bluuebunny/crossref_metadata_2025_split huggingface dataset:
Infantile B-cell acute lymphoblastic leukaemia with the highest recorded count of white blood cells in the literature: case report and literature review
Authors: Asees Mohammad Y. , Shrateh Oadi N. , Assi Ayuob S. , Habbabeh Maysaa , Shiha Haneen Omar , Shakhsheer Shurouq 
Published: November 2023

Introduction:Infantile leukaemia is an uncommon haematological cancer that manifests within the first year of life. This malignancy is highly aggressive and possesses distinctive immunophenotypic, cytogenetic, and molecular attributes. It can originate from either myeloid or lymphoid cells. It often exhibits a higher incidence among females.Case presentation:A 1-month-old male infant, initially seemingly healthy, presented with irritability and feeding difficulties. Born without complications, routine neonatal assessments appeared normal, and physical examination revealed no abnormalities. However, laboratory tests indicated an extremely high white blood cell count, low platelets, and elevated haemoglobin. Further examinations showed a white blood cell count of 1450 × 106/l with a blood film revealing significant leukocytosis dominated by blast cells. Abdominal ultrasound confirmed hepatosplenomegaly which was not present during pregnancy. Subsequent bone marrow analysis and flow cytometry established a diagnosis of B-cell acute lymphoblastic leukaemia (B-ALL).Clinical discussion:It is rare for infantile ALL to manifest within the first month after birth. In most cases, the diagnosis is established before birth. When characteristic signs such as hepatosplenomegaly, leukaemia cutis, or infiltrative involvement of the extramedullary and central nervous systems are present, postnatal diagnoses are relatively straightforward. However, there are instances where children present with non-specific and ambiguous symptoms that resemble other medical conditions.Conclusion:This case underscores the importance of paediatricians being vigilant and attuned to the subtle indicators that differentiate common illnesses from serious conditions such as infantile ALL.
Neglected ureteral stent in a patient with chronic kidney disease and solitary functioning kidney: case report and review of literature
Authors: Sakr Mohamed , Badran Merhan , Pokhrel Prakriti , Asfeen Ummul Z. , Badran Nadin Nouh , Badran Maram Wahed 
Published: November 2023

Introduction:
A ureteral stent is crucial for managing urinary flow obstruction, ureteral reconstructive surgeries, and iatrogenic ureteral injuries. The authors aim to report a case of forgotten double-J stent for 17 years, the longest time reported in literature in a patient with solitary kidney and no typical long-term complications as stones formation and encrustation.

Case presentation:
A 58-year-old male with chronic kidney disease and solitary left kidney presented with left loin pain. With creatinine higher than baseline (6.2 mg/dl), he reported a neglected double-J stent placed 17 years ago in a different hospital. In addition, non-contrast computed tomography and cystoscopy revealed hydronephrosis, cystitis, and an element of infra-vesical obstruction, evident by high bladder neck. Treatment included left percutaneous nephrostomy, but he was readmitted few weeks later for cystoscopy, ureteroscopy, and a new double-J insertion. Due to worsening renal function, he was readmitted four weeks later for cystoscopic removal of the new double-J stent and Transurethral Resection of the Prostate, after which creatinine returned to baseline.

Discussion:
Double-J stents are vital in urological procedures, but neglecting their presence can lead to severe complications like encrustations, stone formation, stent fractures, hydronephrosis, infections, and renal function loss. Treatment of long-term complications is difficult and should consider many factors, including the type and severity of associated complications and the patient’s preoperative status.

Conclusion:
Preventing complications from neglected or forgotten double-J stents through patient education and follow-up is crucial, especially in those with solitary functioning kidneys due to the imminent loss of renal function.
Exercise-induced rhabdomyolysis manifestations and complications: a case report
Authors: Alharbi Kholoud F. , Alfahmi Manal Z. 
Published: November 2023

Introduction:
Rhabdomyolysis is a medical condition that results from damage to striated muscles that causes the release of their components into the bloodstream. Laboratory indications include high levels of creatinine kinase and myoglobin in the serum.

Importance:
This case report emphasizes the importance of having professional trainers in gyms and training centers who respect trainees’ limitations and physical capabilities and ensure that physical exercise programs are being conducted safely and effectively.

Case presentation:
A 39-year-old female healthcare provider presented to the emergency department at a tertiary/quaternary hospital in Saudi Arabia, with progressive right arm pain, swelling, weakness, and dark urine 2 days after an unaccustomed heavy physical exercise session with her personal trainer following a long pause from physical training.

Clinical discussion:
Levels of serum creatinine kinase, aspartate aminotransferase, and alanine transaminase were moderately elevated. There was no evidence of renal impairment, electrolyte disturbance, or coagulopathy. The patient was treated with analgesics, received hydration, and was discharged home under close observation and with a follow-up clinic visit scheduled to check for complications. Data were collected from the hospital’s electronic medical records, including clinical notes and laboratory investigations.

Conclusion:
Awareness campaigns need to be conducted to educate the public about healthy ways to exercise, such as gradually increasing the intensity of physical activity, warming up before exercising, cooling down after each workout, and staying hydrated. It is important that healthcare providers, trainees and trainers are able to recognize the signs of muscular injury following vigorous exercise in order to reduce the incidences of complications that could be deadly if they are not caught and managed early.
Use of Perioperative Advanced Practice Providers to Reduce Cost and Readmission in the Postoperative Hepatopancreatobiliary Population: Results of a Simulation Study
Authors: Smith Savannah R , Blair Catherine M , Lovasik Brendan P , Little Lori A , Sweeney John F , Sarmiento Juan M 
Published: November 2023

BACKGROUND:
Postoperative healthcare use and readmissions are common among the hepatopancreatobiliary (HPB) population. We evaluated the surgical volume required to sustain advanced practice providers (APPs) in the perioperative setting for cost reduction.

STUDY DESIGN:
Using decision analysis modeling, we evaluated costs of employing dedicated perioperative APP navigators compared with no APPs navigators. Simulated subjects could: (1) present to an emergency department, with or without readmission, (2) present for direct readmission, (3) require additional office visits, or (4) require no additional care. We informed our model using the most current available published data and performed sensitivity analyses to evaluate thresholds under which dedicated perioperative APP navigators are beneficial.

RESULTS:
Subjects within the APP navigator cohort accumulated $1,270 and a readmission rate of 6.9%, compared with $2,170 and 13.5% with no APP navigators, yielding a cost savings of $905 and 48% relative reduction in readmission. Based on these estimated cost savings and national salary ranges, a perioperative APPs become financially self-sustaining with 113 to 139 annual HPB cases, equating to 2 to 3 HPB cases weekly. Sensitivity analyses revealed that perioperative APP navigators were no longer cost saving when direct readmission rates exceeded 8.9% (base case 3.7%).

CONCLUSIONS:
We show that readmissions are reduced by nearly 50% with an associated cost savings of $900 when employing dedicated perioperative APPs. This position becomes financially self-sufficient with an annual HPB case load of 113 to 139 cases. High-volume HPB centers could benefit from postdischarge APP navigators to optimize outcomes, minimize high-value resource use, and ultimately save costs.
Modelling of surface reactions and diffusion mediated by bulk diffusion
Authors: Duda Fernando P. , Forte Neto Francisco S. , Fried Eliot 
Published: November 2023

We develop a continuum framework applicable to solid-state hydrogen storage, cell biology and other scenarios where the diffusion of a single constituent within a bulk region is coupled via adsorption/desorption to reactions and diffusion on the boundary of the region. We formulate content balances for all relevant constituents and develop thermodynamically consistent constitutive equations. The latter encompass two classes of kinetics for adsorption/desorption and chemical reactions—fast and Marcelin–De Donder, and the second class includes mass action kinetics as a special case. We apply the framework to derive a system consisting of the standard diffusion equation in bulk and FitzHugh–Nagumo type surface reaction–diffusion system of equations on the boundary. We also study the linear stability of a homogeneous steady state in a spherical region and establish sufficient conditions for the occurrence of instabilities driven by surface diffusion. These findings are verified through numerical simulations which reveal that instabilities driven by diffusion lead to the emergence of steady-state spatial patterns from random initial conditions and that bulk diffusion can suppress spatial patterns, in which case temporal oscillations can ensue. We include an extension of our framework that accounts for mechanochemical coupling when the bulk region is occupied by a deformable solid.
This article is part of the theme issue ‘Foundational issues, analysis and geometry in continuum mechanics’.
Loss of pseudo-momentum, energy-release rate and the effective mass of a moving dislocation
Authors: Markenscoff Xanthippi 
Published: November 2023

In a seminal paper in the Philosophical Transactions of the Royal Society (A244, 87–112). Eshelby (Eshelby 1951
Phil. Trans. R. Soc. Lond. A
244, 87–112. (
doi:10.1098/rsta.1951.0016
)) introduced the concept of ‘the force on an elastic singularity’ and suggested that the extensions to dynamics include the application of the momentum flux. In this direction, it is shown that, in the non-uniformly motion of a dislocation there is a loss in quasi-momentum (or pseudo-momentum) across the scales ε to ε
2
, which induces an effective mass of the dislocation, and a loss in kinetic energy across the scales. It is shown through Noether's theorem that the rate of change of quasi-momentum in the volume enclosing the dislocation is equal to the flux of it through the surface minus a quasi-force, which is the dynamic
J
integral. The connection between the variation in the Hamiltonian and in the Lagrangian relates the quasi-force to the energy-release rate, yielding the same effective mass, while providing physical meaning both through momentum and energy. The effective mass of a dislocation is important in relating the energetics of defects from the micro to the macro scales, and the loss of quasi-momentum can have wider applications in continua.

This article is part of the theme issue 'Foundational issues, analysis and geometry in continuum mechanics'.
Longitudinal stability of individual brain plasticity patterns in blindness
Authors: Amaral Lénia , Thomas Peyton , Amedi Amir , Striem-Amit Ella 
Published: November 2023

AbstractThe primary visual cortex (V1) in individuals born blind is engaged in a wide spectrum of tasks and sensory modalities, including audition, touch, language, and memory. This widespread involvement raises questions regarding the constancy of its role and whether it might exhibit flexibility in its function over time, connecting to diverse network functions in response to task-specific demands. This would suggest that reorganized V1 takes on a role similar to cognitive multiple-demand system regions. Alternatively, it is possible that the varying patterns of plasticity observed in the blind V1 can be attributed to individual factors, whereby different blind individuals recruit V1 for different functions, highlighting the immense idiosyncrasy of plasticity. In support of this second account, we have recently shown that V1 functional connectivity varies greatly across blind individuals. But do these represent stable individual patterns of plasticity or merely instantaneous changes, for a multiple-demand system now inhabiting V1? Here we tested if individual connectivity patterns from the visual cortex of blind individuals are stable over time. We show that over two years, fMRI functional connectivity from the primary visual cortex is unique and highly stable in a small sample of repeatedly sampled congenitally blind individuals. Further, using multivoxel pattern analysis, we demonstrate that the unique reorganization patterns of these individuals allow decoding of participant identity. Together with recent evidence for substantial individual differences in visual cortex connectivity, this indicates there may be a consistent role for the visual cortex in blindness, which may differ for each individual. Further, it suggests that the variability in visual reorganization in blindness across individuals could be used to seek stable neuromarkers for sight rehabilitation and assistive approaches.
Family, community, institutional and policy factors on COVID-19 vaccine perceptions among urban poor adolescents in seven countries: qualitative cross-site analysis
Authors: Ramaiya Astha , Mmari Kristin , Luiza Borges Ana , Cabral Cristiane , Mafuta Eric , Lulebo Aimee , Yu Chunyan , Pinandari Anggriyani Wahyu , Wilopo Siswanto Agus , Chipeta Effie , Hunersen Kara 
Published: November 2023

AbstractPurposeThe number of studies examining family, community, institutional and policy factors on COVID-19 vaccine perceptions is limited, with most concentrating on high-income countries and using predominantly quantitative methods. To address this gap, the goal of this manuscript is to qualitatively explore these factors and how they shape adolescents’ perspectives on COVID-19 vaccines across seven countries.MethodsFocus group discussions (FGDs) were conducted among urban poor adolescent populations (13 - 18 years) across seven countries: Ghent, Belgium; Sao Paulo, Brazil, Shanghai; China, Kinshasa, Democratic Republic of Congo (DRC); Semarang and Denpasar, Indonesia; Blantyre, Malawi and New Orleans, United States of America (USA). An inductive thematic analytical approach was used to understand the emerging themes across the different countries based on the study’s objectives.ResultsThe study found that all influences were inter-connected and contributed towards vaccine perceptions among adolescents, which were largely positive except in the two African countries and to an extent in the USA. Family and community influences played a large role in vaccine perceptions, however, this differed by context. Our findings suggest adolescents’ perceptions about vaccines were more positive in countries with higher vaccination rates, i.e. China and Indonesia versus countries with lower vaccination rates i.e. Malawi and DRC. Vaccine mandates within schools, offices, and public places were also discussed with varying perceptions based on government trust.ConclusionAdolescents’ perceptions of the Covid-19 vaccine are based on a variety of elements, such as families, community, institutions, and policies. Prioritizing one or another path may not be sufficient to improve vaccine adherence during future pandemics, as we experienced with Covid-19. Strategies to make vaccine perceptions more positive among urban poor adolescents should address both family and community perceptions. However, policies and robust programs around immunization are still needed.
Unveiling the Hidden Viromes Across the Animal Tree of Life: Insights from a Taxonomic Classification Pipeline Applied to Invertebrates of 31 Metazoan Phyla
Authors: Alfonso Pau , Butković Anamarija , Fernández Rosa , Riesgo Ana , Elena Santiago F. 
Published: November 2023

AbstractInvertebrates constitute the majority of animal species on Earth, including most disease-causing agents or vectors, with more diverse viromes when compared to vertebrates. Recent advancements in high-throughput sequencing have significantly expanded our understanding of invertebrate viruses, yet this knowledge remains biased toward a few well-studied animal lineages. In this study, we analyze invertebrate DNA and RNA viromes for 31 phyla using 417 publicly available RNA-Seq datasets from diverse environments in the marine-terrestrial and marine-freshwater gradients. This study aims to (i) estimate virome compositions at the family level for the first time across the Animal Tree of Life, including the first exploration of the virome in several phyla, (ii) quantify the diversity of invertebrate viromes and characterize the structure of invertebrate-virus interaction networks, and (iii) investigate host phylum and habitat influence on virome differences. Results showed that a set of few viral families of eukaryotes, comprisingRetroviridae,Flaviviridaeand several families of giant DNA viruses, were ubiquitous and highly abundant. Nevertheless, some differences emerged between phyla, revealing for instance a less diverse virome in Ctenophora compared to the other animal phyla. Compositional analysis of the viromes showed that the host phylum explained over five times more variance in composition than its habitat. Moreover, significant similarities were observed between the viromes of some phylogenetically related phyla, which could highlight the influence of co-evolution in shaping invertebrate viromes.ImportanceThis study significantly enhances our understanding of the global animal virome by characterizing the viromes of previously unexamined invertebrate lineages from a large number of animal phyla. It showcases the great diversity of viromes within each phylum and investigates the role of habitat shaping animal viral communities. Furthermore, our research identifies dominant virus families in invertebrates and distinguishes phyla with analogous viromes. This study sets the road towards a deeper understanding of the virome across the Animal Tree of Life.
The highly abundant mRNA m1A modification: a new layer of gene regulation in dinoflagellates
Authors: Li Chongping , Li Ying , Guo Jia , Wang Yuci , Shi Xiaoyan , Zhang Yangyi , Liang Nan , Yuan Jie , Xu Jiawei , Chen Hao 
Published: November 2023

AbstractThe N1-methyladenosine (m1A) is a positively charged RNA modification known to disrupt base pairing and influence RNA stability. Despite its limited presence in the mRNA of various organism models, including yeast, mouse, and human, the exact processes of m1A biosynthesis, distribution, regulation, and function remain controversial. Dinoflagellates are a major group of single-celled eukaryotic phytoplankton having peculiar crystalline chromosomes. Their genes are arranged in unidirectional gene clusters along the chromosomes and only have minimal transcriptional regulation, implying the involvement of other critical regulatory mechanisms in gene expression. Here, we found that m1A rather than m6A is the most prevalent mRNA modification in dinoflagellates and asymmetrically distributed along mature transcripts. Utilizing the dinoflagellate speciesAmphidinium carteraeas a study model, we identified 13481 m1A peaks characterized by a non-tRNA T-loop-like sequence motif within the transcripts of 10794 genes, many of which are involved in carbon and nitrogen metabolism. With enrichment around stop codon region and 3’ UTR, dinoflagellate mRNA m1A exhibits negative correlation with translation efficiency. Notably, nitrogen depletion (N-depletion) treatment led to significant global decrease of mRNA m1A amount, causing dramatic variation in translation rates with minimal changes in transcription. Additionally, our analysis uncovered distinctive methylation patterns of m1A modification that appears to post-transcriptionally modulate gene expression through regulating translation efficiency. Thus, our findings provide the first comprehensive m1A map of dinoflagellate mRNA, shedding light on its crucial role as a post-transcriptional regulatory layer to compensate the degeneration of transcriptional regulation in dinoflagellate. This study also sets the stage for further investigation into the biogenesis and functional significance of mRNA m1A in eukaryotes.
NASTRA: Accurate analysis of short tandem repeat markers by nanopore sequencing with repeat-structure-aware algorithm
Authors: Ren Zilin , Zhang Jiarong , Zhang Yixiang , Yang Tingting , Sun Pingping , Xue Jiguo , Bo Xiaochen , Zhou Bo , Yan Jiangwei , Ni Ming 
Published: November 2023

ABSTRACTForensic short-tandem repeats (STR) genetic markers are multi-allelic and widely utilized for individual identification, kinship testing, and cell-line authentication. Nanopore sequencing, known for its portability, is emerging as a promising approach for STR typing, facilitating real-time and in-field testing. However, its efficacy is often hampered by sequencing noise. Previous methods rely on alignment-based genotyping, necessitating known alleles, which limits their applicability to unknown alleles. Here, we introduced NASTRA, an innovative allele reference-free tool for precise germline analysis of STR genetic markers. NASTRA incorporates a recursive algorithm to infer repeat structures of allele sequences using only known repeat motifs. Our tests, conducted on 80 individual samples and 8 DNA standards, have demonstrated NASTRA’s exceptional 100% accuracy in genotyping nearly all diploid STRs across various multiplex kits and flow cells. It surpasses alignment-based methods in accuracy and speed. In a paternity testing case study, NASTRA accurately identified three relationships among six individuals within an 18-minute sequencing duration. These results underscore NASTRA’s ability to perform STR analysis on both NGS and nanopore sequencing platforms, significantly enhancing the utility of nanopore sequencing in relevant applications.GRAPHICAL ABSTRACT