bluuebunny/crossref_metadata_2025_split huggingface dataset:
Impact of different genetic mutations on granulocyte development and G-CSF responsiveness in congenital neutropenia
Authors: Meng Xin , Zhang Hai , Dong Lulu , Min Qing , Yu Meiping , Li Yaxuan , Liu Lipin , Wang Wenjie , Ying Wenjing , Sun Jinqiao , Wang Ji-Yang , Hou Jia , Wang Xiaochuan 
Published: January 2024

Abstract
Congenital neutropenia (CN) is a genetic disorder characterized by persistent or intermittent low peripheral neutrophil counts, thus increasing susceptibility to bacterial and fungal infections. Various forms of CN, caused by distinct genetic mutations, exhibit differential responses to granulocyte colony–stimulating factor (G-CSF) therapy, with the underlying mechanisms not fully understood. This study presents an in-depth comparative analysis of clinical and immunological features in 5 CN patient groups (severe congenital neutropenia [SCN]1, SCN3, cyclic neutropenia [CyN], warts, hypogammaglobulinaemia, infections and myelokathexis [WHIM], and Shwachman-Bodian-Diamond Syndrome [SBDS]) associated with mutations in ELANE, HAX1, CXCR4, and SBDS genes. Our analysis led to the identification of 11 novel mutations in ELANE and 1 each in HAX1, CXCR4, and G6PC3 genes. Investigating bone marrow (BM) granulopoiesis and blood absolute neutrophil count after G-CSF treatment, we found that SCN1 and SCN3 presented with severe early-stage disruption between the promyelocyte and myelocyte, leading to a poor response to G-CSF. In contrast, CyN, affected at the late polymorphonuclear stage of neutrophil development, showed a strong G-CSF response. WHIM, displaying normal neutrophil development, responded robustly to G-CSF, whereas SBDS, with moderate disruption from the early myeloblast stage, exhibited a moderate response. Notably, SCN1 uniquely impeded neutrophil development, whereas SCN3, CyN, WHIM, and SBDS also affected eosinophils and basophils. In addition, SCN1, SCN3, and CyN presented with elevated serum immunoglobulins, increased BM plasma cells, and higher A Proliferation-Inducing Ligand levels. Our study reveals a strong correlation between the stage and severity of granulocyte development disruption and the efficacy of G-CSF therapy.
PredictEFC: a fast and efficient multi-label classifier for predicting enzyme family classes
Authors: Chen Lei , Zhang Chenyu , Xu Jing 
Published: January 2024

AbstractBackgroundEnzymes play an irreplaceable and important role in maintaining the lives of living organisms. The Enzyme Commission (EC) number of an enzyme indicates its essential functions. Correct identification of the first digit (family class) of the EC number for a given enzyme is a hot topic in the past twenty years. Several previous methods adopted functional domain composition to represent enzymes. However, it would lead to dimension disaster, thereby reducing the efficiency of the methods. On the other hand, most previous methods can only deal with enzymes belonging to one family class. In fact, several enzymes belong to two or more family classes.ResultsIn this study, a fast and efficient multi-label classifier, named PredictEFC, was designed. To construct this classifier, a novel feature extraction scheme was designed for processing functional domain information of enzymes, which counting the distribution of each functional domain entry across seven family classes in the training dataset. Based on this scheme, each training or test enzyme was encoded into a 7-dimenion vector by fusing its functional domain information and above statistical results. Random k-labelsets (RAKEL) was adopted to build the classifier, where random forest was selected as the base classification algorithm. The two tenfold cross-validation results on the training dataset shown that the accuracy of PredictEFC can reach 0.8493 and 0.8370. The independent test on two datasets indicated the accuracy values of 0.9118 and 0.8777.ConclusionThe performance of PredictEFC was slightly lower than the classifier directly using functional domain composition. However, its efficiency was sharply improved. The running time was less than one-tenth of the time of the classifier directly using functional domain composition. In additional, the utility of PredictEFC was superior to the classifiers using traditional dimensionality reduction methods and some previous methods, and this classifier can be transplanted for predicting enzyme family classes of other species. Finally, a web-server available athttp://124.221.158.221/was set up for easy usage.
Parallels of quantum superposition in ecological models: from counterintuitive patterns to eco-evolutionary interpretations of cryptic species
Authors: Angeler David G. , Fried-Petersen Hannah B. 
Published: January 2024

Abstract
Background
Superposition, i.e. the ability of a particle (electron, photon) to occur in different states or positions simultaneously, is a hallmark in the subatomic world of quantum mechanics. Although counterintuitive at first sight, the quantum world has potential to inform macro-systems of people and nature. Using time series and spatial analysis of bird, phytoplankton and benthic invertebrate communities, this paper shows that superposition can occur analogously in redundancy analysis (RDA) frequently used by ecologists.

Results
We show that within individual ecosystems single species can be associated simultaneously with different orthogonal axes in RDA models, which suggests that they operate in more than one niche spaces. We discuss this counterintuitive result in relation to the statistical and mathematical features of RDA and the recognized limitations with current traditional species concepts based on vegetative morphology.

Conclusion
We suggest that such “quantum weirdness” in the models is reconcilable with classical ecosystems logic when the focus of research shifts from morphological species to cryptic species that consist of genetically and ecologically differentiated subpopulations. We support our argument with theoretical discussions of eco-evolutionary interpretations that should become testable once suitable data are available.
Genomic insights into the endangered white-eared night heron (Gorsachius magnificus)
Authors: Luo Haoran , Lin Qingxian , Fang Wenzhen , Chen Xiaolin , Zhou Xiaoping 
Published: January 2024

Abstract
Objectives
A genome sequence of a threatened species can provide valuable genetic information that is important for improving the conservation strategies. The white-eared night heron (Gorsachius magnificus) is an endangered and poorly known ardeid bird. In order to support future studies on conservation genetics and evolutionary adaptation of this species, we have reported a de novo assembled and annotated whole-genome sequence of the G. magnificus.

Data description
The final draft genome assembly of the G. magnificus was 1.19 Gb in size, with a contig N50 of 187.69 kb and a scaffold N50 of 7,338.28 kb. According to BUSCO analysis, the genome assembly contained 97.49% of the 8,338 genes in the Aves (odb10) dataset. Approximately 10.52% of the genome assembly was composed of repetitive sequences. A total of 14,613 protein-coding genes were predicted in the genome assembly, with functional annotations available for 14,611 genes. The genome assembly exhibited a heterozygosity rate of 0.49 heterozygosity per kilobase pair. This draft genome of G. magnificus provides valuable genomic resources for future studies on conservation and evolution.
Novel compound heterozygous mutations of the NPC1 gene associated with Niemann-pick disease type C: a case report and review of the literature
Authors: Tao Chaoxin , Zhao Min , Zhang Xiaohui , Hao Jihong , Huo Qiuyue , Sun Jie , Xing Jiangtao , Zhang Yuna , Zhao Jianhong , Huang Huaipeng 
Published: January 2024

AbstractBackgroundNiemann-Pick Disease type C is a fatal autosomal recessive lipid storage disorder caused byNPC1orNPC2gene mutations and characterized by progressive, disabling neurological deterioration and hepatosplenomegaly. Herein, we identified a novel compound heterozygous mutations of theNPC1gene in a Chinese pedigree.Case presentationThis paper describes an 11-year-old boy with aggravated walking instability and slurring of speech who presented as Niemann-Pick Disease type C. He had the maternally inherited c.3452 C > T (p. Ala1151Val) mutation and the paternally inherited c.3557G > A (p. Arg1186His) mutation using next-generation sequencing. The c.3452 C > T (p. Ala1151Val) mutation has not previously been reported.ConclusionsThis study predicted that the c.3452 C > T (p. Ala1151Val) mutation is pathogenic. This data enriches theNPC1gene variation spectrum and provides a basis for familial genetic counseling and prenatal diagnosis.
Clinical features and outcomes of influenza and RSV coinfections: a report from Canadian immunization research network serious outcomes surveillance network
Authors: Pott Henrique , J. LeBlanc Jason , S. ElSherif May , Hatchette Todd F. , McNeil Shelly A. , Andrew Melissa K. ,   on behalf of the Serious Outcomes Surveillance (SOS) Network of the Canadian Immunization Research Network (CIRN)
Published: January 2024

Abstract
Background
Influenza and RSV coinfections are not commonly seen but are concerning as they can lead to serious illness and adverse clinical outcomes among vulnerable populations. Here we describe the clinical features and outcomes of influenza and RSV coinfections in hospitalized adults.

Methods
A cohort study was performed with pooled active surveillance in hospitalized adults ≥ 50 years from the Serious Outcomes Surveillance Network of the Canadian Immunization Research Network (CIRN SOS) during the 2012/13, 2013/14, and 2014/15 influenza seasons. Descriptive statistics summarized the characteristics of influenza/RSV coinfections. Kaplan-Meier estimated the probability of survival over the first 30 days of hospitalization.

Results
Over three influenza seasons, we identified 33 cases of RSV and influenza coinfection, accounting for 2.39 cases per 1,000 hospitalizations of patients with acute respiratory illnesses. Adults aged 50 + years commonly reported cough (81.8%), shortness of breath (66.7%), sputum production (45.5%), weakness (33.3%), fever (27.3%), and nasal congestion (24.2%) as constitutional and lower respiratory tract infection symptoms. The mortality rate was substantial (12.1%), and age, comorbidity burden, and frailty were associated with a higher risk for adverse clinical outcomes.

Conclusions
Older adults are at higher risk for complications from influenza and RSV coinfections, especially those over 65 with a high comorbidity burden and frailty.
Obstetric blood transfusion in placenta previa patients with prenatal anemia: a retrospective study
Authors: Zhang Baolian , Liu Hong , Li Haiyan , Wang Jia , Zhu He , Yu Peijia , Huang Xianghua , Wang Wenli 
Published: January 2024

Abstract
Background
The appropriate use of obstetric blood transfusion is crucial for patients with placenta previa and prenatal anemia. This retrospective study aims to explore the correlation between prenatal anemia and blood transfusion-related parameters in this population.

Methods
We retrieved the medical records of consecutive participants who were diagnosed with placenta previa and underwent cesarean section in our hospital. We compared the baseline demographics and clinical characteristics of patients with and without anemia. The correlation between prenatal anemia and obstetric blood transfusion-related parameters was evaluated using multivariate regression analysis.

Results
A total of 749 patients were enrolled, with a mean prenatal hemoglobin level of 10.87 ± 1.37 g/dL. Among them, 54.87% (391/749) were diagnosed with anemia. The rate of obstetric blood transfusion was significantly higher in the anemia group (79.54%) compared to the normal group (44.41%). The median allogeneic red blood cell transfusion volume in the anemia group was 4.00 U (IQR 2.00–6.00), while in the normal group, it was 0.00 U (IQR 0.00–4.00). The prenatal hemoglobin levels had a non-linear relationship with intraoperative allogeneic blood transfusion rate, massive blood transfusion rate, red blood cell transfusion units, and fresh plasma transfusion volume in patients with placenta previa, with a threshold of 12 g/dL.

Conclusions
Our findings suggest that prenatal anemia is associated with a higher rate of blood transfusion-related parameters in women with placenta previa when the hemoglobin level is < 12 g/dL. These results highlight the importance of promoting prenatal care in placenta previa patients with a high requirement for blood transfusion.
When the second comes first– rhabdomyosarcoma preceding heritable retinoblastoma– a case report
Authors: Tripathy Devjyoti , Moulin Alexandre , Bijon Jacques , Gengler Carole , Beck-Popovic Maja , Munier Francis L. , Stathopoulos Christina 
Published: January 2024

Abstract
Background
Retinoblastoma (rb) is the most frequent intraocular tumor, accounting for 3% of all childhood cancers. Heritable rb survivors are germline carriers for an RB1 mutation and have a lifelong risk to develop non-ocular second primary tumors (SPTs) involving multiple other organs like the bones, soft tissues, or skin. These SPTs usually become manifest several years succeeding the diagnosis of rb. In our instance, however, a non-ocular SPT presented prior to the diagnosis of heritable rb.

Case presentation
We report a rare case of a monozygotic twin who presented with primary rhabdomyosarcoma (RMS) preceding the manifestation of heritable rb. The rb was diagnosed when the child developed strabismus while already on therapy for the RMS. The child underwent therapy for both as per defined treatment protocols. The rb regressed well on treatment, but the RMS relapsed and the child developed multiple refractory metastatic foci and succumbed to his disease.

Conclusions
Non-ocular SPTs like sarcomas are usually known to manifest in heritable rb survivors with a lag of two to three decades (earlier if exposure to radiation is present) from the presentation of the rb. However, in our case, this seemed to be reversed with the RMS being manifest at an unusual early age and the rb being diagnosed at a later point in time.
Risk factors on surgical compliance and its impact on survival outcomes in meningioma patients: a SEER-based retrospective propensity-score matched analysis
Authors: Yang Shengkai , Teng Hongwei , Wang Yingdan , Ji Kangkang , Chen Weihua , Zhou Hai 
Published: January 2024

Abstract
Background
This study aimed to analyze the effect of surgical compliance on the survival outcome of patients with meningioma and explore the factors affecting surgical compliance.

Methods
We selected data from the Surveillance, Epidemiology, and End Results database for 122,632 meningioma patients diagnosed between 2004 and 2018. The effect of surgical compliance on patients’ overall survival (OS) was analyzed through Cox regression and Kaplan–Meier curves. Independent risk factors for surgical compliance were identified through multifactorial logistic regression analyses to construct diagnostic nomograms, further assessed by receiver operating characteristic curves. Furthermore, we used univariate and multivariate logistic regression analyses to evaluate relevant variables linked to adherence with meningioma surgery. Moreover, 1:1 propensity score matching was applied to assess the validity of the results in patients with favorable and poor surgical compliance.

Results
A total of 48,735 were eligible from the initial cohort of 122,632 patients with meningioma. Among them, 45,038 (92.40%) exhibited good surgical compliance, while 3697 (7.60%) had poor surgical compliance. The rate of patients with good surgical compliance was significantly higher than that of patients with inadequate surgical compliance (p < 0.001). Moreover, surgical compliance is an independent prognostic factor for OS in meningioma patients. Univariate Cox regression analysis indicated that individuals with poor surgical compliance demonstrated lower OS rates than those with good surgical compliance (hazard ratio [HR 2.404; 95% confidence interval [CI] 2.276–2.54, p < 0.001], consistent with the observation in the multivariate analysis (HR 1.564; 95% CI 1.471–1.663, p < 0.001). We developed a prediction model using seven variables: age, sex, race, tumor behavior recode, tumor size, family income, and residential setting (p < 0.05). Surgical compliance was associated with patient age, sex, race, tumor behavior recode, tumor size, family income, and residential setting by logistic regression analysis.

Conclusions
Surgical compliance emerged as an independent prognostic factor for survival in patients with meningioma. Poor surgical compliance was associated with older age, black and other races, females, advanced-stage tumors, larger tumor size, lower household income, and rural residence. When patients experienced these conditions, OS was shorter, requiring more aggressive treatment.
Knowledge, attitude, and utilization of traditional medicine within the plural medical system in West Java, Indonesia
Authors: Febriyanti Raden Maya , Saefullah Kurniawan , Susanti Raini Diah , Lestari Keri 
Published: January 2024

AbstractBackgroundThe concept of ‘medical pluralism’ has become more popular among scholars in applied health science and prevalent in societies where one medical system alone cannot adequately meet the health care needs of the entire population.MethodsThe data collection is focused on the knowledge-belief-practice and the utilization of three medical systems in Kabupaten Bandung, West Java, Indonesia. Participants were purposively selected from households with at least one member experienced one of the listed diseases in the questionnaire. The extensive survey using a structured questionnaire has been undertaken to collect data on people’s health care utilization behaviour. The dataset is further analyzed using multivariate analysis through non-canonical correlation, with the analytical data provided by Statistical Package for Social Sciences (SPSS).ResultsWith regards to the total utilization by patients, the traditional medical system presents as the dominant medical system in the research area, accounting for 59.3% (n = 419) of total utilization, followed by the modern medical system (33.0%,n = 233), and transitional medical system (7.7%,n = 54). This study identified that village category, illness, illness duration, occupation, belief in traditional medicine, knowledge of modern medicine, accessibility, cost, proximity to the medical service, and insurance have significant (χ2 = 0.000) relationship with the utilization of medical systems. The results of the multivariate analysis show that the block of the predisposing socio-demographic factors and the block of the predisposing psycho-social factors correlate strongly with the utilization of medical systems.ConclusionsIn general, people in Kabupaten Bandung, West Java, Indonesia seeks treatment from various sources, which in the context of the medical system, consists of the traditional, transitional, and modern medical system; therefore, it adopts the patterns of transcultural health care utilization. In terms of the knowledge, beliefs, and practices of traditional medicine in West Java, the inhabitants of the five research villages were commonly familiar with medicinal plants and speak profoundly about their knowledge of traditional medicine, which in the research area is perceived as accessible, efficacious, affordable and culturally appropriate with Sundanese community.
Awareness and practice of airway pressure release ventilation mode in acute respiratory distress syndrome patients among nurses in Saudi Arabia
Authors: Aldhahir Abdulelah M. , Alqarni Abdullah A. , Madkhali Mohammed A. , Madkhali Hussain H. , Bakri Abdullah A. , Shawany Mohammad A. , Alasimi Ahmed H. , Alsulayyim Abdullah S. , Alqahtani Jaber S. , Alyami Mohammed M. , Alghamdi Saeed M. , Alqarni Omar A. , Hakamy Ali 
Published: January 2024

Abstract
Background
This study aimed to assess the knowledge and current practice of using the airway pressure release ventilation (APRV) mode with acute respiratory distress syndrome (ARDS) patients and identify barriers to not using this mode of ventilation among nurses who work in critical areas in Saudi Arabia.

Methods
Between December 2022 and April 2023, a cross-sectional online survey was disseminated to nurses working in critical care areas in Saudi Arabia. The characteristics of the respondents were analyzed using descriptive statistics. Percentages and frequencies were used to report categorical variables.

Results
Overall, 1,002 nurses responded to the online survey, of whom 592 (59.1%) were female. Only 248 (24.7%) nurses had ever used APRV mode, whereas only 229 (22.8%) received training on APRV mode. Moreover, 602 (60.0%) nurses did not know whether APRV was utilized in their hospital. Additionally, 658 (65.6%) nurses did not know whether APRV mode was managed using a standard protocol. Prone positioning was the highest recommended intervention by 444 (43.8%) when a conventional MV failed to improve oxygenation in patients with ARDS. 323 (32.2%) respondents stated that the P-high should be set equal to the plateau pressure on a conventional ventilator, while 400 (39.9%) said that the P-low should match PEEP from a conventional ventilator. Almost half of the respondents (446, 44.5%) stated that the T-high should be set between 4 and 6 s, while 415 (41.4%) said that the T-low should be set at 0.4 to 0.8 s. Over half of the nurses (540, 53.9%) thought that the maximum allowed tidal volume during the release phase should be 4–6 ml/kg. Moreover, 475 (47.4%) believed that the maximum allowed P-high setting should be 35 cm H2O. One-third of the responders (329, 32.8%) stated that when weaning patients with ARDS while in APRV mode, the P-high should be reduced gradually to reach a target of 10 cm H2O. However, 444 (44.3%) thought that the T-high should be gradually increased to reach a target of 10 s. Half of the responders (556, 55.5%) felt that the criteria to switch the patient to continuous positive airway pressure (CPAP) were for the patient to have an FiO2 ≤ 0.4, P-high ≤ 10 cm H2O, and T-high ≥ 10 s. Lack of training was the most common barrier to not using APRV by 615 (61.4%).

Conclusion
The majority of nurses who work in critical care units have not received sufficient training in APRV mode. A significant discrepancy was observed regarding the clinical application and management of APRV parameters. Inadequate training was the most frequently reported barrier to the use of APRV in patients with ARDS.
Mapping cancer biology in space: applications and perspectives on spatial omics for oncology
Authors: Lee Sumin , Kim Gyeongjun , Lee JinYoung , Lee Amos C. , Kwon Sunghoon 
Published: January 2024

AbstractTechnologies to decipher cellular biology, such as bulk sequencing technologies and single-cell sequencing technologies, have greatly assisted novel findings in tumor biology. Recent findings in tumor biology suggest that tumors construct architectures that influence the underlying cancerous mechanisms. Increasing research has reported novel techniques to map the tissue in a spatial context or targeted sampling-based characterization and has introduced such technologies to solve oncology regarding tumor heterogeneity, tumor microenvironment, and spatially located biomarkers. In this study, we address spatial technologies that can delineate the omics profile in a spatial context, novel findings discovered via spatial technologies in oncology, and suggest perspectives regarding therapeutic approaches and further technological developments.