bluuebunny/crossref_metadata_2025_split huggingface dataset:
Deciphering the ghost proteome in ovarian cancer cells by deep proteogenomic characterization
Authors: Tristan Cardon , Rio Diego Garcia-del , Derhourhi Mehdi , Bonnefond Amelie , Leblanc Sebastien , Guilloy Noe , Roucou Xavier , Eyckerman Sven , Gevaert Kris , Salzet Michel 
Published: April 2024

Abstract

Proteogenomics is becoming a powerful tool in personalized medicine by linking genomics, transcriptomics and mass spectrometry (MS)-based proteomics. Due to increasing evidence of alternative open reading frame-encoded proteins (AltProts), proteogenomics has a high potential to unravel the characteristics, variants and expression levels of the alternative proteome, in addition to already annotated proteins (RefProts). To obtain a broader view of the proteome of ovarian cancer cells compared to ovarian epithelial cells, cell-specific total RNA-sequencing profiles and customized protein databases were generated. In total, 128 RefProts and 30 AltProts were identified exclusively in SKOV-3 and PEO-4 cells. Among them, an AltProt variant of IP_715944, translated from DHX8, was found mutated (p.Leu44Pro). We show high variation in protein expression levels of RefProts and AltProts in different subcellular compartments. The presence of 117 RefProt and two AltProt variants was described, along with their possible implications in the different physiological/pathological characteristics. To identify the possible involvement of AltProts in cellular processes, crosslinking-MS (XL-MS) was performed in each cell line to identify AltProt-RefProt interactions. This approach revealed an interaction between POLD3 and the AltProt IP_183088, which after molecular docking, was placed between POLD3-POLD2 binding sites, highlighting its possibility of the involvement in DNA replication and repair.
Antimicrobial Resistance Patterns and Molecular Characterisation of Neisseria Gonorrhoeae Isolated at Regional and National Referral Hospitals in Uganda
Authors: Jackson Were , Petra Nalumaga Pauline , Phiona Twinomugisha , Jude Busingye , Joel Bazira 
Published: April 2024

Abstract

Gonococcal infections (gonorrhoea) are increasingly becoming important sexually spread infections in humans in sub-Saharan countries including Uganda. Antimicrobial resistance associated withNeisseria gonorrhoeaeis rising threatening health crisis. However, the antimicrobial phenotypic and genotypic resistance patterns of the circulatingNeisseria gonorrhoeaestrains in Uganda have not been fully characterized and known. This study was carried out to investigate genetic characterization ofNeisseria gonorrhoeaeisolates and their antibiotic resistance in Western and Central Uganda. Fifty four isolates cultured from July 2019 to June 2021 were examined. The isolates were sub cultured on Thayer-Martin agar. Phenotypic antibiotic resistance was carried out using Kirby-Bauer disc diffusion method as per Clinical and Laboratory Standards Institute (CLSI) standards. Molecular techniques (End-point PCR) was used to screenNeisseria gonorrhoeaeantibiotic resistant strains at three important gene loci; penA, gyr A and parC. 56.8% of participants were male with mean age of 30 years. The adults aged 45 and above were the most sexually active with high odds ratio (OR = 2.88) followed by the middle aged (OR = 1.43). High resistance was observed amongst Penicillin (100%), Tetracycline (98.15%), and Ciprofloxacin (87.04%) and least resistance was with Cefixime (33.33%) and cefoxitin (28.26%). PenA was predominant genetic determinant of resistance. In conclusion, there is high genetic variation among theNeisseria gonorrhoeaestrains with high sensitivity to Cefixime and Ceftriaxome. There is need to strengthen clinical laboratory diagnosis and sensitise population on rational use of drugs in treatment of sexually transmitted infections.
AgroAdvisor: Crop Yield Prediction, Crop and Fertilizer Recommendation System using Random Forest with Gradient Boosting and DeepFM for Precise Agriculture
Authors: Kukkar Ashima , Mohana Rajni , Sharma Aman , Mallik Saurav , Shah Mohd Asif 
Published: April 2024

Abstract

Crop yield prediction plays a very important role in productivity growth. Prediction of the crop yield in particular area helps the farmer to choose the right crop to be grown in the land. With crop yield prediction crop recommendation boosts up the productivity of crop. Recommending the correct type of crop in particular land on the factors of soil pH, rainfall, temperature, humidity etc. helps the farmer to choose specific and most suitable crop. With recommendation and yield prediction of crop, fertilizer recommendation is also necessary for more productivity and yield. It is necessary to use suitable fertilizers on optimal timing for the growth of crops. Therefore, in this paper, we have attempted to address these issues by proposing three model systems that will efficiently manage crop production. In this paper, we designed an integrated system named as AgroAdvisor using the hybrid proposed technique such as Random Forest with Extreme Gradient Boosting (RFXGB) and Deep Factorization Machine (DeepFM). RFGB is applied for processing the features, which improves the DeepFM ability to handle the dense numerical features and increase the prediction performance. The result of RFXGB-DeepFM is compared with classical machine learning and deep learning techniques by using recall, F-value, precision and accuracy parameters. The results show that the proposed RFGB-DeepFM technique gives better accuracy than the classical techniques. The impact of RFGXB on existing techniques is also analyzed using Friedman and post hoc statistical testing and results show that in most cases RFGXB enhanced the performance.
iPSC-derived megakaryocytes and platelets accelerate wound healing and angiogenesis.
Authors: Kosaka Kentaro , Takayama Naoya , Paul Sudip Kumar , Oshima Motohiko , Fukuyo Masaki , Rahmutulla Bahityar , Tajiri Ikuko , Mukai Michiaki , Kubota Yoshitaka , Akita Shinsuke , Furuyama Nobutaka , Kaneda Atsushi , Iwama Atsushi , Eto Koji , Mitsukawa Nobuyuki 
Published: April 2024

Abstract

Background Platelet-rich plasma (PRP), which is prepared by concentrating platelets in autologous blood, shows efficacy in chronic skin wounds via multiple growth factors. However, it exhibits heterogeneity across patients, leading to unstable therapeutic efficacy. Human induced pluripotent stem cell (iPSC)-derived megakaryocytes and platelets (iMPs) are capable of providing a stable supply, holding promise as materials for novel platelet concentrate-based therapies. In this context, we evaluated the effect of iMPs on wound healing and validated lyophilization for clinical applications.
Methods The growth factors released by activated iMPs were measured. The effect of the administration of iMPs on human fibroblasts and human umbilical vein endothelial cells (HUVECs) was investigated in vitro. iMPs were applied to dorsal skin defects of diabetic mice to assess the wound closure rate and quantify collagen deposition and angiogenesis. Following the storage of freeze-dried iMPs (FD-iMPs) for three months, the stability of growth factors and their efficacy in animal models were determined.
Result Multiple growth factors that promote wound healing were detected in activated iMPs. iMPs specifically released FGF2 and exhibited superior enhancement on HUVEC proliferation compared to PRP. Moreover, an RNA-seq analysis revealed that iMPs induce polarization to stalk cells and enhance ANGPTL4 gene expression in HUVECs. Animal studies demonstrated that iMPs promoted wound closure and angiogenesis in chronic wounds caused by diabetes. We also confirmed the long-term stability of growth factors in FD-iMPs and their comparable effects to those of original iMPs in the animal model.
Conclusion Our study demonstrates that iMPs promote angiogenesis and wound healing through the activation of vascular endothelial cells. iMPs exhibited more effectiveness than PRP, an effect attributed to the exclusive presence of specific factors including FGF2. Lyophilization enabled the long-term maintenance of the composition of the growth factors and efficacy of the iMPs, therefore contributing to their stable supply for clinical application. These findings suggest that iMPs provide a novel treatment for chronic wounds.
Positively charged specificity site in cyclin B1 is essential for mitotic fidelity
Authors: Mayer Thomas , Heinzle Christian , Höfler Anna , Yu Jun , Heid Peter , Kremer Nora , Stengel Florian , Bange Tanja , Boland Andreas 
Published: April 2024

Abstract

Phosphorylation of substrates by cyclin-dependent kinases (CDKs) is the driving force of cell cycle progression. Several CDK-activating cyclins are involved, yet how they contribute to substrate specificity is still poorly understood. Here, we discovered that a positively charged pocket in cyclin B1, which is exclusively conserved within B-type cyclins and binds phosphorylated serine- or threonine-residues, is essential for correct execution of mitosis. HeLa cells expressing pocket mutant cyclin B1 are strongly delayed in anaphase onset due to multiple defects in mitotic spindle function and timely activation of the E3 ligase APC/C. Pocket integrity is essential for APC/C phosphorylation particularly at non-consensus CDK1 sites and full in vitro ubiquitylation activity. Our results support a model in which cyclin B1’s pocket serves as a specificity site factor for sequential substrate phosphorylations involving initial priming events that facilitate subsequent pocket-dependent phosphorylations even at non-consensus CDK1 motifs.
Kinetic Simulation of the Reaction between N,N-dimethylazidoethylamine (DMAZ) and Dinitrogen Tetroxide (NTO) based on Density Functional Theory
Authors: Jin Guofeng , Huang Zhiyong , Huang Yuanzheng , Gao Minna , Wang Yingying 
Published: April 2024

Abstract
The long ignition delay time of N,N-dimethylazidoethylamine (DMAZ) and dinitrogen tetroxide (NTO) limits the application of DMAZ. In order to explore the ignition mechanism of DMAZ and NTO and to obtain a theoretical basis for shortening the ignition delay time, the reaction between DMAZ and NO2/NTO was studied based on density functional theory (DFT). The results showed that under the conditions of gas phase and NTO liquid phase, the main path of the reaction is that NO2 attacks the secondary hydrogen atom of DMAZ. The reaction enthalpy is higher than that in the NTO liquid phase, indicating that the gas phase reaction absorbs more energy and is not easy to proceed, while the NTO liquid phase reaction is easier. The combustion mechanism of DMAZ and NTO was preliminarily obtained. It is speculated that under actual working conditions, DMAZ and NTO mainly undergo the liquid-phase reaction。
Immune status of patients with inherited bone marrow failure syndromes: A Single-center analysis
Authors: Lotfy Sohilla , Ghattas Bavly , Elhady Marwa Abd , Meshaal Safa , Hawary Rabab El , Eldash Alia , Galal Nermeen , Elmarsafy Aisha 
Published: April 2024

Abstract

Inherited bone marrow failure syndromes (IBMFS) comprise a heterogeneous group of rare cancer prone genetic disorders with hematologic and physical abnormalities. The immune status of patients with an IBMFS is not entirely clear; however there are some suggestions that a few patients exhibit various degrees of qualitative immune dysfunction. Recently, there are novel and rare PID syndromes that have been associated with cytopenia secondary to bone marrow failure, but they are not always taken into consideration, phenotypic overlap may impair the correct diagnosis. This study included twenty-one patients diagnosed with IBMFS; 17 Fanconi anemia patients and 4 Diamond-Blackfan anemia patients. Evaluation of immune status was done by assessing complete blood count with differential leucocytic count, immunophenotyping of lymphocytes by Flow cytometry (CD3, CD4, CD8, CD19, CD56, B cell maturation, and naïve/memory T cells), as well as immunoglobulins assay (IgG, IgM, IgA levels). Results: Neutropenia was detected in 74% of (N= 15/21) with severity ranging from mild (24%) to severe neutropenia (36%), and all were FA patients. Lymphopenia was detected in 57% of the patients (N=12/21). Low immunoglobulin levels for age were detected in 28.6% of the patients (N=6/21). Most of FA patients had low counts of CD19 B cells, CD27+IgD+ non class switched B cells, CD27+IgD- switched memory B cells, CD27-IgD+ naïve B cells, as well as, low CD4 T Helper cells, CD45 RA naïve T cells, CD56 NK cells, CD45RO memory T cells. In DBA, limited by small sample size, no abnormalities were detected in T cell population, low NK cell counts were reported in two patients. Low CD27-IgD+, CD27+Ig D+ and CD27+IgD were detected in 2/4 of the patients while CD45RA naïve T cells were reduced in only one patient. A positive correlation between the frequency of hospitalization due to infections and degree of bone marrow hypocellularity was found. The degree of lymphopenia, low CD3, CD4, CD8, CD19 and defective T cell maturation subsets were statistically significant variables associated with occurrence of significant infections. Conclusion: IBMFS patients have altered immune status, possibility of the presence of some degree of overlap between IBMFS and certain PIDs associated with cytopenias and special somatic features might be found. Immunological assessment for patients with IBMFS should be considered as a part of routine work up of such patients.
Magnitude of unintended pregnancy among rural reproductive women in Ethiopia: A Multilevel analysis using 2016 EDHS data
Authors: Jejaw Melak , Demissie Kaleb Assegid , Tiruneh Misganaw Guadie , Abera Kaleab Mesfin , Tsega Yawkal , Endawkie Abel , Negash Wubeshet Debebe , Workie Amare Mesfin , Yohannes Lamrot , Getnet Mihiret , Worku Nigusu , Yeshambel Adina , Asmare Lakew , Alemu Hiwot Tadesse , Geberu Demis Mulatu , Hagos Asebe 
Published: April 2024

Abstract

Despite growing utilization of family planning in Ethiopia, many pregnancies in rural areas are still unintended and it remains the main global public and reproductive health challenges with devastating impact on women and child health and general public. Hence, this study was sought to determine the prevalence and associated factors of unintended pregnancy in rural women of Ethiopia. This study used the 2016 Ethiopian Demography and Health Survey data. Total weighted samples of 974 reproductive-aged rural women were included in the analysis. Multilevel mixed logistic regression analysis was employed to consider the effect of hierarchal nature of EDHS data by using stata version 14 to determine individual and community level factors. Variables significantly associated with unintended pregnancy were declared with adjusted odds ratio with 95% CI at p-value < 0.05. The prevalence of unintended pregnancy in rural women was 31.66%( 95%CI: 28.8%, 34.66%). Have no media exposure (AOR: 2.67, 95%CI: 1.48, 4.83), not working (AOR: 0.33, 95%CI: 0.21, 0.52), household size of one to three (AOR: 0.44 95%CI: 0.2, 0.96), primiparous (AOR: 0.41, 95%CI: 0.17, 0.99), poor women (AOR: 2.4, 95%CI: 1.24, 4.56), didn’t have intention to use contraceptive (AOR: 0.24, 95%CI: 0.14, 0.44) were individual factors associated to unintended pregnancy. Large central region (AOR: 4.2, 95%CI: 1.19, 14.62) and poor community level (AOR: 4.3, 95%CI: 1.85, 10.22) were community level factors associated to unintended pregnancy. The present study prevalence of unintended pregnancy in rural women was high. Maternal occupation, household size, media exposure, parity, women wealth, intention to use contraceptive, region and community level wealth were factors statistically associated with unintended pregnancy. Hence, demographer and public health practitioners give great emphasis to set strategies to increase accessibility women to media and improve women financial capacity, and strengthen availability of maternal health service to decrease unintended pregnancy adverse outcome in rural areas.
Identification of Optimal Groundwater Storage Sites in a Semi-Arid Region: A GIS-Based Analytic Hierarchy Process (AHP) Approach
Authors: Qadem Zohair , Abduljaleel Yasir , Amiri Mustapha , Qadem Abdelghani , Lasri Mohamed , Obda Oussama , Pizzo Henrique , Salem Ali 
Published: April 2024

Abstract

Groundwater became a key solution for satisfying water demand for billions of people in many arid and semi-arid regions where climate change has left its negative mark. That poses the necessity of identifying the potential groundwater storage sites to ensure sustainable aquifers. Water resources' availability conditions have a major impact on the socio-economic status of the area, which reflects the necessity of ensuring sustainable water resources, especially groundwater. This study aims to explore potential areas for groundwater storage in the Saïs Plateau and its middle Atlas borders in Morocco using advanced methods such as Remote Sensing (RS) data managed in a Geographic Information System (GIS). The methodology used for evaluation integrates sophisticated methods such as the Analytic Hierarchy Process (AHP) to assess the impact of relevant parameters (precipitation, lithology, rock fractures, and topography) on storage potential. The results reveal significant disparities in storage capacity between the studied regions, highlighting the major influence of climatic and geographical conditions. Areas with high storage potential are mainly concentrated in the Middle Atlas, benefiting from more permeable rocks and abundant precipitation. In contrast, the Saïs Plateau has a more limited storage capacity due to its local geological conditions and lower precipitation levels. This study provides valuable insights for strategic planning of groundwater management, not only as a model for the studied region but also for other regions facing similar challenges of climate change and population growth.
Assembly and analysis of the complete mitochondrial genome of Prunus davidiana (Rosaceae)
Authors: Zhang Yuyan , Guo Xin , Ma Ruijuan , Yu Mingliang , Xu Jianlan , Shen Zhijun , Ren Aihua 
Published: April 2024

Abstract

Background: Prunus davidiana is an excellent woody tree species that has high resistance to various abiotic and biotic stress factors. The species is also a potential gene donor because of its important developmental prospects. While the characteristic of mitochondrial genome (mitogenome) remains unexplored.
Results: In this study, we sequenced and assembled the P. davidiana mitogenome by using the reads from Illumina sequencing and Oxford Nanopore platform. According to the results, the P. davidianamitogenome has a length of 375 671 bp, with a 45.5% GC content. It contains 64 genes, including 39 protein-coding genes, 22 tRNA genes, and 3 rRNA genes. The codon usage, repeated sequences, nonsynonymous to synonymous substitution ratios, RNA editing, synteny, and phylogenetic relationships among Rosaceae species and gene migration event were all examined, respectively. The results of our analyses provide valuable information and a theoretical basis for research on P. davidiana in future.
Conclusions: In this study, we assembled and annotated the mitogenome of P. davidiana, an excellent woody tree species that has high resistance to various abiotic and biotic stress factors. The results of our analyses provide comprehensive information on the P. davidiana mitogenome, which should facilitate evolutionary research and molecular barcoding in Rosaceae.
Characterizing the in vitro motor properties of two kinesin-9 family members from Tetrahymena
Authors: Ishii Hiroto , Yamagishi Masahiko , Yajima Junichiro 
Published: April 2024

Abstract

The kinesin-9 family comprises two subfamilies specific to ciliated eukaryotic cells, and has recently attracted considerable attention because of its importance in ciliary bending and formation. However, only scattered data are available on the motor properties of kinesin-9 family members; these properties have not been compared under identical experimental conditions using kinesin-9 motors from the same species. Here, we report the comprehensive motor properties of two kinesin-9 molecules of Tetrahymena thermophila, TtK9A (Kif9/Klp1 ortholog) and TtK9B1 (Kif6 ortholog), using microtubule-based in vitro assays, including single-motor and multi-motor assays and microtubule-stimulated ATPase assays. Both subfamilies exhibit microtubule plus-end-directed, extremely slow motor activity, both in single and multiple molecules. TtK9A shows lower processivity than TtK9B1. Our findings indicate that the considerable slow movement of kinesin-9 that corresponds to low ATP hydrolysis rates, is a common feature of the ciliary kinesin-9 family.
Psychometric properties of the Depression Anxiety Stress Scales (DASS-21) in women with breast cancer
Authors: Soria-Reyes Lorena Maria , Alarcón Rafael , Cerezo María Victoria , Blanca María J. 
Published: April 2024

Abstract

Breast cancer impacts the psychological well-being of women, leaving them at risk of developing depression, anxiety, and other stress-related disorders. The Depression Anxiety Stress Scales (DASS-21) is a widely used measure, although empirical evidence regarding its psychometric properties in the breast cancer population is limited. The purpose of this study was to conduct an exhaustive analysis of the psychometric properties of the DASS-21 in a sample of Spanish women diagnosed with breast cancer. Participants were 289 breast cancer patients who completed the DASS-21 and other questionnaires measuring life satisfaction, positive and negative affect, flourishing, perceived stress, and breast cancer-specific stressors. In terms of validity evidence based on the internal structure of the DASS-21, adequate fit indices were obtained for the model based on three first-order factors (depression, anxiety, stress) and one second-order factor (general psychological distress). Reliability coefficients (McDonald’s omega) ranged from .84 to .95. Validity evidence based on relationships with other variables was also provided by moderate and strong correlations with well-being indicators and stress measures. The results support the use of the DASS-21 for measuring general psychological distress in the breast cancer context, where it may provide useful information for the design of psychological interventions with patients.
A practical evaluation of AutoML tools for binary, multiclass, and multilabel classification
Authors: Aragão Marcelo V. C. , Afonso Augusto G. , Ferraz Rafaela C. , Ferreira Rairon G. , Leite Sávio , de Figueiredo Felipe A. P. , Mafra Samuel B. 
Published: April 2024

Abstract

Choosing the right Automated Machine Learning (AutoML) tool is crucial for researchers of varying expertise to achieve optimal performance in diverse classification tasks. However, the abundance of AutoML frameworks with varying features makes selection challenging. This study addresses this gap by conducting a practical evaluation informed by a theoretical and bibliographical review and a feature-based comparison of twelve AutoML frameworks. The evaluation, conducted under time constraints, assessed accuracy and training efficiency across binary, multiclass, and multilabel (considering both native and label powerset representations) classification tasks on fifteen datasets. We acknowledge limitations, including dataset scope and default parameter usage, which may not capture the full potential of some frameworks. Our findings reveal no single ``perfect'' tool, as frameworks prioritize accuracy or speed. For time-sensitive binary/multiclass tasks, \claas, \autogluon, and \autokeras showed promise. In multilabel scenarios, \autosklearn offered higher accuracy, while \autokeras excelled in training speed. These results highlight the crucial trade-off between accuracy and speed, emphasizing the importance of considering both factors during tool selection for binary, multiclass, and multilabel classification problems. We made the code, experiment reproduction instructions, and outcomes publicly available on GitHub.