bluuebunny/crossref_metadata_2025 huggingface dataset:
Association of ALDH1A1 Polymorphism With Toxicity From Cyclophosphamide Treatment
Authors: Hwang Mary , Medley Sarah , Shakeel Faisal , Kidwell Kelley M , Hertz Daniel L
Published: February 2022

Purpose: Cyclophosphamide is a commonly used cancer agent that is metabolically activated by polymorphic enzymes. This study aims to investigate the association between genetic polymorphisms of candidate pharmacogenes with severe toxicity during cyclophosphamide treatment.Methods: Genetic data was collected from an institutional genetic data repository. Genetic polymorphisms in CYP2B6, CYP3A4, CYP2C9, CYP2C19, GSTA1, GSTP1, ALDH1A1, ALDH3A1, ABCC1, ABCB1, and ERCC1 were included in the analysis. Treatment and toxicity data were retrospectively collected from the patient’s medical record. The a priori selected primary hypothesis was that patients who have CYP2B6 reduced metabolizer activity (poor or intermediate metabolizer (PM/IM) vs. other) have higher risk of severe toxicity or cyclophosphamide treatment modification due to toxicity. Results: In the primary analysis of 510 cyclophosphamide-treated patients with available genetic data, there was no difference in the odds of severe toxicity or treatment modification due to toxicity in CYP2B6 PM/IM vs. other (Odds ratio=0.97, 95% Confidence Interval: 0.62-1.50, p=0.88). In an exploratory, statistically uncorrected secondary analysis, carriers of the ALDH1A1 rs8187996 variant had a lower risk of the primary toxicity endpoint compared with wild-type homozygous patients (Odds Ratio=0.31, 95% Confidence Interval: 0.09-0.78, p=0.028). None of the other tested phenotypes or genotypes were associated with the primary or secondary endpoints in unadjusted analysis (all p>0.05).Conclusion: Patients who carry ALDH1A1 rs8187996 may have a lower risk of cyclophosphamide toxicity than wild-type patients. Validation of this associations is necessary to justify development of personalized cyclophosphamide dosing strategies to optimize therapeutic outcomes in patients with cancer.
The Analysis of Oral Nutrition Support Needs in Chinese Postoperative Gastric Cancer Patients: Based on Information From Internet
Authors: Tian Qiuju , Qin Liyuan , Zhu Weiyi , Wu Beiwen
Published: February 2022

Purpose: The study aimed to explore oral nutrition support needs in Chinese gastric cancer patients after gastrectomy by analyzing patients question on the internet.Methods: We searched Baidu website for diet question relating to stomach cancer undergoing gastrectomy. Content analysis was used to analyze the data material, Natural language processing & information retrieval sharing platform was used to analyze the sentiment tendency and sentiment attributes of all questions.Results: A total of 1420 diet-related questions were posed during the time before discharge and after gastrectomy several years. About 83.87% of all questions were about what and how to eat after gastric cancer. The results of emotional orientation of oral nutrition problems in patients after gastrectomy was generally positive (positive vs negative score: 1758 VS –1531), but the emotional orientation of diet and symptom problems was generally negative (positive vs negative score: 256.5 VS –410). The oral nutritional requirement of gastric cancer patient included oral nutrition-related solutions provided by professional staff, dietary and prognosis information, food metabolism information, dietary information, oral nutritional supplements information, symptom support, nutrition monitor, psychological support, and exercise information. Conclusions: The dietary problems of patients with gastric cancer after surgery mainly involve how to eat, the causes of diet-related symptoms and treatment methods. Patients and their caregivers need professional person to support their nutrition need, and the nutrition need include dietary and prognosis information, food metabolism information, dietary information, oral nutritional supplements information, symptom support, nutrition monitor, psychological support, and exercise information. The study clarified the specific needs of oral nutrition for patients after gastric cancer surgery, laying a foundation for the formulation of intervention programs.
Biogenic surfactant mediated facile synthesis of visible light sensitized Zn/Mg co-doped TiO2 Nanomaterials– A Green approach: Evaluation of photocatalytic activity by degradation of Amido Black 10B
Authors: Tirukkovalluri Siva Rao , Jaishree Genji , Divya Gorli , Chippada M.L.V. Prasanna , Raju Imandi Manga
Published: February 2022

Visible light driven Zn and Mg co-doped TiO2 nanomaterials were synthesized by varying dopant concentrations in presence of biogenic surfactant Sapindus emerginatus biogenic extract via Solgel method and has been successfully applicated to the degradation of Amido Black 10B, an exemplary anionic textile azo dye pollutant. In this study, explored the potent capping properties of biogenic extract surfactant by encapsulating the Zn/Mg co-doped TiO2. In a view to assess the physical and optical properties of as synthesized catalyst, various advanced instrumental techniques were adopted. The Transmission Electron Microscopy and Scanning Electron Microscopy analysis shows the formation of small particle size (6.92 nm) and rough surface respectively pertaining to ZMT4S2. The substitutional doping of Zn and Mg into TiO2 framework by substituting Ti4+ ion and the encapsulation of surfactant around catalyst was confirmed by Fourier Transform-Infrared Spectroscopy (FTIR) spectral studies. The surface area of the ZMT4S2 was found to be high (195.20 m2 g−1) as compared with undoped TiO2 (32.50 m2 g−1) and ZMT4 (7.02 m2 g−1). The red shift in the absorbance was observed for all the catalysts analyzed using UV-DRS making them active in visible region with maximum shift corresponds to a band energy difference of 2.1 eV for ZMT4S2. The sensitivity of the catalyst towards visible light was confirmed by its band gap energy measurement using UV-vis DRS. The anatase phase of all the catalysts were confirmed using Powder X-ray diffraction. The composition and wt% of dopants revealed the EDX spectra agrees well with the calculated value. The slightly shifted frequency bands (FTIR) further confirmed the doping of Zn and Mg. The characterization analysis reports further accounts for the effective degradation of AB10B dye (99%) taking place within 20 min of irradiation time at optimized reaction parameters such as best dopant concentration ZMT4, catalyst dosage (100 mgL−1), dye concentration (10 mgL−1) and solution pH 3.
Impact of hydrogeological assumptions and their variation on the calculated surface uplift above flooded coal mines
Authors: Vervoort Andre
Published: February 2022

Upward surface movement or uplift has been extensively observed above abandoned deep coal mines. Detailed analysis of measurements indicated that the process of uplift is a complex phenomenon. The observed uplift is linked to the flooding of the underground infrastructure and rock mass. The distribution of water pressure at the end of the mining phase and their increase during the flooding is an important aspect in all estimations. Various assumptions of this distribution at the start of the flooding phase are studied, i.e., from a zero-water pressure to a linear decrease between top and bottom longwall panel. There are also various scenarios possible of how the water pressures change as a function of time, i.e., from filling an open reservoir from bottom to top, to a systematic change in the linear downward trend. The original assumed scenario, i.e., a linear trend, remains the most likely option. It provides the best fit between the estimated uplift values and the large amount of remote sensing measurements, along north-south transects in the Belgian Campine coal basin. However, further improvements and analyses certainly are still needed.
Incidence of preterm births admissions in Uganda, 2015-2019
Authors: Morukileng Job , Mugwanya Wilberforce , Mutumba Robert , Katusiime Maureen , Byaruhanga Aggrey , Gonahasa Doreen N. , Amodan Bob Omoda , Kabwama Steven , Kadobera Daniel , Bulage Lilian , Ario Alex Riolexus
Published: February 2022

Background: Complications of preterm births are the largest cause of neonatal deaths and the second leading cause of deaths among children <5 years globally. The preterm birth rate in Uganda is estimated at 6.6%. Reduction of this rate is needed to achieve the United Nations Sustainable Development Goal to end all preventable deaths among newborns and children aged <5 years by 2030. We describe the trends and distribution of preterm births admissions in Uganda during 2015-2019 for advocacy, planning, and targeted interventions.Methods: We used national preterm birth admissions data from 2015-2019 abstracted from the District Health Information System 2 (DHIS2) to calculate national, regional and district annual incidence of preterm births admissions. DHIS2 defines preterm birth as birth occurring <37 weeks of gestation. We used preterm birth admissions as numerator and the total livebirths (LB) as the denominator. We used line graphs to demonstrate the trend of annual incidence for the national and regional levels and choropleth maps to show district level distribution. Significance of the trend of annual incidence was tested using modified Poisson regression with unbiased sandwich standard errors, considering calendar year as independent and preterm births admissions as dependent variableResults: The national annual incidence of preterm birth admissions/1,000 LB has significantly increased from 3 in 2015 to 14 in 2019 (Incidence Risk Ratio (IRR)=1.3, p=0.003). The annual incidence of preterm birth admissions/1,000 LB increased significantly in three regions of Uganda during 2015 -2019 (Central Region from 3 to 21, IRR=1.5, p<0.0001; Western Region from 4 to 15 IRR=1.2, p=0.039; Northern Region from 3 to 10, IRR=1.2, p=0.008; Eastern Region from 2 to 8, IRR=1.3, p=0.086). The Choropleth map showed minimal clustering of high incidence of preterm birth admissions at district level.Conclusion: Incidence of preterm birth admissions increased nationally and regionally in Uganda from 2015-2019. There is need to plan for and prepare health facilities to manage preterm labor and preterm babies, as well as identifying reasons for the increase. Equipping health facilities and training health workers to manage preterm labor and babies should be prioritized.
Multi-Task Learning to Leverage Partially Annotated Data for PPI Interface Prediction
Authors: Capel Henriette , Feenstra K. Anton , Abeln Sanne
Published: February 2022

Protein protein interactions (PPI) are crucial for protein functioning, nevertheless predicting residues in PPI interfaces from the protein sequence remains a challenging problem. In addition, structure-based functional annotations, such as the PPI interface annotations, are scarce: only for about one-third of all protein structures residue-based PPI interface annotations are available. If we want to use a deep learning strategy, we have to overcome the problem of limited data availability. Here we use a multi-task learning strategy that can handle missing data. We start with the multi-task model architecture, and adapted it to carefully handle missing data in the cost function. As related learning tasks we include prediction of secondary structure, solvent accessibility and buried residue. Our results show that the multi-task learning strategy significantly outperforms single task approaches. Moreover, only the multi-task strategy is able to effectively learn over a dataset extended with structural feature data, without additional PPI annotations. The multi-task setup becomes even more important, if the fraction of PPI annotations becomes very small: the multi-task learner trained on only one-eighth of the PPI annotations -- with data extension -- reaches the same performances as the single-task learner on all PPI annotations. Thus, we show that the multi-task learning strategy can be beneficial for a small training dataset where the protein's functional properties of interest are only partially annotated.
The Timing, Duration And Magnitude of The 8.2 Ka Event In Global Speleothem Records
Authors: Parker Sarah E. , Harrison Sandy P.
Published: February 2022

Abrupt events are a feature of many palaeoclimate records during the Holocene. The best example is the 8.2 ka event, which was triggered by a release of meltwater into the Labrador Sea and resulted in a weakening of poleward heat transport in the North Atlantic. We use an objective method to identify rapid climate events in globally distributed speleothem oxygen isotope records during the Holocene. We show that the 8.2 ka event can be identified in >70% of the speleothem records and is the most coherent signal of abrupt climate change during the last 12,000 years. The isotopic changes during the event are regionally homogenous: positive oxygen isotope anomalies are observed across Asia and negative anomalies are seen across Europe, the Mediterranean, south America and southern Africa. The magnitude of the isotopic excursions in regions close to and far from the North Atlantic are statistically indistinguishable. There is no significant difference in the duration and timing of the 8.2 ka event between regions, or between the speleothem records and Greenland ice core records. Our study supports a rapid and global climate response to the 8.2 ka freshwater pulse into the North Atlantic, likely transmitted globally via atmospheric teleconnections.
H∞ Model Based Control via Mixed Sensitivity for 2DOF Control of Twin Rotor MIMO System With Experimental Validation
Authors: Abbas Nadir , Zar Ali , Raheem Abdur , Shakoor Rabia , Arfeen Zeeshan Ahmad , Rashid Muhammad , Umer Farhana , Safdar Nouman , Liu Xiaodong
Published: February 2022

This article provides a comprehensive study about optimization and real-time implementation of H∞ model-based controller for uncertain systems (having external perturbations) using robust control methods. The complicated air vehicle modeling is quite difficult because of highly nonlinear behavior, un-modeled states, and cross-coupling effect. The helicopter flight control also depends on two rotors generating continuous thrust simultaneously in two different directions. Simple linear feedback controllers cannot ensure the stability of highly nonlinear systems like a helicopter. The controllability and observability full rank matrix output ensure the credibility of the system before a controller design. The design of a robust controller for the desired flight control, demands the availability of all its states and varying parameters for real-time robust feedback control. However, its prototype, Twin-rotor MIMO System (TRMS) facilitates the researchers and control engineers in terms of the real-time environment of a helicopter flight control. Various control strategies are presented to elaborate the behavior of the MIMO system and the limitations of robust control methods. Each control strategy has been comprehensively discussed with the stability analysis and the design requirements. The considered control techniques, such as the loop-shaping control and H∞ model-based control augmented with mixed sensitivity control function, make use of control in such a way that robust stability and robust performance are ensured for highly nonlinear systems. Model-based H∞ optimization technique elaborates the robustness and stability of the system by reducing tracking error of all its states towards origin and thereafter system becomes stable for an infinite period. The loop-shaping control performance as compared to H∞ model-based control has some limitations to ensure closed-loop robustness and real-time implementation under perturbations. The performance evaluation is done at the end which shows that the H∞ model-based control gives optimal robust performance including perturbations and coupling effect. The real-time implementation on MATLAB/Simulation via personal computer validates the worth of the optimization method in the presence of uncertainties (matched, unmatched, coupling effect) of a linearized state-space model of the TRMS system.
Brief Report: Ionising Radiation Induces Autophagy in the Adult Drosophila Brain and Intestine
Authors: Trinca Terrence M , Malik Bilal R
Published: February 2022

Exposure to various genotoxic and oxidative stresses can induce changes in the internal state of a cell leading to cell death. Ionizing radiation is routinely used in clinics to treat various types of cancers, with secondary effects sometimes damaging internal organs particularly the gut. Drosophila melanogaster has become one of the most trusted model organisms to study human disease and various biological pathways. Here we have used gamma radiation to determine for the first time whether they have an effect on autophagy in two different tissues in Drosophila; the gut and the brain. We find that in both tissues exposure to radiation leads to an increase in autophagy.
Metal-to-metal charge transfer driven by electropositive species for stable anionic redox
Authors: Kim Min-Ho , Jang Haeseong , Lee Eun Ryeol , Park Jaehyun , Kim Taewon , Seo Jeongwoo , Jung Young Hwa , Kang Seok Ju , Cho Jaephil , Kim Min , Seo Dong-Hwa , Lee Hyun-Wook
Published: February 2022

Apart from conventional redox chemistries, exploring high-voltage redox processes, such as high-valent redox of a transition metal (TM) or novel anionic redox, is challenging due to unstable energy states correlated with destructive structural disorder in intercalation-type cathode materials. Here, we show a new strategy to design high-energy-density 4d-based Li-excess oxides with strong structural reversibility by substituting electropositive species. It is known that TMs in 4d-based Li-excess oxides, in contrast to 3d-based oxides, actively interact with neighboring oxygen ligands, inducing b1/b1* energy levels. Metal-to-metal charge transfer, driven by covalency competition within the asymmetric TM3d-O-TM4d backbone, induces a larger overlap between electronegative species and oxygen ligands, leading to stable high-voltage redox. Furthermore, we reveal that redox-inactive dopants control the reversibility of cation migration, thereby extending the battery lifetime. These insights open new perspectives for the control of intrinsic redox chemistry and enable rational designs for high-energy-density Li-excess cathodes.
Protective Effect of Resveratrol Against Cadmium-Induced Toxicity On Ovine Oocyte In Vitro Maturation And Fertilization
Authors: Piras Anna Rita , Ariu Federica , Maltana Alessio , Leoni Giovanni Giuseppe , Martino Nicola Antonio , Mastrorocco Antonella , Dell’Aquila Maria Elena , Bogliolo Luisa
Published: February 2022

Background: Heavy metal cadmium (Cd) is a widespread environmental contaminant with a potential toxicity that might negatively affect female reproduction and fertility. It has been reported that Cd exposure impaired the quality of oocytes and led to a defective maturation and fertilization, through oxidative stress induction. Resveratrol (Res) is a natural polyphenol with strong antioxidant properties that exhibited protective role in preventing oocyte redox homeostasis disruption and quality decline. Here, we explored whether the addition of Res to in vitro maturation (IVM) medium might act as a protection against Cd-induced toxicity on ovine oocyte maturation and fertilization. Firstly, we evaluated the effect of supplementing IVM medium with two different Res concentrations (1 and 2 μmol/L) on nuclear maturation and fertilization of oocytes matured under CdCl2 (2 μmol/L) exposure. Therefore, the concentration of 1 μmol/L Res was selected to analyse intracellular ROS levels, mitochondrial (mt) distribution and activity, chromatin configuration, cytoskeleton morphology, cortical granules (CGs) distribution and mRNA expression of genes associated with cellular response to oxidative stress (i.e. SIRT1, SOD 1, GPX1, GSR, CAT ) in Cd-exposed in vitro matured oocytes. Results: We found that 1μmol/L Res was effective to recover the reduced oocyte meiotic competence induced by Cd exposure, while treatment with Res, at both tested concentrations, sustained oocyte ability to be normally fertilized and decreased polyspermic fertilization. Moreover, we demonstrated that 1 μmol/L Res mitigated Cd-induced alterations of oocyte cytoplasmic maturation by reducing reactive oxygen species (ROS) accumulation, preventing mt dysfunction, maintaining the correct meiotic spindle and cortical F-actin assembly and the normal cortical granule distribution as well as up-regulating SIRT1 , SOD1 and GPX1 genes. Conclusions: Taken together, our findings highlighted the beneficial influence exerted by Res in preventing Cd-induced disturbance of nuclear and cytoplasmic maturation and subsequent fertilization in ovine oocytes. Res treatment may help to establish defence strategies counteracting Cd-induced toxicity on the female gamete.
A Novel 7 RNA-Based Signature for Prediction of Prognosis and Therapeutic Responses of Wild-Type BRAF Cutaneous Melanoma
Authors: Sun Ruizheng , Liu Yaozhong , Lei Cheng , Tang Zhenwei , Lu Lulixia
Published: February 2022

Background: The prognosis of wild-type BRAF cutaneous melanoma (WT Bf-CM) patients remains poor due to the lack of therapeutic options. However, few studies have investigated the factors contributing to the prognosis of WT Bf-CM patients.Methods: In this paper, we proposed and validated a novel 7-RNA based signature to predict the prognosis of WT Bf-CM by analyzing the information from TCGA database.Results: Dependence of this signature to other clinical factors were verified and a nomogram was also drawn to promote its application in clinical practice. Functional analysis suggested that the predictive function of this signature might attribute to the prediction of the up-regulation of RNA splicing, transcription, and cellular proliferation in the high-risk group, which have been demonstrated to be linked to malignancy of cancer. Moreover, therapy response analysis supported that this signature could predict the responses of PI3K/Akt/mTOR pathway based drugs in WT Bf-CM patients. Conclusion: Collectively, this study will provide a preliminary bioinformatics evidence for the molecular mechanism and potential drug targets that could improving WT Bf-CM prognosis.
Research on the Application of Surface Wave Method for the Precise Detection of Shallow Coal Seam Mined-Out Area and Overburden
Authors: Li Yu , Yang Zhi , Zou Guangui , Zhao Fei , Liu Yan
Published: February 2022

To finely detect the boundary of a shallow coal mined-out area, as well as the extent of the overburden affected by the mined-out area, and to analyze the factors and interrelationships between the detection depth and lateral resolution of the multichannel analysis of surface waves (MASW) method, a low-frequency focusing factor is introduced into the phase-shift method, and a low-frequency focusing phase-shift method is proposed to improve the detection depth and lateral resolution of the MASW method. The method is applied to the processing and analysis of measured active-source surface waves. The results show that the low-frequency focused phase-shift method has the significant advantage of extracting the dispersion energy at low-frequency side from the short receiver spread. The receiver-spread length of the measured data used to calculate the dispersion energy is 35 m, which meets the 70 m detection depth of the target coal mined-out area. The measured data were processed to obtain high-precision horizontal slices of the shear wave velocity along the coal seam and in the overburden at different depths. The former clearly identify the boundaries of the coal mined-out areas and the locations and geometries of the security coal pillars and estimate the main coal mining direction to be approximately 23° NW, which is in general agreement with the actual direction of 21° NW of the back workings in the mining area of the study site. One mined-out area of approximately 30 m in width, one mined-out area greater than 50 m in width, and one roadway of approximately 10 m in width are inferred. The latter directly shows the extent of the overburden affected by the coal mined-out area gradually decreasing as the depth becomes shallower. The severe influence extent on the surface is delineated and mutually supported by the surface cracks in the village east of the research site. The effectiveness of the low-frequency focused phase-shift method in improving the depth and lateral resolution of the MASW method and the feasibility of the MASW method in precise detection of shallow coal mined-out area and overburden are confirmed.
Clean energy from renewable energy sources, Solar energy for a clean environment and A Case Study: Kars Harakani Airport Solar Power Plant for Kars province
Authors: Aydın Neslihan
Published: February 2022

In this study, the total installation cost was calculated with the selection of solar panels (PV) to be used, Control Monitoring System, number of inverters when applying solar energy from renewable energy sources to Kars Airport in order to obtain a clean environment and clean energy. According to the latest two-year data obtained with the permission of the institution from Kars Harakani Airport Electricity Distribution, the total electricity consumption was calculated by the amount of electricity produced by the SPP project. In the continuation, the cost analysis tables are given when there is an overdraft and non-credit installation with the amortization time required for installation. For installation, statistical data on annual hours of sunshine and rainy days were taken from the General Directorate of Meteorology of Kars province. As a result of calculations; since the service life of a SPP project is 25 years; when the entire project is made without credit,the installation cost of TL 19,917,859.75 ($2.706.157,41) pays off in 4.5 years and the remaining amount of electricity sales earned in 20.5 years is 547,535,115. 02 TL ($74,391,336. 52 ) . It was found that when the entire loan was established, it paid off in 8 years. From these calculations, if the airport uses an overdraft system, it will pay off in about 8 years and the system will generate and sell its own electricity for 17 years . It was calculated that it would have a profit of 495.177.856,89 TL ($67,277,771. 92 ). For the non-credit SPP project,it was found that it will provide an added value of 547.535.115, 02 TL ($74,391,336. 52 ) to the institution, where it can pay off in 4.5 years and produce and sell its own electricity for 20.5 years.
Sunlight-driven nitrate loss records Antarctic surface mass balance
Authors: Akers Pete D. , Savarino Joël , Caillon Nicolas , Servettaz Aymeric P. M. , Meur Emmanuel Le , Magand Olivier , Martins Jean , Agosta Cécile , Crockford Peter , Kobayashi Kanon , Hattori Shohei , Curran Mark , Ommen Tas van , Jong Lenneke , Roberts Jason L.
Published: February 2022

Standard proxies for reconstructing surface mass balance (SMB) in Antarctic ice cores are often inaccurate or coarsely resolved when applied to more complicated environments away from dome summits. Here, we propose an alternative SMB proxy based on photolytic fractionation of nitrogen isotopes in nitrate observed at 114 sites throughout East Antarctica. Applying this proxy approach to nitrate in a shallow core drilled at a moderate SMB site (Aurora Basin North), we reconstruct 700 years of SMB changes that agree well with changes estimated from ice core density and upstream surface topography. For the under-sampled transition zones between dome summits and the coast, this proxy can considerably expand our SMB records by providing high-resolution SMBs that better reflect the local environment and are easier to sample than existing techniques.One Sentence Summary: Nitrate isotopes offer a new way to track past and present changes in Antarctic snowfall and ice sheet mass balance.
A novel twelve-gene signature to evaluate neoadjuvant chemotherapy response and predict prognosis in breast cancer
Authors: Tang Peng , Wu Jin , Tian Yuan , Liao Bin , Wang Minghao , Liu Wei , Yan Yuzhao , Hu Ying , Zheng Hong
Published: February 2022

Background: Accurate evaluation of the response to neoadjuvant chemotherapy (NAC) provides important information about systemic therapies for breast cancer, which implies tumor biology, prognosis, and guide further therapy. Gene profiles overcome many limitations observed with classic histopathological variables but are complicated and expensive. Therefore, it is essential to develop a more accurate, repeatable, and economical evaluation approach for neoadjuvant chemotherapy responses. Methods: We analyzed the transcriptional profiles of chemo-resistant breast cancer cell lines and tumors of chemo-resistant breast cancer patients in the GEO25066 dataset. We preliminarily screened out common significantly differentially expressed genes and constructed a NAC response risk model using least absolute shrinkage and selection operator (LASSO) regression and univariate and multivariate analyses. The differences in prognosis, clinical features, tumor microenvironment components, and immune characteristics were compared between risk groups. The connectivity map (CMap) database was used to screen potential drugs that could reverse chemotherapy resistance in breast cancer. Results: Thirty-six genes were commonly overexpressed or downregulated in both NAC chemo-resistant tumors and cells compared to the sensitive tumors and wild-type cells. Through LASSO regression, we obtained a risk model composed of 12 genes. The risk model divided patients into high-risk and low-risk groups. Univariate and multivariate Cox regression analyses indicated that the risk score can be used as an independent prognostic factor for evaluating NAC response in breast cancer. Tumors in the high-risk and low-risk groups showed significant differences in molecular biological characteristics, tumor-infiltrating lymphocytes, and immunosuppressive molecule expression. Our results showed that the risk score was also an independent prognostic factor for breast cancer. Finally, we screened potential drugs that could reverse chemotherapy resistance in breast cancer. Conclusion: Our results suggest that the novel signature of 12 genes could be used to evaluate NAC response and predict prognosis in breast cancer.
Clinical Phenotype of Filipino Childhood-Onset Systemic Lupus Erythematosus: 12-Year Study in a Tertiary Hospital
Authors: Borromeo Jasper Atillo , Collante Ma. Theresa , Bernal Christine
Published: February 2022

Background
Systemic lupus erythematosus (SLE) is a chronic autoimmune multi-systemic inflammatory disorder that starts at childhood in 10-20% of patients. There is paucity of reports of childhood-onset SLE (cSLE) from developing countries, with little data from Southeast Asia. The purpose of this study is to describe the clinical features at onset and disease manifestation patterns of Filipino patients with cSLE seen in a tertiary hospital in the Philippines.
Methods
This study included patients diagnosed with SLE (age of onset <18 years) seen in the Section of Rheumatology from 2008 to 2019. In-patient and out-patient clinic files of the study population were reviewed. Data collected included demographic profile as well as clinical and laboratory manifestations at initial presentation and during disease course.
Results
A total of 304 cases of cSLE were reviewed. Predominantly affected were females (89.1%). The median age at diagnosis was 13 years (range 3-18 years). The most common presenting features were fever (48.4%), anemia (45%), and arthralgia (40.1%). Predominantly affected systems at diagnosis were hematologic (56.9%), mucocutaneous (55.9%), musculoskeletal (43.4%), and renal (42.1%). Disease activity at diagnosis was generally high (average SLEDAI-2K 12.8). In terms of disease damage, the most common organ damage accrued were renal (20.7%), neuropsychiatric (8.6%), and musculoskeletal (4.6%). All patients were given corticosteroids and hydroxychloroquine, while the most common therapy used for renal disease was intravenous cyclophosphamide.
Conclusion
Among Filipino cSLE patients, the most common features at disease onset and diagnosis were fever, anemia, and arthralgia. Renal involvement occurs in 67.8% of patients throughout the disease course, and is the most predominantly affected in terms of disease damage. Clinical and laboratory features observed were relatively similar to cSLE patients from other series.
Deciphering Nickel-catalyzed Electrochemical Ammonia Synthesis from Nitric Oxide
Authors: Zhao Siwen , Liu Jiyuan , Zhang Zhibin , Wang Qinghe , Zhu Chenyuan , Wu Jing , Yang Chunlei , Shi Guoshuai , Chang Mingwei , Liu Kaihui , Li Shuzhou , Zhang Liming
Published: February 2022

Electrochemical conversion of nitric oxide (NO) to ammonia (NH3) is a highly attractive route to achieve artificial nitrogen fixation and rebalance the global nitrogen-circle. Yet today’s poor mechanistic understanding and unsatisfied selectivity towards NH3 curtails NOR ecologic prospects. Here, we screened a library of transition metals as electrocatalysts, in which non-noble Ni outperformed others at the top of a volcano-shaped plot. To further elucidate the active motifs, we rationally designed and fabricated five single-crystal Ni foils with various surface orientations as electrocatalysts, and observed higher conversion efficiencies on high-index facets. In particular, Ni(210) demonstrates a unique selectivity towards NH3 with a yield rate nearly two-folds higher than those of low-index facets. Under the guidance of density functional theory (DFT) calculation, the energy required for key intermediates switching from hollow to bridge sites in the rate-determining hydrogenation step, was established as a descriptor for the capability towards NH3 production. Our work guides the rational design of NOR electrocatalysts, and more importantly, establishes a paradigm to understand the structure-function correlation in catalysis.
Hypercapnic acidosis microenvironment promoted epithelial-to-mesenchymal transition through activating ASIC3 in lung adenocarcinoma
Authors: Long Dingde , Fang Xingjun , Yuan Peihua , Li Hongtao , Qu Liangchao.
Published: February 2022

Background Epithelial-mesenchymal transition (EMT) plays a major role in tumor invasion and metastasis, which is associated with poor survival in surgically resected lung cancer. Tumor microenvironment, especially extracellular acidity is a favorable factor for tumor progression and metastatic spread, and participates in EMT. However, the effects of Hypercapnic acidosis (HCA) microenvironment on EMT of lung cancer still unknown.Materials and Methods The acid-sensing ion channels (ASICs) gene expression and prognostic value in lung adenocarcinoma (LUAD) and lung squamous cell carcinoma (LUSC) were evaluated using online database. Human lung adenocarcinoma A549 cells were cultured in 10% CO2 and 90% air for 48h to assess the effects of the HCA microenvironment. Transwell assay and wound-healing assay of A549 cells were performed to determine the effects on EMT.Results The mRNA expression levels of ASIC3 may be useful for prediction of lung cancer patient overall survival. The expression of ASIC3 significantly increased , and the invasive and migrate ability of A549 cells was promoted after exposing in HCA microenvironment (10% CO2 and 90% air), and inhibited when ASIC3 was blocked.Conclusion HCA microenvironment induced EMT in lung cancer cells through ASIC3, which may have influence on the FP and OS of lung cancer patients.
NCOA4 is a Prognostic Biomarker Associated with Immune Infiltrates in Glioblastoma
Authors: Liu Lingyu , Liu Yufei
Published: February 2022

Background Glioblastoma (GBM) is a malignant primary craniocerebral tumor with median survival of less than 15 months. Nuclear receptor coactivator 4 (NCOA4) can regulate the growth of various malignant tumors by participating in various biological processes. However, in glioblastoma, the specific regulatory role and mechanism of NCOA4 have not been clearly explained.Methods We collected GBM patient information from the Cancer Genome Atlas (TCGA). The expression of NCOA4 in GBM and normal tissues and the relationship between NCOA4 and various clinicopathological features, further the enrichment pathway of NCOA4 as well as the relationship between NCOA4 and prognosis of patients and the NCOA4-related nomogram for patient survival were analyzed by various bioinformatic tools including Wilcoxon rank sum test, Logistic regression analysis, Gene ontology term analysis (GO), Gene set enrichment analysis (GSEA), single-sample Gene Set Enrichment Analysis (ssGSEA), Kaplan-Meier analysis and Cox regression comprehensively.Results Our study showed that NCOA4 was significantly overexpressed in GBM, and the higher the expression of NCOA4, the longer the survival. In order to further explore the potential role of NCOA4, we conducted enrichment analysis on NCOA4, established a NCOA4-related PPI network. We found that the expression of NCOA4 was negatively interrelated with the infiltration degree of NK CD56bright cells, and positively interrelated with the infiltration degree of mast cells, B cells, T cells, T helper cells. We created a Nomogram in order to predict the prognosis of patients with GBM.Conclusion High expression of NCOA4 is associated with better prognosis and is associated with immune cell infiltration in GBM.
Ensembling Deep Learning and Bioinformatics for Precision Treatment Recommendations: Application in Acute Myeloid Leukemia
Authors: Meng Deyu , Wang Yaru , Guo Hongzhi , Wang Ziheng , Yang Guang
Published: February 2022

The most common kind of acute leukemia, acute myeloid leukemia (AML), has poor clinical outcomes and inadequate therapy. Although there are many therapies for AML, AML patients still have low 5-year overall survival rates. This study aimed to identify key genes and pathways of AML, to predict the prognosis of AML patients, A total of 133 upregulated DEGs and 15 downregulated DEGs were identified. They were enriched in protein binding, insulin secretion regulation, and cancer transcriptional misregulation. The module analysis of the PPI network of DEGs identified ten genes (PCLO, SYT1, STXBP1, GPHN, SYNCRIP, PFN2, ENAH, PAIP1, HNRNPD, STXBP5). SYT1 and PCLO were overexpressed in AML patients and have great potential as prognostic factors and therapeutic targets for AML. Further, by Deep learning, we combined other factors, including age, gender, past malignancy, and prior therapy, to inference whether patients will survive within 6 years by deep learning, the (Ctd)-index was greater than 80%, which indicates DeepHit model can reliably predict the prognosis of AML patients.
Simulated trends in land surface sensible heat flux on the Tibetan Plateau and the possible causes
Authors: Wang Shuzhou , Yuxin Liu , Ma Yaoming
Published: February 2022

Characteristics of spatial distribution and variation of surface sensible heat (SH) flux on the Tibetan Plateau (TP) were studied using the simulation results from the Noah-MP land surface model for the period of 1985-2015. The inter-annual variations and possible causes were also analyzed. It is found that, the western and central TP witnessed much larger 31-yr mean SH fluxes than the eastern TP. Meanwhile, the inter-annual variations of SH fluxes on the central and western TP were larger than that on the eastern TP. All the regions showed a decreasing trend in SH flux from mid-1980s, but an increasing trend since the beginning of the 21st century. However, the eastern TP got the increasing trend later than the western and central TP. On the whole, the increasing trend began from about 2002. The western and central TP had larger values of Ts–Ta (difference between ground and air temperature) than the eastern TP. Overall, the trends of mean Ts–Ta and SH flux were similar to each other. The changes of mean Ts–Ta were the main causes of the decreasing and increasing trends in SH flux on the TP. Meanwhile, the changes of wind speed contributed a lot to the trends of SH flux before 1998. There were no clear trends in heat transfer coefficient CH.
Virus neutralization of SARS-CoV-2 Omicron variant BA.2 in those vaccinated with three doses of BNT162b2 or CoronaVac vaccines.
Authors: Peiris Malik , Cheng Samuel , Chan Karl , Luk Leo , Li John , Tsang Leo , Poon Leo , Mok Chris Ka Pun , Ng Susanna SS , Ko Fanny , Chen Chunke , Yiu Karen , Chan Ken , Hui David , Lam Bosco
Published: February 2022

SARS-CoV-2 Omicron subvariant BA.2 is increasing in some areas of the world and it is important to assess how well current vaccines may protect against this infection. BioNTech Pfizer (BNT162b2) and CoronaVac are widely used COVID-19 vaccines globally. We determined the 50% plaque reduction neutralization test (PRNT50) and PRNT90 antibody titres to BA.2 virus in sera (twenty each collected 3-5 weeks after third dose) from cohorts vaccinated with three doses of BNT162b2, three doses of CoronaVac, two doses of CoronaVac followed by a third dose of BNT162b2 and those convalescent from SARS-CoV-2 (ancestral virus) (143-196 days after infection). We compared the PRNT titres to BA.2 with titres to BA.1 and ancestral virus. We demonstrate that PRNT50 and PRNT90 antibody titres to BA.2 are markedly reduced compared with those to ancestral virus and reduced as much as was observed for BA.1 virus. Those vaccinated with three doses of BNT162b2 or vaccinated with two doses of CoronaVac and a third dose of BNT162b2 develop PRNT antibody titres above the protective threshold from symptomatic infection. Those vaccinated with three doses of CoronaVac fail to achieve protective levels of PRNT50 antibody to BA.2 subvariant of Omicron 3-5 weeks after vaccination.
Comparative Analysis of the Chloroplast Genomes of a novel albino tea "Huabai 1" and the traditional albino tea "Huangjinya" for the revelation of the differences in the gene composition and their evolutionary relationship
Authors: zhao zhenjun
Published: February 2022

The chloroplast genomes of the newly discovered albino tea resource and albino tea variety "Huangjinya" were analyzed comparatively, and DNA barcodes were used to construct phylogenetic trees between albino tea and other plants in theaceae , aiming to clarify the genetic evolutionary relationship between the novel albino tea resource "Huabai 1" and albino tea variety "Huangjinya", other plants in theaceae from the perspective of chloroplast genome. Studies result have shown that the chloroplast genome size of "Huangjinya" and "Huabai 1" is 158,916 bp, 157,028 bp respectively, LSC (large single-copy)、SSC (small single-copy) and IR (inverted repeat) are 86,654 bp, 86,590 bp、18,277 bp, 16,463 bp, and 27,900 bp, 26,081 bp respectively for "Huangjinya" and "Huabai 1", with a total of 113 genes annotated were obtained in the chloroplast genome of both albino tea , these include 84 protein coding genes, 24 tRNA genes and 5 rRNA genes. GC content of chloroplast genome of "Huabai 1" was 37.3%, slightly higher than that of "Huangjinya" (37.22%). The gene composition, classification and codon preference (preferred to use codons ending in A/U) of chloroplast genome in "Huabai 1" were basically the same as that in "Huangjinya", but the main difference was the length of ycf1 fragment in IR region, the length of "Huabai 1" ycf1 fragment was only 987 bp, while that of "Huangjinya" was 2889 bp. The construction of phylogenetic tree was based on the four DNA barcodes ( matK , rbcL , trnH-psbA , and ycf1 ), and the results showed that ycf1 , with the most taxonomic levels, was most suitable for the identification of tea varieties and the interpretation of the evolution of genetic relationships among varieties. Ycf1 cluster showed that the relationship between "Huangjinya" and "Longjing 43" was closer, and that of "Huabai 1" and "Fuding Dabai" was closer. It is speculated that the two tea varieties "Huangjinya" and "Huabai1" may come from different ancestors, and thus led their quite different albino mechanism. This research will provide the basis for the revealing the albino molecular mechanism and phylogenetic development of the novel albino tea resource "Huabai 1".
A computational approach for molecular characterization of Covaxin (BBV152) and its ingredients for assessing its efficacy against COVID-19
Authors: Jena Atala B , Duttaroy Asim K.
Published: February 2022

SARS- CoV-2 vaccination is a life-saving strategy for the entire population living in this pandemic. A dozen vaccines against SARS- CoV-2 were developed and approved for the combat of the COVID-19 pandemic. However, there are many concerns on all vaccines, particularly on the immunogenicity and reactogenicity of vaccines, such as Covaxin. Covaxin (a vaccine code-named BV152), an inactivated COVID-19 vaccine. To address the concern outlined above, we explored the molecular and protein interactions between S protein, angiotensin-converting enzyme 2 (ACE2), and human serum albumin (HSA) with the ingredients of covaxin along with its drug-likeness property. The Autodock Vina shows stronger interactions of 2-phenoxyethanol, imidazoquinolinone (covaxin ingredients) with virus-cell surface S protein, human cell membrane receptor ACE2, and plasma albumin. The molecular and protein-protein interactions of S protein with ACE2 in the presence of 2-phenoxyethanol and imidazoquinolinone may affect the S protein function by reducing the binding energy between these proteins. Covaxin vaccine showed excellent efficacy in averting the virus and may result in herd immunity. As reported here, imidazoquinolinone, used as an ingredient of covaxin, may have the drug-likeness property based on pharmacokinetic and physicochemical parameters. However, the results should be interpreted with caution as there are limitations such as immune response and adverse effects after vaccination.
Stop Oversampling for Class Imbalance Learning: A Critical Review
Authors: Hassanat Ahmad B. , Tarawneh Ahmad S. , Altarawneh Ghada A.
Published: February 2022

For the last two decades, oversampling has been employed to overcome the challenge of learning from imbalanced datasets. Many approaches to solving this challenge have been offered in the literature. Oversampling, on the other hand, is a concern. That is, models trained on fictitious data may fail spectacularly when put to real-world problems. The fundamental difficulty with oversampling approaches is that, given a real-life population, the synthesized samples may not truly belong to the minority class. As a result, training a classifier on these samples while pretending they represent minority may result in incorrect predictions when the model is used in the real world. We analyzed a large number of oversampling methods in this paper and devised a new oversampling evaluation system based on hiding a number of majority examples and comparing them to those generated by the oversampling process. Based on our evaluation system, we ranked all these methods based on their incorrectly generated examples for comparison. Our experiments using more than 70 oversampling methods and three imbalanced real-world datasets reveal that all oversampling methods studied generate minority samples that are most likely to be majority. Given data and methods in hand, we argue that oversampling in its current forms and methodologies is unreliable for learning from class imbalanced data and should be avoided in real-world applications.