bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Benchmark of Pre-processing Effect on Single Cell RNA Sequencing Integration Methods
Authors: Anaissi Ali , Zandavi Seid Miad , Suleiman Basem , Alyassine Widad , Braytee Ali , Vafaee Fatemeh 
Published: November 2022

Abstract
Single-cell data analysis can transform the practice of personalised medicine by facilitating characterisation of disease-associated molecular changes across every single cell. Advanced single-cell multimodal assays can now simultaneously measure different types of molecules (e.g., DNA, RNA, Protein) across hundreds of thousands of individual cells to provide a complete molecular readout of the state of the cell. A key analytical challenge is to integrate single-cell measurements across different modalities. In recent years, different methods have been developed to integrate different molecular modalities of single cell measurements, yet there is no systematic evaluation on the performance of different techniques with respect to different pre-processig strategies. Here, we consider a general pipeline of single-cell data analyses comprising normalisation and data integration followed by the most popular dimensionality reduction methods where several algorithms can be adopted to each module in the pipeline. The performance of different algorithm combinations often depends on the sizes and characteristics of datasets. This paper explores the optimal framework of different algorithms using six datasets across diverse modalities, tissues and organisms. We use three evaluation metrics (Silhouette Coefficient Score, Adjusted Rand Index and Calinski-Harabasz Index) to explore the model's overall performance from the two aspects, including clustering performance and time efficiency. We conduct experiments based on combinations of seven normalization methods, four dimensional reduction methods, and five integration methods. Our results demonstrate that for the data integration module, the clustering performance of Seurat and Harmony are more prominent, but the time efficiency of Harmony was better. At the same time, the performance of Seurat for small data sets is superior. For the dimensionality reduction module, the UMAP method shows promising results in compatibility with the integration methods. The data normalization method could be differentiated according to different integration methods.
A Machine Learning based Resource Efficient Task Scheduler for Heterogeneous Computer Systems
Authors: Hayat Asad , Khalid Yasir Noman , Rathore Muhammad Siraj , Nadir Muhammad Nadeem 
Published: November 2022

Abstract
Heterogeneous computer systems are becoming mainstream due to disparate processing and performance capabilities of multi-core architectures. It consists of different type of devices, i.e., Central Processing Units (CPUs), accelerators, and Graphics Processing Units (GPUs). In the heterogeneous computing environment, if one device is more powerful in terms of computing capability, the scheduling schemes generally favor the powerful device, and that device becomes overloaded while the other device is underutilized. This load imbalance problem results in increased execution time. In this research, we propose load-balanced task scheduler combined with machine learning based device predictor. The device predictor is used to predict execution time both on CPU and GPU devices, and a device with shorter predicted execution time is considered as a suitable device for that particular task. However, it may happen that a high fraction of tasks map only on one type of device since that device is a suitable device for them. Such situation leads to the problem of load imbalance. We use work stealing based task scheduler as part of our solution that allows an idle device to process tasks from the queue of another’s device. In this way we can avoid load imbalance, minimize the overall execution time of tasks, and maximize the device utilization and throughput. We evaluate the performance of our proposed solution into two stages. Firstly, we measure the error rate of our machine learning predictor using three different algorithms (i.e., random forest, gradient boosting, and multiple linear regression). We demonstrate that random forest performs better with marginal error rate. Secondly, we compare the performance of work stealing task scheduler with other scheduling alternatives. Our results show that the proposed solution reduces execution time by 65.63%, increased resource utilization by 93.3%, and throughput by 65.5% in comparison to baseline scheduling schemes.
TUBA1C: a new potential target of LncRNA EGFR-AS1 promotes gastric cancer progression
Authors: Wang Haodong , Cui Huaiping , Yang Xinjun , Peng Lipan 
Published: November 2022

Abstract
Background: The lack of obvious symptoms of early GC as well as the absence of sensitive and specific biomarkers results in poor clinical outcomes. High TUBA1C expression has been shown to be closely related to a poor prognosis in in various cancers, however, the role of TUBA1C in GC have not yet been elucidated. This study, for the first time, revealed that TUBA1C drives the growth of GC cell lines both in vitro and in vivo.
Methods: The expression of lncRNA EGFR-AS1 was detected in human GC cell lines by qRT–PCR. MS experiments following RNA pulldown assays found that EGFR-AS1 directly binds to TUBA1C, the CCK8, EdU, transwell, wound-healing, cell cycle assays and animal experiments were conducted to investigate the function of TUBA1C in GC. Combined with bioinformatics analyses, reveal interaction between E2F1, Ki-67, PCNA and TUBA1C by western blot. Rescue experiments furtherly demonstrated the relationship of EGFR-AS1and TUBA1C.
Results: TUBA1C was proved to be a direct target of EGFR-AS1, TUBA1C promotes gastric cancer proliferation, migration and invasion by accelerating the progression of the cell cycle from the G1 phase to the S phase and activating the expression of tumor suppressor genes: E2F1, Ki-67, and PCNA.
Conclusions: TUBA1C is a new potential target of LncRNA EGFR-AS1 promotes gastric cancer progression and could be a novel biomarker and therapeutic target for GC.
Cobalt and Calcium-based Metal-Organic Frameworks (MOFs) as an Energy and Advanced Electrode material for Supercapacitors
Authors: BM Omkaramurthy , G Krishnamurthy , Foro Sabine 
Published: November 2022

Abstract
Cobalt and Calcium - based metal-organic frameworks (Co-MOF and Ca-MOF) [Co (tpa) (mi) and Ca (tpa)] (tpa = terephthalic acid and mi = methyl imidazole) was synthesized through solvothermal method. Structural characterization revealed that metal centers are equally occupied by Co2+ and Ca2+ ion. Supercapacitive behaviour of synthesized Co-MOF and Ca-MOF were evaluated using cyclic voltammetry (CV), galvano static charge/discharge, and electrochemical impedance spectroscopy (EIS) measurements in 6 M KOH as electrolyte. The Co and Ca-MOFs exhibited outstanding specific capacitance of 1726 and 185Fg− 1 at a discharge current density of 1 Ag− 1, good rate capability, and 97.4% capacitance retention after 3000 cycles. To the best of our knowledge, Co-MOF and Ca-MOFs are used in supercapacitor and its encouraging properties indicate that Co/Ca-MOF can be promising candidate as an advanced electrode material for supercapacitors.
Contributions of vascular burden and amyloid abnormality to cognitive decline in memory clinic patients
Authors: Gils Veerle van , Ramakers Inez , Jansen Willemijn J. , Banning Leonie , Kučikienė Domantė , Costa Ana Sofia , Schulz Jörg Bernhard , Visser Pieter Jelle , Verhey Frans , Reetz Kathrin , Vos Stephanie J.B. 
Published: November 2022

Abstract
Background.
Alzheimer’s disease (AD) pathology and vascular burden are highly prevalent and often co-occur in elderly, but it remains unclear how both are associated with cognitive decline. We aimed to investigate whether amyloid abnormality and vascular burden synergistically contribute to cognitive decline in a memory clinic population.
Methods.
In this longitudinal study, 228 participants across the clinical AD spectrum (SCD, MCI, dementia) were included from Maastricht and Aachen university memory clinics. Amyloid abnormality (A) was measured by cerebrospinal fluid (CSF) Aβ-42, using data-driven cut-offs. Vascular burden (V) was defined as having either moderate to severe white matter lesions (Fazekas score ≥ 2), one or more microbleeds, intracranial hemorrhage or infarcts on MRI. Participants were divided into four groups: A-V-, A-V+, A + V-, and A + V+. Outcome measures were global cognition, memory, processing speed, executive functioning, and language z-scores. Linear mixed models were used, adjusted for age, sex, education, with center as random factor. Effects of individual MRI vascular measures and Aβ-42 abnormality on cognitive decline were also assessed. In secondary analyses, presence of vascular risk factors and disease were used as V definitions.
Results.
At baseline, the A + V + group scored worse on global cognition and language compared to all other groups. The A + V + group also had worse memory scores compared to A-V + and A-V- groups. Over time, with an average follow-up of 2.7 years (SD = 1.5), the A + V + and A + V- groups showed faster decline in global cognition than the A-V + and A-V- groups. Only the A + V- group showed decline on memory and language scores. The A-V + group did not differ from the A-V- group in any domain. Findings were similar in persons without dementia and when vascular risk factors and disease were used as V definitions. When assessing MRI vascular measures individually, no synergistic effects on cognitive decline were shown and only microbleeds were independently associated with executive functioning decline over time.
Conclusions.
Our study shows that amyloid abnormality predicts cognitive decline in a memory clinic population independent from vascular burden. Vascular burden has a minor contribution to cognitive decline in these patients. This has implications for prognostic procedures in memory clinic patients.
Nitrogen release and microbial community characteristics during the decomposition of field-incorporated corn straw in Northeast China
Authors: Yan Chao , Yang Daocheng , Xue Yinghao , Song Qiulai , Hou Zhaofang , Yan Shuangshuang , Lyu Xiaochen , Ma Chunmei , Xu Zhiyu , Gong Zhengping 
Published: November 2022

Abstract

Straw incorporation increases the amount of nutrients in soil and has a significant impact on soil nitrogen and microbial communities. However, no study has quantified the amount of nitrogen released and taken up by straw during its decomposition after it is incorporated into soil in the field. In this study, a method for estimating the amounts of nitrogen released and taken up by field-incorporated straw was proposed based on 15N-labeled corn straw, and the relationships between nitrogen release and uptake amounts and the related microbes were established. The results showed that the amounts of nitrogen released by the straw at different incorporation depths were not significantly different. Among all the treatments, the straw placed 15 cm above the soil surface and the straw mulched on the soil surface had the highest nitrogen uptake, and the straw placed 15 cm above the soil surface had the lowest net nitrogen release. The relative abundances of Burkholderiales, Flavobacteriales, Pseudomonadales, and Sphingobacteriales were significantly positively correlated with the 15N abundance and the nitrogen release speed of the straw. The relative abundances of Rhizobiales and Sphingomonadales were significantly negatively correlated with the 15N abundance in straw and significantly positively correlated with the amount of straw nitrogen uptake.
Optical Frequency Comb Generator Employing Serially Connected LiNbO3 Mach-Zehnder Modulator
Authors: Verma Priyanka , Singh Sukhbir 
Published: November 2022

Abstract
An optical frequency comb having ~ 40 equally spaced frequency lines with 6 dB power deviation is proposed using serially connected LiNbO3 Mach-Zehnder modulator. Semiconductor optical amplifier is employed to get equally spaced and flat optical spectrum. The broadness of ultrashort pulse is enhanced by variation in various factors such as confinement factor and differential gain of SOA. The periodicity of input electrical and central wavelength of optical signal is controlled by tuning frequency and line spacing of equally spaced lines of comb.
Establishment of a new predictive model for the recurrence of upper urinary tract stones
Authors: Xia Kaiguo , Xu Yuexian , Qi Qiao , Huang Qingfeng , Yao Rui , Hao Zongyao 
Published: November 2022

Abstract
The purpose of this study is to construct a new prediction model to evaluate the recurrence risk of upper urinary tract stones in patients. We retrospectively reviewed the clinical data of 657 patients with upper urinary tract stones and divided them into stone recurrence group and non-recurrence group. Blood routine, urine routine, biochemical and urological CT examinations were searched from the electronic medical record, relevant clinical data were collected, including age, BMI, stones number and location, hyperglycemia, hypertension, and relevant blood and urine parameters. Then, independent sample t-test, Wilcoxon rank sum test, and Chi-square test were used to preliminarily analyze the data of two groups, and then LASSO and Logistic regression analysis were used to find out the significant difference indicators. Finally, R software was used to draw a nomogram to construct the model, and ROC curve was drawn to evaluate the sensitivity and specificity. The results showed that multiple stones (OR:1.832,95%CI:1.240–2.706), bilateral stones (OR:1.779,95%CI: 1.226–2.582), kidney stones (OR: 3.268, 95% CI: 1.638–6.518) and kidney ureteral stone (OR: 3.375, 95% CI:1.649–6.906) were high risks factors. And the stone recurrence risk was positively correlated with creatinine (OR:1.012,95%CI:1.006–1.018), urine pH (OR:1.967, 95%CI:1.343–2.883), Apo B (OR:4.189, 95%CI:1.985–8.841) and negatively correlated with serum phosphorus (OR:0.282, 95%CI:0.109–0.728). In addition, the sensitivity and specificity of the prediction model were 73.08% and 61.25%, diagnosis values were greater than any single variable. It means the model can effectively evaluate the recurrence risk of upper urinary stones, especially suitable for stone postoperative patients, to help reduce the possibility of postoperative stone recurrence.
Association between Available Blastocyst Formation Rate and Pregnancy Outcome Following Fresh Embryo Transfer
Authors: Wang Longmei , Qiu Pingping , Jiang Lizhi , Jiang Yufei , Li Ping 
Published: November 2022

Abstract
Background: Embryo quality usually has been regarded as a key predictor of successful implantation and pregnancy potential. The identification of embryos that have the capacity to implant and result in a healthy pregnancy is a crucial part of in vitro fertilization (IVF). Usually, the morphologically high quality embryos are chosen for embryo transfer in IVF treatment. The aim of this study was to assess the association between available blastocyst formation rate with pregnancy outcome following first fresh embryo transfer cycles. Our objective was to predict pregnancy outcome according to embryonic development potential, and provide a systematical individual treatment to adjust endometrial receptivity for the next transfer cycle.
Methods: This retrospective, single-center study including 512 fresh embryo transfers conducted between 11/2019–08/2021, which consisted of 385 cleavage-stage (day 3) and 127 blastocyst-stage (day 5) transfers. The two groups were divided into clinical pregnancy group and non-clinical pregnancy group respectively for comparison. The association with available blastocyst formation rate and the clinical pregnancy rate between day 3 or day 5 transfer groups were concerned.
Results: In the day 3 group, there were 275 clinical pregnancies, and the clinical pregnancy rate was 71.43%. Although the 2PN oocytes rate and available embryo rate at day 3 were significantly higher in clinical pregnancy group compared with non-clinical pregnancy group (P < 0.05), the blastocyst formation rate and the available blastocyst formation rate had no significant differences between the clinical pregnancy group and non-clinical pregnancy group (P > 0.05).
In the day 5 group, there were 81 clinical pregnancies, and the clinical pregnancy rate was 63.78%. All the baseline characteristics had no obvious differences between the clinical pregnancy group and non-clinical pregnancy group (P > 0.05). The blastocyst formation rate in the non-clinical pregnancy group was higher than that in the clinical pregnancy group, but the difference was not statistically significant (81.06% vs. 77.03%, P = 0.083). Interestingly, the available blastocyst formation rate was significantly higher than the clinical pregnancy group (66.19% vs. 60.79%, P = 0.014).
Conclusions: In fresh cycles, available blastocyst formation rate was not associated with pregnancy outcome with a day 3 embryo transfer. However, available blastocyst formation rate was negatively associated with pregnancy outcome with a day 5 embryo transfer.
A complicated aortic graft infection case after Bentall’s procedure
Authors: Zhang HongYu , Ke Yingjie , Chen Jiansong , Sun Tucheng , Yu Changjiang 
Published: November 2022

Abstract
Background: The aortic graft infection (AGI) is fatal and has rare evidences of treatment. Here, we report a complicated AGI case after Bentall’s procedure.
Case presentation: A 54-year-old male with a history of Bentall’s procedure, ruptured right sinus aneurysm, ventricular septal defect(VSD) repair and right ventricular outflow tract stenosis(RVOTS) repair was admitted in our hospital with the chief complaint of poor heeling of incision, chilling and fever. Transthoracic echocardiography(TTE), contrast enhanced computed tomography(CECT) found a perigraft leakage pseudoaneurysm. After conservative treatment, the patient was underwent re-operation due to the growing giant pseudoaneurysm. After 8 weeks antibiotic therapy, the patient discharged with no complications.
Conclusions: The treatment of AGI is comprehensive. Successful management requires a prompt diagnosis,sensitive and long-term postoperative antimicrobial therapy, and early surgery depending on the patients’ status and clinician’s experience.
WITHDRAWN: Rapid quantitative analysis of calcium in infant formula powder assisted by long short-term memory with variable importance using laser-induced breakdown spectroscopy
Authors: Ding Yu , Yang Lin-yu , Chen Wen-jie , Chen Jing , Zhao Xing-qiang , Luo Yong 
Published: November 2022

Abstract
Calcium is the main mineral responsible for healthy bone growth in infants. In this study, LIBS was combined with a variable importance-based long short-term memory (VI-LSTM) for the quantitative analysis of calcium in infant formula powder. Firstly, the full spectra were used to establish PLS and LSTM models. The R2 and root-mean-square error (RMSE) of the test set (R2P and RMSEP) were 0.1460 and 0.0093 in the PLS method, respectively, and 0.1454 and 0.0091 in the LSTM model, respectively. To improve the quantitative performance, variable selection based on variable importance was introduced to evaluate the contribution of input variables. The variable importance-based PLS (VI-PLS) model had R2P and RMSEP of 0.1454 and 0.0091, respectively, whereas the VI-LSTM model had R2P and RMSEP of 0.9845 and 0.0037, respectively. Compared with the LSTM model, the number of input variables in the VI-LSTM model was reduced to 276, R2P was improved by 114.63%, and RMSEP was reduced by 46.38%. The mean relative error of the VI-LSTM model was 3.33%. This study confirms the predictive ability of the VI-LSTM model for calcium element in infant formula powder. Thus, combining VI-LSTM modeling and LIBS has great potential for the quantitative elemental analysis of dairy products.
Variations in wood traits and specific gravity in male clone of Populus deltoides Bartr. Ex Marsh
Authors: Aziz Massarat 
Published: November 2022

Abstract
The present study deals with the variations of wood anatomical characters and specific gravity in male F 1 offspring of Populus deltoides. ANOVA indicated that within-ramet difference between the means at differents heights of male offspring clone were significant for specific gravity only and non-significant for other wood traits studied. The specific gravity also increases from base to top of the ramet following an increasing trend. The variations for fiber length and vessel element length were significant for direction. The fiber length, fiber wall thickness and vessel element length significantly varied for different radial position. The interactions of height*direction and direction*position were non-significant for all wood traits except fiber outer diameter in height*direction interaction. The non-significant variations in different wood elements of single ramet of Populus deltoides due to peripheral and radial-direction may be related to the early maturity of clone raised tree. It seems non-significant variations in the wood element dimension’s at different directions of Populus deltoides regulate the homogenous wood properties in the discs. The different types of ratios such as Runkel Ratio, shape factor, fiber length/diameter ratio and wall ratio were determined and are important particularly for determining the suitability of a particular material for pulping and paper making. The objectives of the study is to evaluate the wood quality on the basis of specific gravity, Vessel and fiber morphology and other wood anatomical parameters in the F1 male clone of Populus deltoides.
Interpolation numerical integration method for extremely high-accuracy calculation of ordinary differential equations
Authors: Fukuchi Tsugio 
Published: November 2022

Abstract
There are three types of problems that arise in the numerical analysis of differential equations: (i) the initial value problem (IVP), (ii) the boundary value problem (BVP), and (iii) IVP + BVP. In general, it is natural that (i) and (ii) are thoroughly examined before the study of (iii). Thus far, it has been shown that the BVP of one-dimensional (1D) Poisson equations can be solved with extremely high accuracy and speed using the interpolation finite difference method (IFDM). Furthermore, it has been found that a high-accuracy numerical calculation system for the IVP can be constructed by applying the polynomial interpolation method, as in the case of the BVP of the 1D Poisson equation. This method is called the interpolation numerical integration method (INIM). Numerical integration is possible with an arbitrary accuracy order by specifying the degree of the interpolation polynomial for representing the integrand. The proposed calculation method enables numerical calculations that seem to have no error. IVPs are usually calculated by the fourth-order accuracy Runge‒Kutta method, which is often sufficient for engineering purposes. However, in this paper, we report that a numerical algorithm that agrees with the exact solution up to 15 significant digits has theoretical value.