bluuebunny/crossref_metadata_2025_split huggingface dataset:
Systematic Analysis Identifies NUF2 as an Immunological and Prognostic Biomarker for Non-small cell lung cancer
Authors: li xia , yi zhongquan , zhang lianlian , zhou jin , song wenchun , zhao panwen , wu jixiang , song jianxiang , Ni qinggan 
Published: August 2021

Abstract
Background

Non-small cell lung cancer (NSCLC) is a part of the most common cancers in the world. A lot of efforts have been made to clarify the etiology of non-small cell lung cancer, but the molecular mechanism of non-small cell lung cancer is still unclear.

Methods

In order to identify candidate genes in the occurrence and progression of non-small cell lung cancer, GSE19804 GSE118370 GSE19188 GSE27262 and GSE33532 microarray data sets were downloaded from the Gene Expression General (GEO) database. Identify differentially expressed genes (DEGS) and perform functional enrichment analysis. The protein-protein interaction network (PPI) was constructed, and the module analysis was performed using STRING and Cytoscape. A total of 562 DEGS were identified, consisting of 98 downregulated genes and 464 upregulated genes. Abundant functions and pathways of DEGS include p53 signaling pathway, Cell adhesion molecules,Leukocyte transendothelial migration,Vascular smooth muscle contraction,Complement and coagulation cascades and Axon guidance. Tumor immunity was assessed to investigate the functions of hub genes.

Results

Totally 562 genes were found to be dysregulated. 12 genes were considered to be the hub genes. NUF2 was considered as the potential immunotherapeutic targets with future clinical significance.12 hub genes were detected, and biological process analysis showed that these genes are mainly enriched in p53 signaling pathway,Progesterone-mediated oocyte maturation,Cell cycle, Oocyte meiosis and Cellular senescence Survival analysis shows that NUF2 may be linked to the occurrence, invasion or recurrence of non-small cell lung cancer.

Conclusion

NUF2 genes discovered in this study help us include the molecular mechanisms of the occurrence and progression of non-small cell lung cancer, and provide candidate targets for the diagnosis and treatment of non-small cell lung cancer.
Theoretical Modelling of High-efficiency Perovskite Solar Cells and Reduction of Internal Heat Generation using Hot-Electron Extraction
Authors: Rostami Ali , Tofigi Isun , Barzinjy Azeez , Mirtagioglu Hamit 
Published: August 2021

Abstract
Perovskite single crystals have received enormous attention in recent years. This is, perhaps, due to their simplistic synthesis and excellent optoelectronic properties including the long carrier diffusion length, high carrier mobility, low trap density, and tuneable absorption edge ranging from ultra-violet (UV) to near-infrared (NIR). These distinguishing features offer numerous potential applications in energy-related fields like solar cells, photodetectors (PDs), lasers, etc. Efficiency enhancement and stability, in general, are the main challenges to obtain better solar cells. One of the main reasons for the early degradation of solar cells is heat generation due to high energy electrons and holes in the conduction and valance bands. In this study, the authors trying to introduce the concept of selective energy contacts in perovskite solar cells. Also, they investigate how this concept affects the power conversion efficiency (enhancement) and heat generation due to hot electrons and holes (reduction) scattering in the conduction and valance bands. Both efficiency enhancement and reduction in heat generation have been calculated in this study. Thus, for mathematical modeling of the anticipated idea, the Methylammonium lead halide (CH3NH3PbI3) material is used in a PIN structure for a single-junction solar cell. Also, for the proposed structure, analytical modeling was introduced and it is shown that the efficiency of a single contact cell is around 25%, and after applying the second contact, the efficiency was increased to 35%. Finally, due to the reduction of heat loss in the structure, the stability of perovskite material is significantly increased.
The Relationship Between Triglycerides, High-Density Lipoprotein, Triglyceride/High-Density Lipoprotein, and Hospital Death in Patients with Sepsis: A Retrospective Cohort Study
Authors: Gong Rongpeng , Tian Yu , Hu Tianyang , Xu Zixin , Deng Xiao , Shen Xiaofang , Wei Xiaoxin 
Published: August 2021

Abstract
Background: Sepsis remains the leading cause of death in the ICU. There is still controversy about the association between TG, HDL and TG/HDL and sepsis. Our aim was to explore the relationship between TG, HDL, TG/HDL and the hospitalized mortality of sepsis by using the MIMIC-IV database.Methods: Selected from patients admitted to MIMIC-IV database (2008-2019). A total of 1032 eligible participants were included. Multivariate Cox regression model was used to analyze the correlation between TG, HDL, TG/HDL and sepsis hospitalization death after excluding potential confounding factors, and the smooth curve fitting graph and survival curve were drawn. Subgroup analysis was performed to test the results.ResultsThere was a negative correlation between TG , TG/HDL and the poor prognosis of sepsis, while HDL was positively correlated with the poor prognosis of sepsis.
Neoadjuvant PD-1 blockade induces T cell and cDC1 activation but fails to overcome the immunosuppressive tumor associated macrophages in recurrent glioblastoma
Authors: Lee Alexander , Sun Lu , Mochizuki Aaron , Reynoso Jeremy , Orpilla Joey , Chow Frances , Kienzler Jenny , Everson Richard , Nathanson David , Bensinger Steven , Liau Linda , Cloughesy Timothy , Hugo Willy , Prins Robert 
Published: August 2021

Abstract
Primary brain tumors, such as glioblastoma (GBM), have been remarkably resistant to immunotherapy, even though pre-clinical models suggest effectiveness. To understand this better in patients, we took advantage of our recent neoadjuvant treatment paradigm to map the infiltrating immune cell landscape of GBM and how this is altered following PD-1 checkpoint blockade using high dimensional proteomics, single cell transcriptomics, and quantitative multiplex immunofluorescence. Neoadjuvant PD-1 blockade increased T cell infiltration and proportion of a progenitor exhausted population of T cells found within the tumor. We identified an early activated and clonally expanded CD8+ T cell cluster whose TCR overlapped with a CD8+ PBMC population. Distinct changes were also observed in conventional type 1 dendritic cells that may facilitate T cell recruitment. Macrophages and monocytes still constituted the majority of infiltrating immune cells, even after anti-PD-1 therapy. Interferon-mediated changes in the myeloid population were consistently observed following PD-1 blockade; these also mediated an increase in chemotactic factors that recruit T cells. However, sustained high expression of T-cell-suppressive checkpoints in these myeloid cells continued to prevent the optimal activation of the tumor infiltrating T cells. Therefore, future immunotherapeutic strategies may need to incorporate the targeting of these cells for clinical benefit.
Use of Moringa Oleifera Seeds as a Biosorbent and Antimicrobial Agent in Acidic Mineral Effluents
Authors: Ncube Pauline , Ntuli Freeman , Falayi Thabo 
Published: August 2021

Abstract
Moringa Oleifera (MO) seed extract was used as an antimicrobial agent and a biosorbent to remove heavy metals from acidic mineral effluents. Biosorption experiments were conducted in a thermostatic shaker using synthetic acidic mineral effluent(SAME) of composition, 20 ppm, 20 ppm, 100 ppm, and 500 ppm for Ni, Cu, Mn, and Fe, respectively. The Quanti-tray and SimPlate standard procedures were used for the antimicrobial tests. The aqueous seed extract achieved microbial reductions of 100% total coliform and 90.5% Heterotrophic Plate Count (HPC). Ni and Cu were the most removed metals and optimum sorption conditions achieved were pH = 3, Temperature = 308 K, solid loading = 10% m/v, and residence time = 90 minutes. The biosorption process was endothermic for all the metals but only feasible and spontaneous for Cu and Ni. The Langmuir model and second-order kinetics best fit the adsorption process for Ni, Cu, and Fe, while ion-exchange/ chemisorption was the possible mechanism of adsorption. Overall, MO seed extract was an effective antimicrobial agent and bio-sorbent for Ni, Cu, and Fe removal in acidic mineral effluent. The use of MO in acidic medium is a novel technique.
Determinants of Elderly Pedestrian Traffic Behavior in Iran: The Role of Socio Economic and Cognition Status
Authors: Ghasemi Masoumeh , Bazargani Homayoun Sadeghi- , Aghdam Fatemeh Bakhtari , Ponnet Koen , Papi Shahab , Rostami Zahra 
Published: August 2021

Abstract
Background: Elderly pedestrians are among the most vulnerable groups in terms of traffic-related injuries. This study aimed to investigate traffic behavior and its determinants among elderly pedestrians in Iran.Methods: This cross-sectional study examined the traffic behavior of 600 elderly pedestrians in Zanjan, northwestern Iran. Pedestrian traffic behavior was evaluated in five domains (traffic violations, traffic distraction, adherence to traffic rules, aggressive behaviors, and positive behaviors) using the Pedestrian Behavior Questionnaire (PBQ). Participants’ socioeconomic status (SES) was assessed by an SES questionnaire, and cognitive function was assessed by the Abbreviated Mental Test score (AMTS). The participants were selected using the multistage random sampling method.Results: 50% of elders were man. 488 (81.3%) of them had 60-74 and 112 (18.7%) were 75 years old and above. More than 90% of elderly pedestrians showed unsafe traffic behavior. This included traffic violations and failure to adhere to traffic rules. Almost half the elders were aggressive and distracted when walking and crossing the street. Higher SES was associated with both higher cognitive status and safer traffic behavior. Higher SES, healthy cognitive function, male sex, walking more than 1 hour a day, higher levels of education, and being married were among the determinants of safe traffic behavior.Conclusion: The majority of the elders showed unsafe traffic behavior Elderly pedestrians with high SES and healthy cognitive function were more likely to exhibit safe behavior than those with low SES and cognitive dysfunction. . Interventions are needed to improve the traffic behavior of elderly pedestrians special with low SES.
WITHDRAWN: Study of Biofilm Formation and Antibiotic Resistant Profile in Multidrug Resistant and Extensive Drug Resistance Pseudomonas Aeruginosa Isolated from Burn Wound Infections in Southwest Iran
Authors: dezfuli Aram asareh zadegan , Avarvand Arshid Yousefi 
Published: August 2021

Abstract
Background: Pseudomonas aeruginosa is an opportunistic pathogen that has remained on the ‘top 10’ common hospital ‘superbugs’ worldwide for more than a decade. Study of biofilm formation and antibiotic resistant profile in multidrug resistant and extensive drug resistance P. aeruginosa isolated from burn wound infections in southwest IranMethods and Results: This study, which was performed in 110 P. aeruginosa isolates culture-positive reports. Assessment of biofilm formation via microtiteplate and congo red agar. Overall, 110 clinical P. aeruginosa isolates were confirmed from wound burn infections. The maximum resistance rate among P. aeruginosa isolates to antibiotics tested was as follow Piperacillin, ceftazidime, and minimum resistance rate among P. aeruginosa isolates to antibiotics tested such as ticarcillin-clavulanic acid. The isolates were then evaluating the MICs by using the E-test. only 7 isolates were confirmed as colistin-resistant. Colistin reference MICs for the The prevalence of MDR P. aeruginosa was 38% and XDR- P. aeruginosa was 22% respectively. One of P. aeruginosa isolates were PDR. In microtiteplate assay,76% of the isolates have ability for biofilm, formation, 40% were categorized as strong biofilm-formers; 32% were moderate; 21% were weak biofilm formers and 43% could not form any detectable biofilm. Conclusion: in our study development of resistance by P. aeruginosa to many antimicrobial agents is a great challenge in controlling its infections. Therefore, the transmission of these isolates to patients leads to higher resistance. Therefore, the necessary hygiene measurements should be taken for the prevention of transferring the P. aeruginosa isolates to hospitalized patients.
A Pilot Study for the Prediction of Liver Function Related Scores Using Breath Biomarkers and Machine Learning
Authors: Patnaik Rakesh Kumar , Lin Yu-Chen , Agarwal Ashish , Ho Ming Chih , Yeh J. Andrew 
Published: August 2021

Abstract
Liver function test is the first step to diagnose various liver diseases by measuring certain proteins and liver enzymes from the blood sample. After getting the required data of the clinical parameters from the blood test it is possible to calculate Child-Pugh (CTP), AST to PLT ratio (APRI) and Model for end-stage liver disease (MELD) clinical scores that help the doctors about the severity of the disease progression. Volatile organic compounds (VOCs) found in-breath and monitoring their concentration may be a prevailing method for disease diagnosis. In this work, Isoprene, Limonene, and Dimethyl sulphide (DMS) are considered as a potential breath biomarker related to liver disease. A dataset is designed, that includes the biomarkers concentration analysed from the breath sample before and after study subjects performed an exercise. Four regression methods are performed to predict the clinical scores using breath biomarkers data as features set by the machine learning techniques. Regression methods on the dataset for prediction are evaluated by mean absolute error and root mean square error. A significant difference observed for isoprene concentration (p<0.01) and for DMS concentration (p<0.0001) between liver patients and healthy subjects breath sample. Ensemble regression methods are found best suited for the dataset. The mean absolute error for CTP score is 0.07, for APRI score 0.1 and for MELD score 0.7. The R-square value between actual clinical score and predicted clinical score is found to be 0.78, 0.95, and 0.85 for CTP score, APRI score, and MELD score, respectively. These results suggest that breath biomarkers hold a promising approach for non-invasive test and mass screening related to liver disease.
Quantitative assessment of near-infrared fluorescent proteins
Authors: Piatkevich Kiryl , Zhang Hanbin , Papadaki Stavrini , Sun Xiaoting , Yao Luxia , Wang Xinyue , Köster Reinhard , Wu Lianfeng , Namikawa Kazuhiko 
Published: August 2021

Abstract
Recent progress in fluorescent protein development has generated a large diversity of near-infrared fluorescent proteins, which are rapidly becoming popular probes for a variety of imaging applications. To assist end-users with a selection of the right near-infrared fluorescent protein for a given application, we will conduct a quantitative assessment of intracellular brightness, photostability, and oligomeric state of 19 near-infrared fluorescent proteins in cultured mammalian cells. The top-performing proteins will be further validated for in vivo imaging of neurons in C. elegans, zebrafish, and mice. We will also assess the applicability of the selected NIR FPs for expansion microscopy and two-photon imaging.
High-throughput nanofluidic real-time PCR to discriminate Pneumococcal Conjugate Vaccine (PCV)-associated serogroups 6, 18, and 22 to serotypes using modified oligonucleotides.
Authors: Downs Sarah Leah , Madhi Shabir Ahmed , Merwe Lara van Der , Nunes Marta Coelho , Olwagen Courtney Paige 
Published: August 2021

Abstract
Current real-time Polymerase Chain Reaction (qPCR) methods are unable to distinguish serotypes 6A from 6B, 18C from 18A/B and 22F from 22A. We established a nanofluidic real-time PCR (Fluidigm) for serotyping that included Dual-Priming-Oligonucleotides (DPO), a Locked-Nucleic-Acid (LNA) probe and TaqMan assay-sets for high-throughput serotyping. The designed assay-sets target capsular gene wciP in serogroup 6, wciX and wxcM in serogroup 18, and wcwA in serogroup 22. An algorithm combining results from published assay-sets (6A/B/C/D; 6C/D; 18A/B/C; 22A/F) and designed assay-sets for 6A/C; 18B/C/F; 18C/F, 18F and 22F was validated through blind analysis of 1973 archived clinical samples collected from South African children ≤ 5-years-old (2009-11), previously serotyped with the culture-based Quellung method. All assay-sets were efficient (92–101%), had low variation between replicates (R2 > 0.98), and were able to detect targets at a limit of detection (LOD) of < 100 Colony-Forming-Units (CFU)/ml of sample. There was high concordance (Kappa = 0.73–0.92); sensitivity (85–100%) and specificity (96–100%) for Fluidigm compared with Quellung for serotyping 6A; 6B; 6C; 18C and 22F. Fluidigm distinguishes vaccine-serotypes 6A, 6B, 18C, next-generation PCV-serotype 22F and non-vaccine-serotypes 6C, 6D, 18A, 18B, 18F and 22A. Discriminating single serotypes is important for assessing serotype replacement and the impact of PCVs on vaccine- and non-vaccine serotypes.
Global predictions of short- to medium-term COVID-19 transmission trends : a retrospective assessment
Authors: Bhatia Sangeeta , Parag Kris , Wardle Jack , Imai Natsuko , Elsland Sabine van , Lassmann Britta , Cuomo-Dannenburg Gina , Jauneikaite Elita , Unwin H. Juliette , Riley Steven , Ferguson Neil , Donnelly Christl , Cori Anne , Nouvellet Pierre 
Published: August 2021

Abstract
From 8th March to 29th November 2020, we produced weekly estimates of SARS-CoV-2 transmissibility and forecasts of deaths due to COVID-19 for 81 countries with evidence of sustained transmission. We also developed a novel heuristic to combine weekly estimates of transmissibility to produce forecasts over a 4-week horizon. We evaluated the robustness of the forecasts using relative error, coverage probability, and comparisons with null models. During the 39-week period covered by this study, both the short- and medium-term forecasts captured well the epidemic trajectory across different waves of COVID-19 infections with small relative errors over the forecast horizon. The model was well calibrated with 56.3\% and 45.6\% of the observations lying in the 50\% Credible Interval in 1-week and 4-week ahead forecasts respectively. We could accurately characterise the overall phase of the epidemic up to 4-weeks ahead in 84.9\% of country-days. The medium-term forecasts can be used in conjunction with the short-term forecasts of COVID-19 mortality as a useful planning tool as countries continue to relax public health measures.
Co-Culture of Mesenchymal Stem Cell Spheres with Hematopoietic Stem Cells Under Hypoxia: A Cost-Effective Method to Maintain Self-Renewal and Homing Marker Expression
Authors: Amiri Fatemeh , Kiani Ali Asghar , Bahadori Marzie , roudkenar mehryar habibi 
Published: August 2021

Abstract
Background: Hematopoietic stem cell (HSC) transplantation is considered a possible treatment option capable of curing various diseases. The aim of this study was the co-culturing of mesenchymal stem cell (MSC) spheres with HSCs under hypoxic condition to enhance the proliferation, self-renewal, stemness, and homing capacities of HSCs.Methods and results: HSCs were expanded after being subjected to different conditions including cytokines without feeder (Cyto), co-culturing with adherent MSCs (MSC), co-culturing with adherent MSCs+ hypoxia (MSC+ Hyp), co-culturing with MSCs spheres (Sph-MSC), co-culturing with MSCs spheres+ hypoxia (Sph-MSC+ Hyp), co-culturing with MSC spheres+ cytokines (Sph-MSC+Cyto). After 10 days, total nucleated cell (TNC) and CD34+/CD38- cell counts, colony-forming unit assay (CFU), long-term culture initiating cell (LTC-IC), the expression of endothelial protein C receptor (EPCR), nucleostemin (NS), nuclear factor I/X (Nfix) CXCR4, and VLA-4 were evaluated. The TNC, CD34+/CD38- cell count, CFU, and LTC-IC were higher in the Sph-MSC+ Hyp and Sph-MSC+ Cyto groups as compared with those of the MSC+ Hyp group (P<0.001). The expanded HSCs co-cultured with MSC spheres in combination with hypoxia expressed more EPCR, CXCR4, VLA-4, NS, and Nfix mRNA. The protein expression was also more up-regulated in the Sph-MSC+Cyto and Sph-MSC+ Hyp groups.Conclusion: Co-culturing HSCs with MSC spheres under hypoxic condition not only leads to higher cellular yield but also increases the expression of self-renewal and homing genes. Therefore, we suggest this approach as a simple and non-expensive strategy that might improve the transplantation efficiency of HSCs.
Addressing the Need for Patient-friendly Medical Communications: Adaptation of the 2019 Recommendations for the Management of MPS VI and MPS IVA
Authors: Bruce Iain A. , Ezgü Fatih S. , Kampmann Christoph , Kenis Vladimir , Mackenzie William , Stevens Bob , Walker Robert , Hendriksz Christian Johannes 
Published: August 2021

Abstract
BackgroundPatients are the most important stakeholders in the care of any disease and have an educational need to learn about their condition and the treatment they should receive. Considering this need for patient-focused materials, we present a directed approach for mucopolysaccharidosis (MPS) VI and MPS IVA, a pair of rare, inherited diseases that affects multiple organs and parts of the body. Independent guidelines on the treatment of these diseases were recently published, providing evidence- and expertise-driven recommendations to optimize patient management. However, while healthcare providers may have the training and knowledge to understand these guidelines, patients and their caregivers can find the technical content challenging. Hence, we aimed to develop plain language summaries (PLS) of the MPS VI and MPS IVA guidelines with patients as the primary audience.ResultsA review of the guidelines by an expert team identified six domains of information relevant to patients: The multidisciplinary team, regular tests and check-ups, disease-modifying and supportive treatments, general anesthetics, ear-nose-throat/respiratory care, and surgeries. This information was adapted into a series of infographics specific to either MPS VI or MPS IVA, designed to appeal to patients and clearly present information in a concise manner.ConclusionsThe use of patient-friendly materials, like the infographics we have developed, has the potential to better inform patients and engage them in their care. We issue a “call to arms” to the medical community for the development of similar PLS materials in rare diseases intended to inform and empower patients.