bluuebunny/crossref_metadata_2025_split huggingface dataset:
Breaking the Limits - Multichromosomal Structure of an Early Eudicot Pulsatilla Patens Mitogenome Reveals Extensive RNA-editing, Longest Repeats and Chloroplast Derived Regions Among Sequenced Land Plant Mitogenomes
Authors: Szandar Kamil , Krawczyk Katarzyna , Myszczyński Kamil , Ślipiko Monika , Sawicki Jakub , Szczecińska Monika 
Published: November 2021

Abstract
Background: The mitogenomes of vascular plants are one of the most structurally diverse molecules. In the present study we characterize mitogenome of a rare and endangered species Pulsatilla patens. We investigated the gene content and its RNA editing potential, repeats distribution and plastid derived sequences.Results: The mitogenome structure of early divergent eudicot, endangered Pulsatilla patens does not support the master chromosome hypothesis, revealing the presence of three linear chromosomes of total length 986 613 bp. The molecules are shaped by the presence of extremely long, exceeding 87 kbp, repeats and multiple chloroplast derived regions including nearly complete inverted repeat. Since the plastid IR content of Ranunculales is very characteristic, the incorporation into mitogenome could be explained rather by intracellular transfer than mitochondrial HGT. The mitogenome contains an almost complete set of genes known from other vascular plants with exception of rps10 and sdh3, the latter being present but pseudogenised. Analysis of long ORFs enabled the identification of genes which are rarely present in plant mitogenomes, including RNA and DNA polymerases, albeit their presence even at species level is variable. Mitochondrial transcripts of P. patens were edited with a high frequency, exceeding the level known in other analyzed angiosperms, despite strict qualification criteria of editing event’s count and analysis of generally less frequently edited leaf transcriptome. The total number of edited sites was 902 and nad4 was identified as the most edited gene with 65 C to U changes. Non-canonical, reverse U to C editing was not detected. Comparative analyses of mitochondrial genes of three Pulsatilla species revealed a level of variation comparable to chloroplast CDS dataset and much higher infrageneric differentiation than in other known angiosperm genera. The variation found in CDS of mitochondrial genes is comparable to values found among Pulsatilla plastomes. Despite a complicated mitogenome structure, 14 single copy regions not splitted by repeats or MTPT of 329 kbp revealed potential for phylogenetic, phylogeographic and population genetics studies by revealing intra- and interspecific collinearity.Conclusions: This studies provides valuable new information about mitochondrial genome of early divergent eudicots, Pulsatilla patens, revealed multi-chromosomal structure and shed new light on mitogenomics of early eudicots.
FAM201A, a Long Noncoding RNA Potentially Associated With Atrial Fibrillation Identified by ceRNA Network Analyses and WGCNA
Authors: Chen Xi , He Xiang-Yu , Dan Qing , Li Yang 
Published: November 2021

Abstract
Background: Atrial fibrillation (AF) is the most common cardiac arrhythmia that contributes to various complications. However, little is known about lncRNAs associated with AF susceptibility. In the present study, we aim to identify lncRNAs involved in pathogenesis of AF based on competing endogenous RNA (ceRNA) network analyses and weighted gene co-expression network analysis (WGCNA).Methods: Two lncRNA and mRNA microarray datasets GSE41177 and GSE79768 were retrieved from the Gene Expression Omnibus (GEO) database. Differentially expressed lncRNAs (DElncRNAs), mRNAs (DEmRNAs) between AF patients and patients with sinus rhythm (SR) were identified from dataset GSE41177. Then, those DElncRNAs associated target miRNAs were predicted. The ceRNA network was constructed based on DElncRNAs, predicted miRNAs and DEmRNAs. To validate the role of AF-related lncRNAs, all lncRNAs form dataset GSE79768 were selected to perform WGCNA. LncRNA modules relevant to AF were identified. Crucial lncRNAs in the module that was most relevant to AF were screened according to the criteria of | Gene significance (GS)| > 0.6 and |Module membership (MM)| > 0.5. Results: A total of 18 DElncRNAs and 350 DEmRNAs were identified between AF patients and SR patients. The final ceRNA network contained 5 lncRNAs, 10 miRNAs, and 21 mRNAs. According to the ceRNA theory, combined with the comparative toxicogenomics database (CTD) database, the ceRNA axis FAM201A-miR-33a-3p-RAC3 was considered associated with AF susceptibility. By WGCNA, the blue module was detected most highly relevant with AF. The lncRNA FAM201A was proved in the blue module and highly related to AF. Conclusions: These results demonstrated that FAM201A might have great potential for susceptibility of AF based on ceRNA network analyses and WGCNA. FAM201A may function, at least partly, as ceRNA to regulate RAC3 in AF susceptibility.
Hierarchical generative modelling for autonomous robots
Authors: Yuan Kai , Sajid Noor , Friston Karl , Li Zhibin 
Published: November 2021

Abstract
Humans can produce complex movements when interacting with their surroundings. This relies on the planning of various movements and subsequent execution. In this paper, we investigated this fundamental aspect of motor control in the setting of autonomous robotic operations. We consider hierarchical generative modelling—for autonomous task completion—that mimics the deep temporal architecture of human motor control. Here, temporal depth refers to the nested time scales at which successive levels of a forward or generative model unfold: for example, the apprehension and delivery of an object requires both a global plan that contextualises the fast coordination of multiple local limb movements. This separation of temporal scales can also be motivated from a robotics and control perspective. Specifically, to ensure versatile sensorimotor control, it is necessary to hierarchically structure high-level planning and low-level motor control of individual limbs. We use numerical experiments to establish the efficacy of this formulation and demonstrate how a humanoid robot can autonomously solve a complex task requiring locomotion, manipulation, and grasping, using a hierarchical generative model. In particular, the humanoid robot can retrieve and deliver a box, open and walk through a door to reach the final destination. Our approach, and experiments, illustrate the effectiveness of using human-inspired motor control algorithms, which provide a scalable hierarchical architecture for autonomous performance of complex goal-directed tasks.
An intra-cytoplasmic route for SARS-CoV-2 transmission unveiled by Helium-ion microscopy
Authors: Merolli Antonio , Kasaei Leila , Ramsamy Santhamani , Kolloli Afsal , Kumar Ranjeet , Subbian Selvakumar , Feldman Leonard 
Published: November 2021

Abstract
SARS-CoV-2 virions enter the host cells by docking their spike glycoproteins to the membrane-bound Angiotensin Converting Enzyme 2. After intracellular assembly, the newly formed virions are released from the infected cells to propagate the infection, using the extra-cytoplasmic ACE2 docking mechanism. However, the molecular events underpinning SARS-CoV-2 transmission between host cells are not fully understood. Here, we report the findings of a scanning Helium-ion microscopy study performed on Vero E6 cells infected with mNeonGreen-expressing SARS-CoV-2. Our data reveal, with unprecedented resolution, the presence of: 1)-long tunneling nanotubes that connect two or more host cells over submillimeter distances; 2)-large scale multiple cell fusion events (syncytia); and 3)-abundant extracellular vesicles of various sizes. Taken together, these ultrastructural features describe a novel intra-cytoplasmic connection among SARS-CoV-2 infected cells that may act as an alternative route of viral transmission, disengaged from the well-known extra-cytoplasmic ACE2 docking mechanism. Our findings may explain the elusiveness of SARS-CoV-2 to survive from the immune surveillance of the infected host.
Vaccination Coverage in Cancer Outpatients: An Interventional Multicenter Before-and-After Study
Authors: Riviere Pierre , Penel Nicolas , Faure Karine , Marie Guillaume , Najem Abeer , Rivière Marie-Karelle , Panaget Sophie 
Published: November 2021

Abstract
Purpose: Despite widely disseminated guidelines, pneumococcal and influenza vaccination coverage (VC) remains insufficient in cancer patients receiving chemotherapy. We aimed to perform an interventional study to evaluate and improve VC in cancer patients treated in the medical oncology departments of three North-of-France hospitals. Methods: A standardized questionnaire assessed VC in adult cancer patients receiving anticancer treatment in three day hospitals from December 2–7, 2019. Subsequently (January 2020), we organized educational training sessions for medical staff in each hospital to discuss the current vaccination guidelines. To assess the impact of training on pneumococcal and influenza VC, we re-administered the same questionnaire in March 2020. Because there were no specific guidelines on Diphtheria-Tetanus-Pertussis (DTP) vaccination and no improvement was expected, DTP VC acted as an internal control. Results: In total, 272 patients were enrolled in the “before study” in all three hospitals; 156 patients were enrolled in the “after study” in only two hospitals, as data collection in the third was impossible because of COVID-19 pandemic national containment. The predictors were age for DTP VC, treatment center for pneumococcal VC, and age, sex, and tumor histology (adenocarcinoma vs. others) for influenza VC. Influenza VC was significantly improved post-intervention (42.6% vs. 55.1%, p=0.0169), especially in fragile patients, whereas pneumococcal VC was not (11.8% vs. 15.4%, p=0.3575).Conclusion:As expected, VC was very low in cancer patients, consistent with the literature. The intervention’s impact was limited for pneumococcal VC. The increased influenza VC may reflect the result of the national influenza vaccination campaign.
Stress Analysis of the Lower Lumbar Spine Three-joint Complex According to Different Pelvic Incidences
Authors: Lai Qi , Yin Jun , Zhang Zi Zhen , Yang Jie , Wan Zongmiao 
Published: November 2021

Abstract
Background: Pelvic incidence is closely related to degeneration of the facet joint and intervertebral disc and is related to the orientation of the facet joints. Currently, very few studies have been conducted on the force analysis of the three-joint complex in patients with different pelvic incidence measurements under different sports postures. We designed this study to better assess the influence of pelvic incidence on the stress of the lumbar three-joint complex. Finite element analysis can provide a biomechanical basis for the relationship between different pelvic incidences and degenerative diseases of the lower lumbar spine.Methods: We developed three nonlinear finite element models of the lumbar spine (L1-S1) with different pelvic incidences (27.44°, 47.05°, and 62.28°) and validated them to study the biomechanical response of facet joints and intervertebral discs with a follower preload of 400 N, under different torques (5 Nm, 10 Nm, and 15 Nm), and compared the stress of the three-joint complex of the lower lumbar spine (L3-S1) in different positions (flexion-extension, left-right bending, and left-right torsion).Results: In the flexion position, the stress of the disc in the low pelvic incidence model was the largest among the three models; the stress of the facet joint in the high pelvic incidence model was the largest among the three groups during the extension position. During torsion, the intradiscal pressure of the high pelvic incidence model was higher than that of the other two models in the L3/4 segment, and the maximum von Mises stress of the annulus fibrosus in the L5/S1 segment with a large pelvic incidence was greater than that of the other two models.Conclusions: Pelvic incidence is related to the occurrence and development of degenerative lumbar diseases. The stress of the lower lumbar facet joints and fibrous annulus of individuals with a high pelvic incidence is greater than that of individuals with a low pelvic incidence or a normal pelvic incidence. Although this condition only occurs in individual segments, to a certain extent, it can also reflect the influence of pelvic incidence on the force of the three-joint complex of the lower lumbar spine.
Anemia Requiring Transfusion in Breast Cancer Patients on Dose-dense Chemotherapy: Prevalence, Risk Factors, Cost and Effect on Disease Outcome.
Authors: Sharma Parth , Georgy Josh Thomas , Andrews Anand George , John Ajoy Oommen , Joel Anjana , Chacko Raju Titus , Singh Ashish 
Published: November 2021

Abstract
Purpose: Dose dense chemotherapy improves survival but also increases toxicity and treatment related cost. Here we report the prevalence of anemia, understand the risk factors of chemotherapy related anemia and determine the cost and time-delay associated with transfusion requirement in Indian non-metastatic breast cancer patients on dose dense preoperative chemotherapy.Methods: In this study, 116 triple negative breast cancer (TNBC) patients were treated preoperatively with Docetaxel and Cyclophosphamide alternating with Epirubicin and Cisplatin every 2-weekly. Patients were evaluated for anemia pre- and post-chemotherapy. We examined trends in the cell counts, transfusion requirement, time to transfusion as well as risk factors associated with transfusion during treatment, along with delay in treatment due to anemia and the additional cost incurred.Results: One hundred and sixteen women with high-risk non-metastatic TNBC were treated. Median age was 44.5 years. 56.1% had stage III disease. Delivery of 6/8 planned doses was achieved in 98.3% of patients, and all 8 doses in 86% patients. Anemia was detected at baseline in 54(46.5%) patients with mild(10-12g/dl) anemia in 42(36.2%) patients and moderate(8-10g/dl) in 12(10.3%) patients. Forty-four patients (37.9%) required transfusion during chemotherapy with 55(47.4%) patients having grade 1-2 anemia and 40(34.5%) patients having grade 3 anemia. The factors associated with transfusion were low grade of tumor (OR 2.48 (95% CI 1.08 - 5.68), p = 0.025), hemoglobin post 2 cycles of chemotherapy (OR 1.74 (95% CI 1.21- 2.51), p = 0.003), thrombocytopenia grade 3 or 4 (OR 4.35 (95% CI 1.062-17.827), p = 0.034) and drop in hemoglobin after 2 cycles (OR 1.65 (95% CI 1.09-2.48), p = 0.017). Nearly one fourth of the study population had a delay between two cycles of chemotherapy due to anemia. A median additional cost of Rs 7000 (IQR-Rs 7000 – Rs 14000) was incurred on transfusion.Conclusion: Anemia is a common toxicity associated with dose dense chemotherapy during curative breast cancer treatment leading to delay in treatment and increased cost. Low grade tumor, grade 3 or 4 thrombocytopenia and Grade 2 or higher anemia after 2 cycles of chemotherapy are risk factors for blood transfusions during treatment.
Use of Cellular Automata-Based Artificial Neural Networks For Detection and Prediction of Land Use Changes in North Eastern Dhaka City
Authors: Rahman Foyezur , Rahman Md. Tauhid Ur 
Published: November 2021

Abstract
The purpose of this study was to examine the pattern of change in Land Use Land Cover (LULC) and Land Surface Temperature (LST) in Mirpur and its surrounding area (north-eastern part of Dhaka) over the last 30 years using Landsat Satellite images and remote sensing indices, and to develop relationships between LULC types and LST, as well as to analyze their impact on local warming. Using this analyzed data, a further projection of LULC and LST change over the next two decades was made. From 1989 to 2019, five-year intervals of Landsat 4-5 TM and Landsat 8 OLI pictures were utilized to track the relationship between LULC changes and LST. Cellular Automata-based Artificial Neural Network (CA-ANN) algorithm was used to model the LULC and LST maps for the year 2039. Two environmental indices were analyzed to determine their link with LST: the Normalized Difference Vegetation Index (NDVI) and the Normalized Difference Built-up Index (NDBI). The link between LST and LULC types indicates that built-up area raises LST by substituting non-evaporating surfaces for natural vegetation. The average surface temperature has been increasing steadily for the previous 30 years. For the year 2019, it was determined that roughly 86 percent of total land area has been converted to built-up area and that 89 percent of land area has an LST greater than 28°C. According to the study, if the current trend continues, 72 percent of the Mirpur area is predicted to see temperatures near 32°C in 2039. Additionally, LST had a significant positive association with NDBI and a negative correlation with NDVI. The overall accuracy of LULC was greater than 90%, with a Kappa coefficient of 0.83. The study may assist urban planners and environmental engineers in comprehending and recommending effective policy measures and plans to mitigate the consequences of LULC.
Stress Detection using Natural Language Processing and Machine Learning over social Interactions
Authors: Nijhawan Tanya , Attigeri Girija , T Ananthakrishna 
Published: November 2021

Abstract
Cyberspace is a vast soapbox for people to post anything that they witness in their day-to-day lives. Subsequently, it can be used as a very effective tool in detecting the stress levels of an individual based on the posts and comments shared by him/her on social networking platforms. We leverage large-scale datasets with tweets to successfully accomplish sentiment analysis with the aid of machine learning algorithms. We take the help of a capable deep learning pre-trained model called BERT to solve the problems which come with sentiment classification. The BERT model outperforms a lot of other well-known models for this job without any sophisticated architecture. We also adopted Latent Dirichlet Allocation which is an unsupervised machine learning method that’s skilled in scanning a group of documents, recognizing the word and phrase patterns within them, and gathering word groups and alike expressions that most precisely illustrate a set of documents. This helps us predict which topic is linked to the textual data. With the aid of the models suggested, we will be able to detect the emotion of users online. We are primarily working with Twitter data because Twitter is a website where people express their thoughts often. In conclusion, this proposal is for the well- being of one’s mental health. The results are evaluated using various metric at macro and micro level and indicate that the trained model detects the status of emotions bases on social interactions.
Evaluation of ECMWF's forecasting system for probabilistic urban flood prediction: a case study in Mexico City
Authors: López López Marco R. , Pedrozo-Acuña Adrián , Severiano Covarrubias Marcela L. 
Published: November 2021

Abstract
As the world continues urbanizing, including efforts to forge a new framework of urban development is necessary. Recent studies related to flood prediction and mitigation have shown that Ensemble Prediction Systems (EPSs) constitute a valuable and essential tool for an Early Warning System. However, the use of EPS for flood forecasting in urban zones has yet to be understood. This work has the objective to investigate the potential use of the Operational EPS, issued by the European Centre for Medium-Range Weather Forecasts (ECMWF), for probabilistic urban flood prediction. In this research, a precipitation forecast verification was carried out in two study zones: (1) Mexico Valley Basin and (2) Mexico City, where for the latter, forecasts were compared against real-time observed data. The results showed good forecast reliability for a rain threshold of up to 20 mm in 24-hourly accumulations, with the first 36 h of the forecast horizon being the most reliable. The EPS has sufficient resolution and precision for flood prediction in Mexico City, which represents a further step toward developing a flood warning system at the local level based on ensemble forecasts.
Research and application of parameter estimation method in hydrological model based on dual ensemble Kalman filter
Authors: Lu Mengtian , Lu Sicheng , Liao Weihong , Lei Xiaohui , Yin Zhaokai , Wang Hao 
Published: November 2021

Abstract
Although field measurements and using long hydrological datasets provide a reliable method for parameters' calibration, changes in the underlying basin surface and lack of hydrometeorological data may affect parameter accuracy in streamflow simulation. The ensemble Kalman filter (EnKF) can be used as a real-time parameter correction method to solve this problem. In this study, five representative Xin'anjiang model parameters are selected to study the effects of the initial parameter ensemble distribution and the specific function form of the parameter on the EnKF parameter estimation process for both single and multiple parameters. Results indicate: (1) the method of parameter calibration to determine the initial distribution mean can improve the assimilation efficiency; (2) there is mutual interference among the parameters during multiple parameters' estimation which invalidates some conclusions of single-parameter estimation. We applied and evaluated the EnKF method in Jinjiang River Basin, China. Compared to traditional approaches, our method showed a better performance in both basins with long hydrometeorological dataset (an increase of Kling–Gupta efficiency (KGE) from 0.810 to 0.887 and a decrease of bias from −1.08% to −0.74%); and in basins with a lack of hydrometeorological data (an increase of KGE from 0.536 to 0.849 and a decrease of bias from −15.55% to −11.42%).
Urban water conundrums in Zimbabwe – the role of water policy and its implementation gaps
Authors: Taonameso Solomon , Mudau Lutendo Sylvia , Traoré Afsatou Ndama , Potgieter Natasha 
Published: November 2021

Abstract
Zimbabwe's urban areas are experiencing a dearth of water services, which is epitomized by acute water shortages and high morbidity due to waterborne diseases. The possible contribution of failures of water policy implementation to this state of affairs is explored. This review identifies and assesses 122 studies in Zimbabwe and in other countries that have analyzed water policies, in order to understand the factors which create gaps in policy implementation. It was found that these implementation gaps are mainly a result of capacity limitations in institutions, finances, and social and technical/human resources. There is currently very limited literature available that analyses water policy in Zimbabwe. In order to overcome the water conundrums in Zimbabwe's urban areas it is recommended that a literature review combined with an empirical study of both qualitative and quantitative gaps between the Zimbabwe National Water Policy and its implementation be undertaken. In particular, the review and study should focus on capacity limitations in institutions, finances, and social and technical/human resources in Zimbabwe.