bluuebunny/crossref_metadata_2025_split huggingface dataset:
The prognostic value of tumor-associated macrophages in glioma patients
Authors: Shen Yang , Zheng Dingke , Hu Dong , Ma Baoxin , Cai Chunsheng , Chen Wei , Zeng Jiahao , Luo Junran , Xiao Dan , Zhao Yao , Wu Zhiyan , Jing Guojie , xie yituan 
Published: April 2023

Abstract
Glioma is a complex tumor composed of both neoplastic and non-neoplastic cells, including tumor-infiltrating leukocytes (TILs), and each cell type contributes to tumor formation and malignant progression. Among TILs, tumor-associated macrophages (TAMs) are of great importance and play a key role in the immune response to cancer. In this study, 22 types of adaptive and innate TILs were evaluated in gliomas. TAMs, which account for 38.7% of all these cells, are the most abundant immune infiltrates in the tumor microenvironment (TME). In addition, we observed different immune cell patterns in low-grade glioma (LGG) and glioblastoma (GBM). Our research indicated that there was a connection between TILs, and 13 of 22 TILs were significantly associated with patient outcomes. Finally, the prognosis and diagnostic value of TAMs were revealed using Kaplan-Meier analysis. We identified the optimal cut-off point of TAMs at an infiltrating level of 0.47 to predict patient prognosis, with a median overall survival (OS) of 448 days in patients with higher TAM infiltration levels and 2660 days in patients with lower TAM infiltration levels. These findings provide a new idea for glioma to regulate tumor-specific immunity, clarify the potential effects of TAMs on disease pathology, and provide a theoretical basis for immune intervention treatment of gliomas.
Establishment of a basement membrane-related prognosis model and characterization of tumor microenvironment infiltration in acute myeloid leukemia
Authors: Zhu Zongsi , Zhao Mingming , Guan Jiaqiang , Zheng Cuiping 
Published: April 2023

Abstract
Background Basement membrane is a special component of extracellular matrix of epithelial and endothelial tissues, which can maintain their normal morphologies and functions. It can also participate in tumor progression and affect tumor treatment. However, the roles of basement membrane-related genes (BMGs) in acute myeloid leukemia (AML) remain unknown.
Methods We downloaded the data of AML and normal samples from TCGA, GTEx, and GEO. Then, we performed bioinformatics analysis to identify differential BMGs. We calculated the risk score of the training cohort and divided it into two risk groups. In addition, we also introduced external cohorts, serving as validation cohorts, to estimate the accuracy of risk score. A nomogram was established based on the risk score and clinicopathological characteristics to predict the prognosis. Based on BMGs, AML patients of TCGA were clustered into 2 subtypes. To investigate the biological features and the association between immune cells and tumor microenvironment (TME), we performed GSVA and ssGSEA analyses. Lastly, we performed the analysis of genetic mutation and drug sensitivity.
Results We obtained 3 differential BMGs between AML and normal samples. The training cohort was divided into high- and low-risk groups based on the risk score. The Kaplan-Meier survival analysis indicated that the two groups had significant differences. The nomogram could be used to predict the survival outcomes of AML patients. Based on the clustering result, we found significant differences between the two gene clusters. Sankey’s diagram suggested that cluster B was associated with the high-risk group and poor prognosis. GSVA analysis showed that cluster B was also related to the upregulation of intercellular and intracellular signal transduction pathways. In TME, resting mast cells, follicular helper T cells, and plasma cells decreased while monocytes increased in the high-risk group. In addition, the high-risk group was more sensitive to BTK and AKT inhibitors.
Conclusion Our study indicated that the nomogram model of BMGs could predict the prognosis of AML patients. Meanwhile, BMGs were correlated with immune TME in AML. A correct and comprehensive assessment of the mechanisms of BMGs in individuals will help guide more effective treatment.
Adaptive wave-particle decomposition in UGKWP method for high-speed flow simulations
Authors: Wei Yufeng , Cao Junzhe , Ji Xing , Xu Kun 
Published: April 2023

Abstract
With wave-particle decomposition, a unified gas-kinetic wave-particle (UGKWP) method has been developed for the multiscale flow simulations. With the variation of cell's Knudsen number, the UGKWP method captures the transport process in all flow regimes without kinetic solver's constraint on the numerical mesh size and time step being less than the particle mean free path and collision time. In the current UGKWP method, the cell's Knudsen number, which is defined as the ratio of particle collision time to numerical time step, is used to distribute the components in the wave-particle decomposition. However, the adaptation of particle in UGKWP is mainly for the capturing of the non-equilibrium transport, and the cell's Knudsen number alone is not enough to identify the non-equilibrium state. For example, in the equilibrium flow regime with a Maxwellian distribution function, even at a large cell's Knudsen number, the flow evolution can be still modelled by the Navier-Stokes solver. More specifically, in the near space environment both the hypersonic flow around a space vehicle and the plume flow from a satellite nozzle will encounter a far field rarefied equilibrium flow in a large computational domain. In the background dilute equilibrium region, the large particle collision time and a uniform small numerical time step can result in a large local cell's Knudsen number and make UGKWP track a huge number of particles for the far field background flow. But, in this region the analytical wave representation can be legitimately used in UGKWP to capture the nearly equilibrium flow evolution. Therefore, to further improve the efficiency of UGKWP for multiscale flow simulations, an adaptive UGKWP (AUGKWP) method will be developed with the introduction of an additional local flow variable gradient-dependent Knudsen number. As a result, the wave-particle decomposition in UGKWP will be determined by both cell's and gradient's Knudsen numbers, and the use of particle in UGKWP is solely to capture the non-equilibrium flow transport. The current AUGKWP becomes much more efficient than the previous one with the cell's Knudsen number only in the determination of wave-particle composition. Many numerical tests, including Sod shock tube, normal shock structure, hypersonic flow around cylinder, flow around reentry capsule, and an unsteady nozzle plume flow, have been conducted to validate the accuracy and efficiency of the AUGKWP method. Compared with the original UGKWP method, the AUGKWP method achieves the same accuracy, but has advantages in memory reduction and computational efficiency in the simulation for the flow with the co-existing of multiple regimes.
In vitro adventitious regeneration and plantlet transplantation of Atractylodes chinensis (DC.) Koidz., a valuable medicinal plant
Authors: Jia Wenhao , Rong Junbo , Zhang Mengyang , Peng Wenyue , He Xutong , Lei Xiujuan , Wang Yingping 
Published: April 2023

Abstract
Triploid Atractylodes chinensis (DC.) Koidz. (A. chinensis) is a valuable genetic resource for medicinal plant breeding, and there is a demand to develop an efficient in vitro regeneration protocol to resolve triploid sterility in production. In this study, the effects of sterilization, bud type, 6-benzyladenine (6-BA) combined with 1-naphthaleneacetic acid (NAA) or indole-3-butyric acid (IBA) and transplanting materials on shoot regeneration, rooting and growth were explored. The genetic stability of regenerated plants was verified using flow cytometry (FCM) and simple sequence repetition (SSR) molecular markers. When axillary buds were sterilized with sodium hypochlorite for 30 min and cultured on Murashige and Skoog (MS) + 1.5 mg·L-1 6-BA + 0.4 mg·L-1 NAA medium, the regeneration rate was 61.33%. Strong roots occurred on 1/2 MS combined with 3% sucrose and 0.6 mg·L-1 IBA medium. Rooting plantlets transplanted into a mixture of peat soil: perlite (1:1, v/v), the survival rate up to 90.00%. Histological analyses revealed that shoot meristematic cells derived from cambium cells developed into the apical meristem and formed shoots. FCM analysis determined that the ploidy levels of 20 random regenerated plants were coincident with explants, the number and size of bands obtained by 6 pairs of SSR polymorphic primers were consistent. The results of this study show that our in vitro adventitious regeneration and plantlet transplantation protocol of triploid A. chinensis was efficient and produced strong genetic stability.
Ileoileal knotting a rare cause of double loop small bowel obstruction,diagnostic and intraoperative challenge at Ethiopian Leku district hospital,sidama region,April 2023 ,case report
Authors: Kibret Asfaw 
Published: April 2023

Abstract
Baground
Intestinal obstruction is a common cause for abdominal surgeries. Among the causes for intestinal obstruction ileal knotting is the unusual and rare cause with very few case reports in the globe and in Ethiopia.Almost all cases were intraoperative surprises.We report a case of strangulated closed loop obstruction caused by ileoileal knotting at distal ileum near ileocecal junction,its diagnostic and management challenges and the role of the “Integrated Emergency surgical officers’’ for early emergency surgical interventions in district primary hospitals in Ethiopia where there is scarce general specialist surgeon.
Case presentation
Here we discuss a 78yrs old male Ethiopian patient presented to our district hospital with sign symptoms of strangulated small bowel obstruction and exploratory laparatomy was done with intraoperative surprise of ileoileal knot with gangreneous closed loop obstruction at ileocecal junction.The gangreneous segment was resected and ileo ascending colon anastomosis was done.The post operative stay was uneventful and patient discharged on his 7th post operation date.
Conclusion
Here we present this case to highlight difficulty of preoperative diagnosis and the need of high index of suspicion as well as the management challenges of resection anastomosis when the knot is near to ileocecal junction and the undeniable role of emergency surgical officers for early intervension such emergency cases who need early intervensios.
Quantitative measurement of positive and negative ion species ejected from a Li-O-H surface by hydrogen and noble gas ion irradiation
Authors: Abe Shota , Ostrowski Evan , Maan Anurag , Krstic Predrag , Majeski Richard , Koel Bruce 
Published: April 2023

Abstract
We report sputtering yields of Li+, H−, O−, and OHx− ion species from an Li-O-H surface for H, D, He, Ne, and Ar ion irradiation at 45° incidence in the energy range of 30 − 2,000 eV. A Li film was deposited on a stainless steel target using Li evaporators in the LTX-β vessel, using the LTX-β Sample Exposure Probe (SEP), which includes an ultrahigh vacuum suitcase for transferring targets without significant contamination from air exposure. The SEP was used to transfer the Li-coated target from LTX-β to a separate Sample Exposure Station (SES) to perform ion exposure measurements. The SEP was also used for characterization of the Li-coated target utilizing X-ray photoelectron spectroscopy (XPS) in a different chamber, showing that the lithium film surface was oxidized. Ion exposures were performed using an electron cyclotron resonance (ECR) plasma source in the SES. Sputtered/ejected species were sampled by a quadrupole mass spectrometer with capabilities for detecting positive and negative ions, and an energy filter for determining the mean kinetic energy of the ejected ion species. All ion irradiations caused Li+ ions to be ejected, while causing impurity ions such as H+, H−, O− and OH− to be ejected. Our results for the sputtering yields of ejected ion species and their associated ion energies from a Li-O-H surface indicates that lithium sputtering is suppressed and impurity removal is enhanced due to the sheath potential at the divertor surface for fusion reactor applications.
Alcohol use disorder among patients diagnosed with Tuberculosis in a large urban case-finding project in central Uganda: prevalence, associated factors and lived experiences
Authors: Bayigga Josephine , Kakai Ilona , Odongpiny Eva Laker , Wiltshire Christine Sekaggya , Ddungu Ahmed , Semakula Lynn , Nansereko Martha , Stavia Turyahabwe , Zawedde-Muyanja Stella 
Published: April 2023

Abstract
Background Heavy consumption of alcohol increases the risk of developing active tuberculosis (TB), contributes to delayed diagnosis and affects adherence to treatment. Within a large urban case-finding project, we sought to determine the prevalence of and factors associated with AUD and to understand the lived experiences of patients with alcohol use disorder (AUD).Methods We carried out a mixed methods study in two large urban districts in Uganda. We collected quantitative data on the prevalence of alcohol use disorder using the Cut, Annoyed, Guilty, Eye opener (CAGE) tool. We conducted focus group discussions (FGDs) to understand lived experiences of patients with AUD particularly challenges with adhering to TB treatment. Factors associated with AUD were examined using a multilevel logistic regression model. Focus group discussions were transcribed, data was analysed inductively and coded into themes.Results Out of 325 TB patients interviewed, 62 (18.7% 95% confidence interval [CI] 18–31%) had AUD. Majority 82.3% (51/62) were men. Being male aOR 3.26 (95% CI 1.45, 7.33) and living in an urban area aOR 1.89 (95% CI: 1.01, 3.53) were significantly associated with AUD. Among patients with AUD, there was a trend towards suboptimal TB treatment outcomes, although this did not reach significance aOR 2.15 (95% CI: 0.95, 4.90). Fourteen patients (eight men and six women) with AUD attended two FGDs. Patients with AUD often did not disclose alcohol use and missed clinic refill appointments due to lack of money to pay the transport fare to the clinic. In addition, lack of food coupled with the long treatment duration were challenges to TB treatment completion.Conclusion A large proportion of TB patients have undisclosed AUD and experience several challenges while on TB treatment. TB care programs need to design interventions in order to address AUD.
Learning Food Composition Knowledge from scientific literature
Authors: Jiomekong Azanzi 
Published: April 2023

Abstract
Food Composition Tables (FCT) or Food Composition Databases (FCD) contains the food we eat and what it contains. It is built by using chemical analysis to determine the different composition and structure of foods. However, the chemical analysis of food requires significant financial resources and skilled laboratory investigators. These resources are not always available. Thus, in many cases, to build Food Composition Tables, many people rely on existing resources such as scientific papers. Scientific papers contain key-insights organized in text, tables figures, etc. that are used to understand the scientific contribution of its author. Many FCT are stored in scientific papers related to food, nutrition, food chemistry, etc. in the form of tables. Acquiring these tables manually as it is currently done by domain experts is costly, not scalable and cumbersome work because one has to open the paper, copy the elements one by one and save in a file such as CSV files. This paper proposes to learn Food Composition Knowledge (FCK) stores in tables of scientific papers. It consists of using Deep Learning techniques for the automatic detection of tables, text recognition from these tables, text extraction and table reconstruction. This approach was used to extract over 10,000 tables from around 5000 scientific papers. To validate the knowledge extracted, we presented 100 tables selected manually to a Professor in Food Science and Nutrition. On the other hand, the validation by Ontology Recommender of Bioportal showed that the knowledge extracted are relevant to the biomedical domain in general and can be used to enrich food ontologies.
Intraperitoneal paclitaxel combined with FOLFOX/CAPOX plus bevacizumab for colorectal cancer with peritoneal carcinomatosis (the iPac-02 trial): study protocol of a single arm, multicenter, phase 2 study
Authors: Murono Koji , Yokoyama Yuichiro , Nozawa Hiroaki , Sasaki Kazuhito , Emoto Shigenobu , Matsuzaki Hiroyuki , Kashiwabara Kosuke , Ishigami Hironori , Gohda Yoshimasa , Yamaguchi Hironori , Kitayama Joji , Ishihara Soichiro 
Published: April 2023

Abstract
Background The safety of intraperitoneally administrated paclitaxel (ip PTX) was demonstrated in the phase I trial of ip PTX combined with conventional systemic chemotherapy for colorectal cancer with peritoneal carcinomatosis. Moreover, the median survival time was 29.3 months, which was longer than that observed in previous studies. Here, we planned the phase II trial of ip PTX: the iPac-02 trial.Methods This multicenter, open-label, single assignment interventional clinical study includes patients with colorectal cancer with unresectable peritoneal carcinomatosis. FOLFOX-bevacizumab or CAPOX-bevacizumab is administered concomitantly as systemic chemotherapy. PTX 20 mg/m2 is administered weekly through the peritoneal access port in addition to these conventional systemic chemotherapies. The response rate is the primary endpoint. Progression-free survival, overall survival, peritoneal cancer index improvement rate, rate of negative peritoneal lavage cytology, safety, and response rate to peritoneal metastases are the secondary endpoints. A total of 38 patients are included in the study. In the interim analysis, the study will continue to the second stage if at least 4 of the first 14 patients respond to the study treatment. The study has been registered at the Japan Registry of Clinical Trials (jRCT2031220110).
On Computing the Topological Invariant of Metal-Organic Network
Authors: Yang Jun , Malik Mehar Ali , Aqib Muhammmad 
Published: April 2023

Abstract
This study focuses on the application of Metal-Organic Networks (MON’s) as a structural support for chemical compounds in the energy department. MON’s have diverse properties in various elds and are frequently used to restore chemical compounds, particularly those with elements like hydrogen and carbon as energy sources. The topological indices (TIs) of MON structures provide a relationship between the physical and chemical properties of the ligands, including melting and boiling points, chemical stability, pressure, and chemical reaction factors. In this paper, we calculate various TIs based on degrees for two diierent metal-organic networks with expanding layers of metal vertices and organic ligands. We provide a comparison of various TIs using numerical values and graphical representations.
In this paper, we compute various topological invariant based on degree partitioning for two metal-organic networks with increasing layers of organic ligands and metal vertices. We also analyze their behavior in higher-dimensional graphs and present pairwise comparisons of their values for these invariants, supported by relevant graphs.
A CNN-LSTM-att Hybrid Model for Classification and Evaluation of Growth status under Drought and Heat stress in Chinese fir (Cunninghamia lanceolata)
Authors: Xing Dong , Wang Yulin , Sun Penghui , Huang Huahong , Lin Erpei 
Published: April 2023

Abstract
Background Cunninghamia lanceolata (Chinese fir), is one of the most important timber trees in China. With the global warming, to develop new resistant varieties to drought or heat stress has become an essential task for breeders of Chinese fir. However, classification and evaluation of growth status of Chinese fir under drought or heat stress are still labor-intensive and time-consuming. Here, we proposed a CNN-LSTM-att hybrid model for classification of growth status of Chinese fir seedlings under drought and heat stress, respectively. Two RGB image datasets of Chinese fir seedling under drought and heat stress were generated for the first time, and utilized in this study. By comparing four base CNN models with LSTM, the Resnet50-LSTM was identified as the best model in classification of growth status, and LSTM would dramatically improve the classification performance. Moreover, attention mechanism further enhanced performance of Resnet50-LSTM, which was verified by Grad-CAM.
Results By applying the established Resnet50-LSTM-att model, the accuracy rate and recall rate of classification was up to 96.91% and 96.79% for dataset of heat stress, and 96.05% and 95.88% for dataset of drought, respectively. Accordingly, the R2 value and RMSE value for evaluation on growth status under heat stress were 0.957 and 0.067, respectively. And, the R2 value and RMSE value for evaluation on growth status under drought were 0.944 and 0.076, respectively.
Conclusion In summary, our proposed model provides an important tool for stress phenotyping in Chinese fir, which will be a great help for selection and breeding new resistant varieties in future.
A case of SARS-CoV-2 Omicron variant co-infection with Influenza A-H3N2 from India
Authors: Vaman Raman Swathy , Jolly Bani , Bhoyar Rahul C. , Augustine Anu Elizabeth , Mohan Anuja , PM Anitha , Vignesh Harie , Sivadas Saritha , Sivasubbu Sridhar , Scaria Vinod 
Published: April 2023

Abstract
We report a case of SARS-CoV-2 Omicron variant co-infection with influenza A H3N2 detected from Kerala, India. The patient, a 10-year-old girl, had symptoms of low-grade fever, cough, and cold. As part of the ongoing surveillance, a throat swab was taken and sent for testing, and the influenza A virus isolated from the patient was identified as subtype H3N2. Whole-genome sequencing and analysis of the viral isolates suggested that the SARS-CoV-2 isolate belonged to BA.4.1 sublineage of Omicron while the influenza A isolate belonged to the 2a.3 clade of H3N2 and clustered with other H3N2 genomes from Maldives, India, Bangladesh, and the United Arab Emirates. The report highlights the importance of genomic surveillance of SARS-CoV-2 co-infections with other respiratory illnesses for understanding the prevalence of co-infections and their rapid detection and prevention.