, this study provides high-quality haplotype-resolved assemblies and a comprehensive set of benchmarking resources for two Chinese monozygotic twin samples which, relative to existing benchmarks, offers expanded genomic coverage and insight into complex variant categories.
Optic nerve sheath diameter measurement for the paediatric patient with an acute deterioration in consciousness
Authors: Ali Ahmed , McCreary David J. 
Published: December 2023

AbstractOcular Point of Care Ultrasound (PoCUS) is emerging as a valuable utility within emergency medicine. Optic nerve sheath diameter (ONSD) has been demonstrated to correlate closely with intracranial pressure (ICP) and an elevated measurement can detect raised ICP readily, where fundoscopy may not, owing to both technical challenges and insufficient clinical skills. A previously fit and well 10-year-old girl presented to the paediatric emergency department with worsening headache, fever and lethargy. On examination, her left pupil was large, and not reactive to light. Initially, her GCS was 15 but suddenly dropped to 8/15. Her blood tests showed raised inflammatory markers. A CT head was reported as possible pansinusitis and MRI of her brain was initially reported as showing evidence of meningeal irritation only. Due to her drop in GCS PoCUS of optic nerve sheath was conducted which showed evidence of increased ICP with increased optic nerve sheath diameter of 6.8mm. This led to a reassessment of the MRI imaging by the neurosurgical team who felt there was evidence of subdural empyema. The patient was transferred to the tertiary neurosurgical centre, where an emergency evacuation of subdural empyema was carried out. Staphylococcus aureus and Streptococcus pyogenes were grown from pus samples. Early detection of raised ICP is of paramount importance in terms of being able to instigate neuroprotective measures and prevent adverse neurological outcomes. PoCUS is a readily available, non-irradiating, easily repeatable, well-tolerated and readily teachable ultrasound modality and a useful tool which should be employed in paediatric and adult emergency departments.
A multi-scale digital twin for adiposity-driven insulin resistance in humans: diet and drug effects
Authors: Herrgårdh Tilda , Simonsson Christian , Ekstedt Mattias , Lundberg Peter , Stenkula Karin G. , Nyman Elin , Gennemark Peter , Cedersund Gunnar 
Published: December 2023

Abstract
Background
The increased prevalence of insulin resistance is one of the major health risks in society today. Insulin resistance involves both short-term dynamics, such as altered meal responses, and long-term dynamics, such as the development of type 2 diabetes. Insulin resistance also occurs on different physiological levels, ranging from disease phenotypes to organ-organ communication and intracellular signaling. To better understand the progression of insulin resistance, an analysis method is needed that can combine different timescales and physiological levels. One such method is digital twins, consisting of combined mechanistic mathematical models. We have previously developed a model for short-term glucose homeostasis and intracellular insulin signaling, and there exist long-term weight regulation models. Herein, we combine these models into a first interconnected digital twin for the progression of insulin resistance in humans.

Methods
The model is based on ordinary differential equations representing biochemical and physiological processes, in which unknown parameters were fitted to data using a MATLAB toolbox.

Results
The interconnected twin correctly predicts independent data from a weight increase study, both for weight-changes, fasting plasma insulin and glucose levels, and intracellular insulin signaling. Similarly, the model can predict independent weight-change data in a weight loss study with the weight loss drug topiramate. The model can also predict non-measured variables.

Conclusions
The model presented herein constitutes the basis for a new digital twin technology, which in the future could be used to aid medical pedagogy and increase motivation and compliance and thus aid in the prevention and treatment of insulin resistance.
Coronavirus disease 2019 (COVID-19)-associated brain abscesses caused by Pseudomonas aeruginosa and Aspergillus fumigatus: two case and a review of the literature
Authors: Yassin Zeynab , Farid Armita , Ahmadi Sayedali , Emamikhah Maziar , Motamedi Omid , Jafari Mohammadamin , Goodarzi Azadeh 
Published: December 2023

Abstract
Background
Bacterial and fungal superinfections are commonly reported in patients with coronavirus disease 2019.

Case presentation
We report the first case of brain and intramedullary abscesses caused by Pseudomonas aeruginosa and a rare case of brain abscesses caused by Aspergillus fumigatus in two post-coronavirus disease 2019 patients. The first patient—34-year-old Iranian woman—presented with weakness of the left upper limb, headaches, and lower limb paresthesia. She had a history of undiagnosed diabetes and had received corticosteroid therapy. The second patient—45-year-old Iranian man—presented with right-sided weakness and had a history of intensive care unit admission. Both patients passed away despite appropriate medical therapy.

Conclusion
The immune dysregulation induced by coronavirus disease 2019 and its’ treatments can predispose patients, especially immunosuppressed ones, to bacterial and fungal infections with unusual and opportunistic pathogens in the central nervous system. Pseudomonas aeruginosa and Aspergillus fumigatus should be considered as potential causes of brain infection in any coronavirus disease 2019 patient presenting with neurological symptoms and evidence of brain abscess in imaging, regardless of sinonasal involvement. These patients should get started on appropriate antimicrobial therapy as soon as possible, as any delay in diagnosis or treatment can be associated with adverse outcomes.
Adhatoda vasica and Tinospora cordifolia extracts ameliorate clinical and molecular markers in mild COVID-19 patients: a randomized open-label three-armed study
Authors: Verma Mukta , Rawat Neha , Rani Ritu , Singh Manju , Choudhary Aditi , Abbasi Sarfaraz , Kumar Manish , Kumar Sachin , Tanwar Ankur , Misir Bishnu Raman , Khanna Sangeeta , Agrawal Anurag , Faruq Mohammed , Rai Shalini , Tripathi Richa , Kumar Anil , Pujani Mukta , Bhojani Meera , Pandey Anil Kumar , Nesari Tanuja , Prasher Bhavana 
Published: December 2023

Abstract
Background
SARS-CoV-2 infections caused mild-to-moderate illness. However, a sizable portion of infected people experience a rapid progression of hyper-inflammatory and hypoxic respiratory illness that necessitates an effective and safer remedy to combat COVID-19.

Methods
A total of 150 COVID-19-positive patients with no to mild symptoms, between the age groups 19–65 years were enrolled in this randomized, open-labeled three-armed clinical trial. Among them, 136 patients completed the study with RT-PCR negative reports. The patients received herbal drugs orally (Group A (Adhatoda vasica; AV; 500 mg; n = 50); Group B (Tinospora cordifolia; TC; 500 mg; n = 43), and Group C (AV + TC; 250 mg each; n = 43)) for 14 days. Clinical symptoms, vital parameters, and viral clearance were taken as primary outcomes, and biochemical, hematological parameters, cytokines, and biomarkers were evaluated at three time points as secondary outcomes.

Results
We found that the mean viral clearance time was 13.92 days (95% confidence interval [CI] 12.85–14.99) in Group A, 13.44 days (95% confidence interval [CI] 12.14–14.74) in Group B, and 11.86 days (95% confidence interval [CI] 10.62–13.11) days in Group C. Over a period of 14 days, the mean temperature in Groups A, and B significantly decreased linearly. In Group A, during the trial period, eosinophils, and PT/INR increased significantly, while monocytes, SGOT, globulin, serum ferritin, and HIF-1α, a marker of hypoxia reduced significantly. On the other hand, in Group B hsCRP decreased at mid-treatment. Eosinophil levels increased in Group C during the treatment, while MCP-3 levels were significantly reduced.

Conclusions
All the patients of the three-armed interventions recovered from COVID-19 and none of them reported any adverse effects from the drugs. Group C patients (AV + TC) resulted in a quicker viral clearance as compared to the other two groups. We provide the first clinical report of AV herbal extract acting as a modifier of HIF-1α in COVID-19 patients along with a reduction in levels of ferritin, VEGF, and PT/INR as the markers of hypoxia, inflammation, and thrombosis highlighting the potential use in progression stages, whereas the TC group showed immunomodulatory effects.
Trial registration Clinical Trials Database -India (ICMR-NIMS), CTRI/2020/09/028043. Registered 24th September 2020, https://www.ctri.nic.in/Clinicaltrials/pdf_generate.php?trialid=47443&EncHid=&modid=&compid=%27,%2747443det%27

Graphical Abstract
A Concise on the Effect of Calcium Oxide on the Properties of Alkali-Activated Materials: A Manual for Civil Engineers
Authors: Rashad Alaa M. 
Published: December 2023

AbstractAs known, calcium oxide (CaO) is an alkaline material, which can be used widely to increase the clay-containing soils load carrying capacity, to produce aerated concrete and calcium aluminate cement. In the last few years, introducing CaO into alkali-activated materials (AAMs) became a hot topic and attained more attention than other times. Generally, CaO can be incorporated into AAMs as an additive/a part of the main precursor and a sole activator without/with an auxiliary activator. Incorporating CaO into the matrices may improve some properties and worsen others. This mainly depends on the ratio of CaO, curing conditions, activator type and activator concentration, precursor type and testing age. This review collected, summarized and analyzed the available studies focused on the effect of CaO on the fresh (reaction kinetic, workability, setting time) and hardened (mechanical strength, durability and length change) properties of AAMs. In addition, some recommendations for future works were included. The results showed that the inclusion of CaO in AAMs decreased workability and setting time. In spite of there are contradictory results about the effect of CaO on the compressive strength of AAMs, most of them reported higher compressive strength, especially at the early ages. The incorporation of CaO up to 5% in the matrix is more effective than the incorporation of higher ratios. The inclusion of CaO in the matrix decreased water absorption, decreased total porosity, increased wetting/drying as well as acid attack resistivity. The CaO (5–10%) can be used as a sole activator for precursors. Auxiliary activators such as Al2(SO4)3, Na2CO3, Na2SiO3, Na2SO4, CaSO4, NaOH, Ca(NO3)2, NaNO3, Mg(NO3)2, Mg(HCOO)2, Ca(HCOO)2, SO3, gypsum and MgO can be used to enhance the compressive strength of CaO-activated materials, especially at the early ages.
Study on the structural stability of the blistering of the Vajrasana pagoda in Miaozhan Temple, Kunming, Yunnan, China
Authors: Li Bo , Zhang Yao , Bao Xun , Wang Yu , Zhang Ying , Cui Deshan , Guo Hong 
Published: December 2023

Abstract
The Vajrasana pagoda is the only stone overturned-bowl pagoda among the 12 existing Vajrasana pagodas built during the Ming Dynasty in the Guandu District, Kunming City, Yunnan Province, China. The location of the Vajrasana pagoda is in an earthquake-active zone with high rainfall. The small towers on the upper side were damaged by an earthquake in 1696 AD. All the stone statues representing religious figures have blistered and may peel further due to external factors, such as sunshine and rainfall. To assess the structural stability of the blistering, we employed 3D laser scanning to record the building’s geometry over time. Subsequently, X-ray diffraction, thin section identification, and uniaxial compressive strength tests were conducted on the pagoda stone to reveal physical–mechanical properties. Finally, a finite element model was constructed to analyze stress and displacement in various scenarios. The results revealed: (1) Blistering on the pagoda stone is secure under self-gravity and heavy rainfall. (2) In an earthquake, the upper blistering near the junction of two sides may break. (3) A 3D color deviation model of blistering over 8 months showed peeling and bursting within the finite element simulation's predicted range. This research offers a fresh approach to stone tower preservation, shifting from reactive measures to proactive prevention and prediction. These methods and concepts hold relevance for stone towers in similar high-rainfall and earthquake-prone regions.
Added value of regional 18F-FDG PET/MRI-assisted whole-body 18F-FDG PET/CT in malignant ascites with unknown primary origin
Authors: Fu Yiru , Ruan Weiwei , Sun Xun , Hu Fan , Lan Xiaoli , Liu Fang 
Published: December 2023

Abstract
Background
Comparing to PET/CT, integrative PET/MRI imaging provides superior soft tissue resolution. This study aims to evaluate the added value of regional delayed 18F-FDG PET/MRI-assisted whole-body 18F-FDG PET/CT in diagnosing malignant ascites patients.

Results
The final diagnosis included 22 patients with ovarian cancer (n = 11), peritoneal cancer (n = 3), colon cancer (n = 2), liver cancer (n = 2), pancreatic cancer (n = 2), gastric cancer (n = 1), and fallopian tube cancer (n = 1). The diagnosis of the primary tumor using whole-body PET/CT was correct in 11 cases. Regional PET/MRI-assisted whole-body PET/CT diagnosis was correct in 18 cases, including 6 more cases of ovarian cancer and 1 more case of fallopian tube cancer. Among 4 cases that were not diagnosed correctly, 1 case had the primary tumor outside of the PET/MRI scan area, 2 cases were peritoneal cancer, and 1 case was colon cancer. The diagnostic accuracy of regional PET/MRI-assisted whole-body PET/CT was higher than PET/CT alone (81.8% vs. 50.0%, κ 2 = 5.14, p = 0.023). The primary tumor conspicuity score of PET/MRI was higher than PET/CT (3.67 ± 0.66 vs. 2.76 ± 0.94, P < 0.01). In the same scan area, more metastases were detected in PET/MRI than in PET/CT (156 vs. 86 in total, and 7.43 ± 5.17 vs. 4.10 ± 1.92 per patient, t = 3.89, P < 0.01). Lesion-to-background ratio in PET/MRI was higher than that in PET/CT (10.76 ± 5.16 vs. 6.56 ± 3.45, t = 13.02, P < 0.01).

Conclusion
Comparing to whole-body PET/CT alone, additional delayed regional PET/MRI with high soft tissue resolution is helpful in diagnosing the location of the primary tumor and identifying more metastases in patients with malignant ascites. Yet larger sample size in multicenter and prospective clinical researches is still needed.
The genomes of Scedosporium between environmental challenges and opportunism
Authors: Venice Francesco , Spina Federica , Davolos Domenico , Ghignone Stefano , Varese Giovanna Cristina 
Published: December 2023

AbstractEmerging fungal pathogens are a global challenge for humankind. Many efforts have been made to understand the mechanisms underlying pathogenicity in bacteria, and OMICs techniques are largely responsible for those advancements. By contrast, our limited understanding of opportunism and antifungal resistance is preventing us from identifying, limiting and interpreting the emergence of fungal pathogens. The genus Scedosporium (Microascaceae) includes fungi with high tolerance to environmental pollution, whilst some species can be considered major human pathogens, such as Scedosporium apiospermum and Scedosporium boydii. However, unlike other fungal pathogens, little is known about the genome evolution of these organisms. We sequenced two novel genomes of Scedosporium aurantiacum and Scedosporium minutisporum isolated from extreme, strongly anthropized environments. We compared all the available Scedosporium and Microascaceae genomes, that we systematically annotated and characterized ex novo in most cases. The genomes in this family were integrated in a Phylum-level comparison to infer the presence of putative, shared genomic traits in filamentous ascomycetes with pathogenic potential. The analysis included the genomes of 100 environmental and clinical fungi, revealing poor evolutionary convergence of putative pathogenicity traits. By contrast, several features in Microascaceae and Scedosporium were detected that might have a dual role in responding to environmental challenges and allowing colonization of the human body, including chitin, melanin and other cell wall related genes, proteases, glutaredoxins and magnesium transporters. We found these gene families to be impacted by expansions, orthologous transposon insertions, and point mutations. With RNA-seq, we demonstrated that most of these anciently impacted genomic features responded to the stress imposed by an antifungal compound (voriconazole) in the two environmental strains S. aurantiacum MUT6114 and S. minutisporum MUT6113. Therefore, the present genomics and transcriptomics investigation stands on the edge between stress resistance and pathogenic potential, to elucidate whether fungi were pre-adapted to infect humans. We highlight the strengths and limitations of genomics applied to opportunistic human pathogens, the multifactoriality of pathogenicity and resistance to drugs, and suggest a scenario where pressures other than anthropic contributed to forge filamentous human pathogens.
‘Smart’ BLE wearables for digital contact tracing in care homes during the COVID-19 pandemic—a process evaluation of the CONTACT feasibility study
Authors: Thompson Carl A. , Daffu-O’Reilly Amrit , Willis Thomas , Gordon Adam , Noakes Catherine , Khaliq Kishwer , Farrin Amanda , Kemp Andrew , Hall Tom , Bojke Chris , Spilsbury Karen 
Published: December 2023

Abstract
Background
Rapid and mass transmission of the SARS-CoV-2 virus amongst vulnerable people led to devastating effects from COVID-19 in care homes. The CONTACT intervention introduced Bluetooth Low Energy ‘smart’ wearable devices (BLE wearables) as a basis for automated contact tracing in, and feedback on infection risks and patterns to, care homes to try and improve infection prevention and control (IPC). We planned a cluster randomised controlled trial (RCT) of CONTACT. To be feasible, homes had to adopt CONTACT’s technology and new ways of working. This paper reports on the process evaluation conducted alongside CONTACT’s feasibility study and explains why it lacked the feasibility and acceptability for a definitive RCT.

Methods
This mixed method process evaluation used Normalisation Process Theory (NPT) qualitative (interviews, field notes, study case report forms and documents, and observation) and quantitative (survey instruments, counts of activity) data to plan, implement, and analyse the mechanisms, effects, and contextual factors that shaped the feasibility and acceptability of the CONTACT intervention.

Results
Thirteen themes within four core NPT constructs explained CONTACT’s lack of feasibility. Coherence: the home’s varied in the scale and extent of commitment and understanding of the technology and study procedures. Leadership credibility was important but compromised by competing priorities. Management and direct care staff saw CONTACT differently. Work to promote (cognitive participation) and enact (collective action) CONTACT was burdensome and failed to be prioritised over competing COVID-19-related demands on time and scarce human and cognitive resources. Ultimately, staff appraisal of the value of CONTACT-generated information and study procedures (reflexivity) was that any utility for IPC was insufficient to outweigh the perceived burden and complexity involved.

Conclusions
Despite implementation failure, dismissing BLE wearables’ potential for contact tracing is premature. In non-pandemic conditions, with more time, better co-design and integration of theory-driven implementation strategies tailored to care homes’ unique contexts, researchers could enhance normalisation in readiness for future pandemic challenges.

Trial registration
ISRCTN registration: 11,204,126 registered 17/02/2021.