bluuebunny/crossref_metadata_2025_split huggingface dataset:
Accurate prediction of RNA secondary structure including pseudoknots through solving minimum-cost flow with learned potentials
Authors: Gong Tiansu , Ju Fusong , Bu Dongbo 
Published: September 2022

Abstract
Pseudoknots are key structure motifs of RNA and pseudoknotted RNAs play important roles in a variety of biological processes. Here, we present KnotFold, an accurate approach to the prediction of RNA secondary structure including pseudoknots. The key elements of KnotFold include a learned potential function and a minimum-cost flow algorithm to find the secondary structure with the lowest potential. KnotFold learns the potential from the RNAs with known structures using a self-attention-based neural network, thus avoiding the inaccuracy of hand-crafted energy functions.
The specially-designed minimum-cost flow algorithm used by KnotFold considers all possible combinations of base pairs and selects from them the optimal combination. The algorithm breaks the restriction of nested base pairs required by the widely-used dynamic programming algorithms, thus facilitating the identification of pseudoknots.
Using a total of 1605 RNAs as representatives, we demonstrate the successful application of KnotFold in predicting RNA secondary structures including pseudoknots with accuracy significantly higher than the state-of-the-art approaches.
We anticipate that KnotFold, with its superior accuracy, will greatly facilitate the understanding of RNA structures and functionalities.
A dynamical system based on projection operator for solving absolute value equations associated with second-order cone
Authors: Chen Cairong , Yu Dongmei , Han Deren , Ma Changfeng 
Published: September 2022

Abstract
A new equivalent reformulation of the absolute value equations associated with second-order cone (SOCAVEs) is emphasised, from which a dynamical system based on projection operator for solving SOCAVEs is constructed. Under mild conditions, it is proved that the equilibrium points of the dynamical system exist and could be (globally) asymptotically stable. The effectiveness of the proposed method is illustrated by some numerical simulations.
Evaluation of Groundwater Quality Using Water Quality Index and GIS, The Case of Debre Tabor Town, Ethiopia
Authors: Tasew Adugnaw Shega , Berihune Zigiybel Firiew 
Published: September 2022

Abstract
Assessing the quality of groundwater for better management of the water sources is essential. This study is aimed at evaluating the groundwater quality of Debre Tabor town. Twelve groundwater samples were collected at hand dung wells during the wet season (Mid July-Mid August 2020) and dry season (1st February –Mid-March 2021). Various Physico-chemical parameters (pH, electrical conductivity (EC), Total dissolved solids (TDS), Temperature, Turbidity, Calcium (Ca2+), Magnesium (Mg2+), Chloride (Cl−), Nitrate (No3−), and microbiological parameters (Total coliform and Feacal coliform)) were analyzed and compared with the standard guidelines recommended by WHO. GIS was used to show the distribution of groundwater quality throughout the study area. WQI created by Canadian Council of Minster of the Environment (CCME) was applied to evaluate the suitability of the groundwater for drinking purposes. Also, the result shows that total coliform and faecal coliform at all groundwater wells were not suitable for drinking purpose. The result shows that Electrical conductivity, Temperature, Nitrate, Chloride and Magnesium at all groundwater wells were suitable for drinking purpose for both dry and wet season whereas Turbidity, pH, Calcium and Total Dissolved Solids are suitable for drinking purpose at some groundwater wells but not suitable at some wells. The water quality analysis result shows that spatial and seasonal variations of the parameters are significant throughout the study area(p < 0.05). According to CCMEWQI result seven groundwater samples show poor water quality status of 40.53-44 while, five groundwater samples show marginal water quality status of 44.19–55.82. Based on the information provided by the study, it is recommended to identify the source of contamination, provide properly designed sanitation systems and to monitor water quality at least once per year for effective and proper management of the groundwater quality.
Temporal trend of sediment accumulation in the Xuan Thuy Natural Wetland Reserve (Ba Lat coastal area of the Red River) and prediction on the future coastal wetland development
Authors: Dung Buidac , Thang Duongduc , Hau Doanthuy , Trang Nguyenhuyen , Cuong Ledinh , Khanh Nguyenvan , Thang Duongvan , Nam Phamtuan , Bac Vuongthu , Ha Nguyenthithu 
Published: September 2022

Abstract

An important task for future planning and management is predicting how the coastal wetland will develop. In order to calculate the rates of sediment accumulation, five sediment cores A, B, C, D, and E were taken from the Xuan Thuy National Park. Results show that the wetland experienced two to three sedimentation periods of different sedimentation rates in the last 100 years. At the core A site, the sedimentation rate has decreased over the past 40 years from1.70 ± 0.18 to 0.77 ± 0.11 cm year‑1. For the past 20 years, the average sedimentation rates at sites B, C, D, and E have been 1.53 ± 0.18, 1.80 ± 0.32, 2.02 ± 0.22, and 2.03 ± 0.25 cm year‑1, respectively. According to the recent temporal trend of sedimentation, it is predicted that in about 35 (±10) years from now, site A will be no longer receiving sediment from the tidal creeks and will be lying above the high tidal water level. Site B, D, and E will be lying above the high tidal water level in about 75 (± 10) years. In about 80 (± 15) years, the Tra tributary riverwill be filled up with sediment and become a swamp like today site B, D and E.
Single-Time-Point Dosimetry Using Model Selection and Non-Linear Mixed-Effects Modelling
Authors: Hardiansyah Deni , Riana Ade , Beer Ambros J. , Glatting Gerhard 
Published: September 2022

Abstract
Note: Please see pdf for full abstract with equations.
Purpose
This project aims to develop and evaluate a method for accurately determining time-integrated activities (TIAs) in single-time-point (STP) dosimetry for molecular radiotherapy (MRT). It performs a Model Selection (MS) within the framework of the Non-Linear Mixed-Effects (NLME) model (MS-NLME).
Methods
Biokinetic data of 111 In-DOTATATE in kidneys at T1=(2.9±0.6) h, T2=(4.6±0.4) h, T3=(22.8±1.6) h, T4=(46.7±1.7) h, and T5=(70.9±1.0) h post injection were obtained from eight patients using planar imaging. Eleven functions were derived from various parameterisations of mono-, bi-, and tri-exponential functions. The functions' fixed and random effects parameters were fitted simultaneously (in the NLME framework) to the biokinetic data of all patients. The Akaike weights were used to select the fit function most supported by the data. The relative deviations (RD) and the Root-Mean-Squared Error (RMSE) of the calculated TIAs for the STP dosimetry at T3=(22.8±1.6) h and T4=(46.7±1.7) h p.i. were determined using the best model of the MS-NLME (TIA MS-NLME ) and the bi-exponential function from the literature (TIA LIT ).
Results
The function [[EQUATION]] was selected as the function most supported by the data with an Akaike weight of (39±6) %. RD and RMSE values show that the MS-NLME method has a better performance than the bi-exponential function from the literature. The RMSEs of TIA NLME-PBMS and TIA LIT were 7.8% and 10.9% (for STP at T3), and 4.9% and 10.7% (for STP at T4), respectively.
Conclusion
An MS-NLME method was developed to determine the best fit function for calculating TIAs in STP dosimetry for a given radiopharmaceutical, organ and patient population. This STP dosimetry based on the MS-NLME method performs better than the STP dosimetry based on the NLME method using the bi-exponential function reported in the literature.
Identification of hub genes and pathways associated with abdominal subcutaneous fat deposition in pig using a comprehensive bioinformatics strategy
Authors: Yang Yongli , Wang Xiaoyi , Li Mingli , Wang Huiyu , Chen Qiang , Lu Shaoxiong 
Published: September 2022

Abstract
Background
Abdominal subcutaneous fat deposition (ASFD) is not only related to meat quality in pig industry, but also to human health in medicine. It is of great value to elucidate the potential molecular mechanisms of ASFD. However, the molecular mechanisms of ASFD are still unclear. The present study aims to identify hub genes and key pathways correlated with ASFD using porcine mature adipocytes (MAs).
Results
Totals of 565 differentially expressed genes (DEGs) were identified between three obese and three lean pigs, and these DEGs were mainly involved in p53 signaling pathway, MAPK signaling pathway and fatty acid metabolism. A protein-protein interaction (PPI) network including 540 nodes and 1065 edges was constructed, and top ten genes with the highest degree scores were identified as hub genes (ABL1, HDAC1, CDC42, HDAC2, MRPS5, MRPS10, MDM2, JUP, RPL7L1, and UQCRFS1) in the whole PPI network. A miRNA-hub gene network including 563 miRNAs and ten hub genes was established, and three genes with more links including MDM2, HDAC2 and CDC42 were identified as key genes in miRNA-gene regulatory network.
Conclusions
The present study identified some hub genes and key pathways associated with ASFD by a comprehensive analysis, which provided some novel insights into the molecular mechanism involved in ASFD.
Prolongation of seed viability and grain quality in rice by editing OsLOX1 using CRISPR/Cas9
Authors: Chen Yaping , Zhang Ping , Tong Qikai , Zhu Ziyan , Ma Tengfei , Wang Ping , Fu Kai , Chen Cheng , Mou Changling , Huang Yunshuai , Zhang Fulin , Hao Qixian , Zhang Min , Liu Shijia , Jiang Ling , Wan Jianmin 
Published: September 2022

Abstract
Storage tolerance is an important agronomic character in rice (Oryza sativa L.). Lipoxygenase (LOX) is a key enzyme in lipid metabolism, and its activity directly affects the rate of aging in rice. Here, lipoxygenase gene OsLOX1 was edited by CRISPR/Cas9 in Ningjing 4. We found that OsLOX1 knock-out can delay seed vigor loss, lipid metabolism and quality deterioration after aging. In addition, combining the transcriptome analysis, we could conclude that OsLOX1 affected the transcription of multiple genes during storage, and was involved in seed storage tolerance by regulating lipid metabolism and antioxidant pathways such as phosphatase and acetaldehyde dehydrogenase. By knocking out LOX1 gene, a new rice material with high vigor and no exogenous vector skeleton was bred to improve the storage tolerance of seeds and provide material support for rice breeding in China.
Titanium Dioxide and Zinc Oxide Nanoparticles in Sunscreen: Potential Impact on Cytokine Expression in Human Skin Pre- and Post-UVB Exposure
Authors: Ailawadi Shaina , Talreja Raghav , Panstingel Nicole , Sulentic Courtney 
Published: September 2022

Abstract
Background
Nanoparticles have been widely used in sunscreen products to prevent UVB-mediated skin damage. Research has shown that ZnO and TiO2 nanoparticles effectively scatter, reflect, and absorb light in the UV range. However, little is known regarding the impact of nanoparticle and UVB exposure on cytokine expression. This study investigates the influence of ZnO and TiO2 nanoparticles on the expression of pro- and anti-inflammatory cytokines in human skin exposed to UVB radiation.
Methods
De-identified, discarded skin from three abdominoplasty surgeries were exposed to UVB with or without the application of ZnO or TiO2 nanoparticles. Samples were analyzed using a BioRad Bio-Plex Pro Human Cytokine 27-plex Assay to determine cytokine levels of various pro- and anti-inflammatory cytokines.
Results
UVB exposure or application of ZnO or TiO2 nanoparticles had very little effect on cytokine levels compared to the no treatment control when evaluated 24 hrs after exposure. However, application of TiO2 following UVB exposure resulted in increased cytokine levels for nearly all the cytokines evaluated. This effect was absent when a combination of ZnO and TiO2 nanoparticles were applied. Interestingly, pre-, and post-UVB application of ZnO or a combination of ZnO and TiO2 nanoparticles decreased IL-6 levels or IL-6 and IL-8 levels, respectively.
Discussion
These results suggest a potential for nanoparticle sunscreen to enhance or reduce the inflammatory response in skin depending on conditions of UVB exposure and the nanoparticle composition and how it is applied. Further studies to evaluate the safety and efficacy of using nanoparticle sunscreens are warranted.
Electrochemical Monitoring of Trace-level Mercury in water sample using ZnO/GCE Modified Electrode
Authors: Bakhsh Hadi , Batool Madeeha , Mallah Arfana , Hassan Syeda Sara , Buledi Jamil A. , Solangi Amber R. , Sherazi Syed Tufail.H 
Published: September 2022

Abstract
Modification of glassy carbon electrode to electrochemically determine metal ions in water samples is of great interest these days. In this research, modified ZnO/GCE has been used to electrochemically sense mercury, which is toxic and harmful to human and aquatic life. ZnO NPs were synthesized by chemical aqueous growth procedure. Characteristic size and shape of ZnO NPs were determined by XRD and TEM whereas their elemental composition and functional group study were measured by EDX and FTIR, respectively. ZnO NPs were fabricated over GCE and electrochemical performance of modified ZnO/GCE was checked by employing cyclic voltammetry. The GCE fabricated with ZnO NPs was used to determine Hg (II) ions as a pollutant in real samples of water collected from Larkana district, Sindh, Pakistan. The linear dynamic range for mercury was found to be 1–80 µM with LOD and LOQ calculated as 0.001 µM .003 µM, respectively. The recovery percentage was obtained as; lowest 95% and highest 99% for canal water sample, while it was 92.5 to 100.2% for the samples ground water. The obtained results showed that the modified electrochemical sensor was stable for the selective detection of mercury ions even at low concentration.
Solvothermal synthesis, crystal structure and properties of selenidostannate containing zero-dimensional cluster structure
Authors: Jia Guo-Xin , Jiang Qi-Qi , Baiyin Menghe , Teri Gele 
Published: September 2022

Abstract
New selenidostannate compound [Ni(tren)(en)]SnSe3∙H2O (1) have been solvothermally synthesized and structurally characterized. Compound 1 consists of a transition metal complex [Ni(tren)(en)]2+, dimer [Sn2Se6]4−, and water molecules. The compound 1 is combination of metal complex and dimer that form unique zero-dimensional (0-D) structure. In this work, the photocurrent response was studied, and the results showed that compound 1 have good photocurrent response performance that higher photoelectron transfer efficiency and photoelectron hole pair separation efficiency. In addition, the optical properties, thermal stability and infrared spectra of the compound 1 was also studied.
A Janus Textile Capable of Radiative Subambient Cooling and Warming for Personal Thermal Management in Harsh Climates
Authors: Li Keqiao , Li Meng , Lin Chongjia , Liu Gongze , Li Yang , Huang Baoling 
Published: September 2022

AbstractTextiles with radiative cooling/warming capabilities provide a green and effective solution to personal thermal comfort in different climate scenarios. However, developing multiple-mode textiles for wearing in harsh climates with large temperature variation remains a challenge. Here we report a Janus textile comprising a polyethersulfone (PES)-Al2O3cooling layer optically coupled with a Ti3C2Txwarming layer, which can realize sub-ambient radiative cooling, solar warming and active Joule heating. Owing to the intrinsically high refractive index of PES and the rational design of the fiber topology, the nanocomposite PES textile features a record high solar reflectance of 0.97. Accompanied by an infrared emittance of 0.91 in the atmospheric window, sub-ambient cooling of 0.5-2.5 °C was achieved near noontime in humid summer under ~1000 W m-2solar irradiation in Hong Kong. The simulated skin covered with the textile was ~10 °C cooler than that with white cotton. The Ti3C2Txlayer provides a high solar-thermal efficiency of ~80% and a Joule heating flux of 66 W m-2at 2V due to its excellent spectral selectivity and electrical conductivity. The switchable multiple working modes enable effective and adaptive personal thermal management in different harsh environments.
Preoperative psychological competitive ability is associated with emotional states six months after anterior cruciate ligament reconstruction with hamstring autograft
Authors: Sengoku Takuya , Nakase Junsuke , Yoshimizu Rikuto , Kimura Mitsuhiro , Kanayama Tomoyuki , Kitaoka Katsuhiko , Tsuchiya Hiroyuki 
Published: September 2022

Abstract
Psychological state has been reported as one of the factors strongly related to return to sports after anterior cruciate ligament (ACL) reconstruction. However, its relationship with the emotional state remains unclear. This study aimed to investigate whether the preoperative psychological competitive ability is related to emotional states preoperatively and six months after ACL reconstruction. Patients who regularly performed sports activities and who underwent ACL reconstruction were divided into two groups according to the Diagnostic Inventory of Psychological Competitive Ability for Athletes (DIPCA.3) score. The emotional states preoperatively and at six months postoperatively were assessed using the Profile of Mood States, 2nd Edition (POMS2) and compared between the groups. Eighty-four patients were included and divided into high (DIPCA.3 score of 4 or higher, n = 23) and low (DIPCA.3 less than 4, n = 61) groups. Vigour-activity and friendliness were significantly higher in the high group than in the low group preoperatively. The difference was even greater at six months after ACL reconstruction. In addition, the high group showed statistically better results postoperatively for fatigue-inertia and total mood disturbance. Athletes with higher psychological competitive ability were in a positive emotional state preoperatively and six months after ACL reconstruction.
Current Control of EAST Fast Control Power Supply Based on BP Neuron Network Predictive PI
Authors: Chen Zhao , Huang Haihong , Wang Haixin 
Published: September 2022

Abstract
The dynamic response speed of output current is one of the most important performance indexes of EAST fast control power supply. To further improve the response speed of output current, a predictive PI control algorithm of BP neural network is proposed to overcome the shortcomings of large computation and slow convergence in traditional BP neural network. A branch current prediction model of EAST fast control power supply is established. Based on linear PI control, the BP neural network structure is combined, and the current prediction model is used as the adaptive objective function. To simplify the calculation process of the processor and speed up the convergence rate, a piecewise linear activation function is adopted. The learning rate of BP neural network structure and the activation function factor of the output layer are adjusted in real time according to the error between the predicted current and the reference signal. The online predictive adaptive setting of PI control parameters is realized by the steepest gradient descent method. Simulation and experiments results show that the proposed control algorithm has faster dynamic response speed than the traditional PI control.
Integrating untargeted and targeted metabolomics coupled with pathway analysis reveals muscle disorder in osteoporosis on orchiectomized mice
Authors: Ge Fei , Che Yanting , Wei Ziheng , Zheng Xiangtai , Sun Xiaodong , Qian Qingqing , Song Jinfei , Chen Junjie , Ding Gangyi , Zhao Hongxia , Wu Si , Dong Xin 
Published: September 2022

Abstract
Most osteoporosis (OP) fracture accidents in men are not only due to low BMD but also because of unhealthy muscle support. However, it has been a limited number of reports about how muscle metabolism is disturbed by OP in male patients. In this work, pathway analysis based on metabolomic research was carried out to fill this gap. Classical orchiectomy procedure was adapted to create OP animal model. Micro-CT and pathological section were applied for bone and muscle phenotype assessment and pathology analysis. UPLC-Q-TOF/MS and UPLC-QQQ-MS/MS were applied to measure metabolites in skeletal muscle samples among groups. In total, 31 significantly differential metabolites were detected by comparing between healthy model and OP animals, and 7 representative metabolites among the 31 significantly differential metabolites were identified and validated experimentally by UPLC-QQQ-MS/MS (xanthine, L-phenylalanine, choline, hypoxanthine, L-tryptophan, succinic acid, and L-tyrosine). Ingenuity Pathway Analysis analysis revealed significantly enriched pathways involved in inflammatory, oxidative stress, and necrosis. To our best knowledge, this is the first study that investigated early muscle disorder processes in OP cases at metabolic level, which facilitate early intervention and protection from OP fracture for aged men.
Endophenotype-based polygenic risk scores: Prediction of biomarker and clinical progression and dementia
Authors: Chasioti Danai , Jacobson Tanner , Nho Kwangsik , Risacher Shannon L. , Gao Sujuan , Yan Jingwen , Saykin Andrew J. 
Published: September 2022

Abstract

BACKGROUND: Biomarkers provide a framework for a biological diagnosis of Alzheimer’s disease (AD) whereas polygenic risk scores (PRS) provide method to estimate genetic risk. We derive biomarker-based PRS by incorporating endophenotype genetic risk relevant to amyloid, tau, neurodegeneration and cerebrovascular (A/T/N/V) pathology. METHODS: Endophenotype-PRSs (PRSA, PRST, PRSN, PRSV) and combined-PRSs (PRSAT, PRSATNV) were generated using the Alzheimer’s Disease Neuroimaging Initiative (ADNI) data. Prediction performance of the PRSs was assessed in terms of dementia risk, age at onset (AAO) and longitudinal change of 14 important AD biomarkers. RESULTS: PRSAand PRSTexplained more amyloid and tau variability than combined PRSs (CSF-amyloid: R2PRSA= 9.22%; CSF-tau: R2PRST= 6.37%; CSF-ptau: R2PRST= 7.10%). Combined-PRSs explained more neurodegeneration-related variability (R2PRSATNVrange: 1.22%-4.20%) and were strong predictors of dementia risk (HR and OR p-value<8.3e-03) and AAO (AAO(predicted_vs_observed): rAT=0.76). CONCLUSIONS: PRSAand PRSTare AD-specific, while combined-PRSs are linked to neurodegeneration in general. Biomarker-derived PRSs provide mechanistic insights beyond aggregate disease susceptibility, supporting development of precision medicine for dementia.