bluuebunny/crossref_metadata_2025_split huggingface dataset:
R5hmCFDV: computational identification of RNA 5-hydroxymethylcytosine based on deep feature fusion and deep voting
Authors: Shi Hongyan , Zhang Shengli , Li Xinjie 
Published: August 2022

AbstractRNA 5-hydroxymethylcytosine (5hmC) is a kind of RNA modification, which is related to the life activities of many organisms. Studying its distribution is very important to reveal its biological function. Previously, high-throughput sequencing was used to identify 5hmC, but it is expensive and inefficient. Therefore, machine learning is used to identify 5hmC sites. Here, we design a model called R5hmCFDV, which is mainly divided into feature representation, feature fusion and classification. (i) Pseudo dinucleotide composition, dinucleotide binary profile and frequency, natural vector and physicochemical property are used to extract features from four aspects: nucleotide composition, coding, natural language and physical and chemical properties. (ii) To strengthen the relevance of features, we construct a novel feature fusion method. Firstly, the attention mechanism is employed to process four single features, stitch them together and feed them to the convolution layer. After that, the output data are processed by BiGRU and BiLSTM, respectively. Finally, the features of these two parts are fused by the multiply function. (iii) We design the deep voting algorithm for classification by imitating the soft voting mechanism in the Python package. The base classifiers contain deep neural network (DNN), convolutional neural network (CNN) and improved gated recurrent unit (GRU). And then using the principle of soft voting, the corresponding weights are assigned to the predicted probabilities of the three classifiers. The predicted probability values are multiplied by the corresponding weights and then summed to obtain the final prediction results. We use 10-fold cross-validation to evaluate the model, and the evaluation indicators are significantly improved. The prediction accuracy of the two datasets is as high as 95.41% and 93.50%, respectively. It demonstrates the stronger competitiveness and generalization performance of our model. In addition, all datasets and source codes can be found at https://github.com/HongyanShi026/R5hmCFDV.
Advanced bioengineering of female germ cells to preserve fertility
Authors: Ghorbani Sadegh , Eyni Hossein , Norahan Mohammad Hadi , Zarrintaj Payam , Urban Nadine , Mohammadzadeh Alireza , Mostafavi Ebrahim , Sutherland Duncan S 
Published: August 2022

Abstract
Oogenesis and folliculogenesis are considered as complex and species-specific cellular differentiation processes, which depend on the in vivo ovarian follicular environment and endocrine cues. Considerable efforts have been devoted to driving the differentiation of female primordial germ cells toward mature oocytes outside of the body. The recent experimental attempts have laid stress on offering a suitable microenvironment to assist the in vitro folliculogenesis and oogenesis. Despite developing a variety of bioengineering techniques and generating functional mature gametes through in vitro oogenesis in earlier studies, we still lack knowledge of appropriate microenvironment conditions for building biomimetic culture systems for female fertility preservation. Therefore, this review paper can provide a source for a large body of scientists developing cutting-edge in vitro culture systems for female germ cells or setting up the next generation of reproductive medicine as feasible options for female infertility treatment. The focal point of this review outlines advanced bioengineering technologies such as 3D biofabricated hydrogels/scaffolds and microfluidic systems utilized with female germlines for fertility preservation through in vitro folliculogenesis and oogenesis.
Optimal row-column designs
Authors: Zhou Zheng , Zhou Yongdao 
Published: August 2022

Summary
Row-column designs have been widely used in experiments involving double confounding. Among them, one that provides unconfounded estimation of all main effects and as many two-factor interactions as possible is preferred, and is called optimal. Most current work focuses on the construction of two-level row-column designs, while the corresponding optimality theory has been largely ignored. Moreover, most constructed designs contain at least one replicate of a full factorial design, which is not flexible as the number of factors increases. In this study, a theoretical framework is built up to evaluate the optimality of row-column designs with prime level. A method for constructing optimal row-column designs with prime level is proposed. Subsequently, optimal full factorial three-level row-column designs are constructed for any parameter combination. Optimal fractional factorial two-level and three-level row-column designs are also constructed for cost saving.
Phylogeography of the desert scorpion illuminates a route out of Central Asia
Authors: Shi Cheng-Min , Zhang Xue-Shu , Liu Lin , Ji Ya-Jie , Zhang De-Xing 
Published: August 2022

AbstractA comprehensive understanding of phylogeography requires the integration of knowledge across different organisms, ecosystems, and geographic regions. However, a critical knowledge gap exists in the arid biota of the vast Asian drylands. To narrow this gap, here we test an “out-of-Central Asia” hypothesis for the desert scorpion Mesobuthus mongolicus by combining Bayesian phylogeographic reconstruction and ecological niche modeling. Phylogenetic analyses of one mitochondrial and three nuclear loci and molecular dating revealed that M. mongolicus represents a coherent lineage that diverged from its most closely related lineage in Central Asia about 1.36 Ma and underwent radiation ever since. Bayesian phylogeographic reconstruction indicated that the ancestral population dispersed from Central Asia gradually eastward to the Gobi region via the Junggar Basin, suggesting that the Junggar Basin has severed as a corridor for Quaternary faunal exchange between Central Asia and East Asia. Two major dispersal events occurred probably during interglacial periods (around 0.8 and 0.4 Ma, respectively) when climatic conditions were analogous to present-day status, under which the scorpion achieved its maximum distributional range. M. mongolicus underwent demographic expansion during the Last Glacial Maximum, although the predicted distributional areas were smaller than those at present and during the Last Interglacial. Development of desert ecosystems in northwest China incurred by intensified aridification might have opened up empty habitats that sustained population expansion. Our results extend the spatiotemporal dimensions of trans-Eurasia faunal exchange and suggest that species’ adaptation is an important determinant of their phylogeographic and demographic responses to climate changes.
Concurrent cardiac and central nervous system complications of acute infective endocarditis: case report
Authors: Prandi Francesca Romana , Anastasius Malcolm O , Matsoukas Stavros , Zhang Lily , Scaggiante Jacopo , Fifi Johanna T , Romeo Francesco , Lerakis Stamatios 
Published: August 2022

Abstract

Background
Cerebral mycotic aneurysms represent a rare but life-threatening complication of infective endocarditis (IE), with high mortality rate when ruptured. Due to the lack of randomized controlled trials, management of infectious aneurysms complicating endocarditis remains a controversial topic.

Case summary
We describe a case of Streptococcus salivarius bicuspid aortic and mitral valve endocarditis with concurrent spontaneous mycotic aneurysm rupture and acute subarachnoid haemorrhage (SAH). A 40-year-old man with history of intravenous drug abuse presented to our emergency department with altered mental status and dyspnoea. Echocardiography documented large vegetations on a bicuspid aortic valve and on the mitral valve, causing acute severe aortic and mitral regurgitation. Brain computed tomography imaging documented a ruptured fusiform aneurysm in a distal branch of the right middle cerebral artery causing acute SAH and acute obstructive hydrocephalus. An external ventricular drain was emergently placed and endovascular embolization of the aneurysm was achieved with deployment of six coils. Blood cultures grew S. salivarius and antibiotic therapy according to microbiological sensitivities was administered. Hospital stay was complicated by acute heart failure, ST-elevation myocardial infarction, conduction disturbances, cerebral vasospasm, recurrent mycotic aneurysm rupture, and death.

Discussion
Clinicians should be mindful of the rare, potentially severe complication of IE with cerebral mycotic aneurysms to enable prompt treatment. Generally, central nervous system procedures are performed prior to cardiac surgical management of IE, since cardiopulmonary bypass may exacerbate cerebral haemorrhage, ischaemic damage, and oedema in areas of blood–brain barrier disruption. A multidisciplinary collaboration is crucial for optimal patient management.
Understanding the digital impact of World Hypertension Day: key takeaways
Authors: Malhotra Kashish , Kalra Ankur , Kumar Ashish , Majmundar Monil , Wander Gurpreet Singh , Bawa Ashvind 
Published: August 2022

Abstract

Aim
To understand the global digital impact of World Hypertension Day and identify areas for further improvement to steer future policy development.

Methods and results
We used three social media assessment tools (Sprout Social, SocioViz, and Symplur) and Google Trends to obtain data about the total tweets and global impressions from countries worldwide about World Hypertension Day. Social network analysis of top influencers, associated hashtags, and keywords was performed to understand the context of the posts. With over 60 000 tweets reaching more than 250 million impressions, World Hypertension Day was a highly impactful event. A large spike of over 800% yearly increase was seen in 2021 that has greatly facilitated wider dissemination. However, there was limited collaboration among the top influencers and negligible participation from several African and non-English-speaking European countries.

Conclusion
With support from several governmental bodies, organizations and media outlets, World Hypertension Day is a highly impactful healthcare awareness day and presents a global case study of effectively utilizing digital resources for creating awareness among the global audience. Prioritizing equitable involvement from underrepresented and underprivileged communities must be focused. Future policy development of other awareness events shall extract the constructive feedback from these findings to promote global and public health.
Modified slide tracheoplasty technique in the management of a long-segment tracheoesophageal fistula
Authors: Duan Liang , Li Qiuyuan , Dai Jie , Jiang Gening 
Published: August 2022

Abstract
Post-tracheotomy tracheoesophageal fistula remains a challenge because it frequently involves a considerable length of the trachea. We report a case in which a modified slide tracheoplasty was successfully used to repair a long-segment, subglottic post-tracheotomy tracheoesophageal fistula. This technique not only shortened the length of the resected tracheal segment but also maintained the patency of the tracheal lumen.
Bacterial methyltransferases: from targeting bacterial genomes to host epigenetics
Authors: Rolando Monica , Silvestre Cristina Di , Gomez-Valero Laura , Buchrieser Carmen 
Published: August 2022

ABSTRACTMethyltransferase (MTases) enzymes transfer methyl groups particularly on proteins and nucleotides, thereby participating in controlling the epigenetic information in both prokaryotes and eukaryotes. The concept of epigenetic regulation by DNA methylation has been extensively described for eukaryotes. However, recent studies have extended this concept to bacteria showing that DNA methylation can also exert epigenetic control on bacterial phenotypes. Indeed, the addition of epigenetic information to nucleotide sequences confers adaptive traits including virulence-related characteristics to bacterial cells. In eukaryotes, an additional layer of epigenetic regulation is obtained by post-translational modifications of histone proteins. Interestingly, in the last decades it was shown that bacterial MTases, besides playing an important role in epigenetic regulations at the microbe level by exerting an epigenetic control on their own gene expression, are also important players in host–microbe interactions. Indeed, secreted nucleomodulins, bacterial effectors that target the nucleus of infected cells, have been shown to directly modify the epigenetic landscape of the host. A subclass of nucleomodulins encodes MTase activities, targeting both host DNA and histone proteins, leading to important transcriptional changes in the host cell. In this review, we will focus on lysine and arginine MTases of bacteria and their hosts. The identification and characterization of these enzymes will help to fight bacterial pathogens as they may emerge as promising targets for the development of novel epigenetic inhibitors in both bacteria and the host cells they infect.
Genomic evidence of paternal genome elimination in the globular springtailAllacma fusca
Authors: Jaron Kamil S , Hodson Christina N , Ellers Jacintha , Baird Stuart J E , Ross Laura 
Published: August 2022

AbstractPaternal genome elimination—a type of reproduction in which males inherit but fail to pass on their father’s genome—evolved independently in 6–8 arthropod clades. Thousands of species, including several important for agriculture, reproduce via this mode of reproduction. While paternal genome elimination is well established in some of the clades, the evidence in globular springtails (Symphypleona) remains elusive, even though they represent the oldest and most species-rich clade putatively reproducing via paternal genome elimination. We sequenced genomic DNA from whole bodies of Allacma fusca males with high fractions (&gt;27.5%) of sperm to conclusively confirm that all the sperm carry 1 parental haplotype only. Although it is suggestive that the single haplotype present in sperm is maternally inherited, definitive genetic proof of the parent of origin is still needed. The genomic approach we developed allows for the detection of genotypic differences between germline and soma in all species with sufficiently high fraction of germline in their bodies. This opens new opportunities for scans of reproductive modes in small organisms.
Resolution enhancement of airborne gravity data based on remove–compute–restore scheme (RCR) and downward continuation (DWC) technique
Authors: Elghrabawy Osama 
Published: August 2022

SUMMARY
This study aims to present a strategy to enhance the short wavelengths of airborne gravity signal, which attenuate due to the altitude and low-pass filtering based on remove–compute–restore (RCR) scheme and downward continuation (DWC) technique using fast Fourier transform (FFT). The airborne gravity data are measured at an altitude 1 km above the geoid using a GT-1A gravimeter. The enhancement strategy was applied in four cases. In case 1, the original airborne gravity anomaly was downward continued from 1 km to terrain level directly without applying the RCR scheme. In case 2, the XGM2019_2190 was removed from the original airborne gravity anomaly at flight level and back substituted at terrain level after applying the DWC technique. In case 3, the residual terrain model (RTM) was used instead of the XGM2019_2190 model, following the same sequence. Finally, in case 4, both regional and terrain signals were used in the same manner as applied in cases 2 and 3. The downward continued gravity anomalies were compared to the terrestrial gravity anomalies. The statistical results show that the most significant improvement was related to cases 3 and 4 in terms of the mean difference, which reveals 0.48 and 0.36 mGal, respectively. In conclusion, removing the terrain signal before applying the DWC process and back substituting it at terrain level plays a significant role in improving the resolution of the gravity signal-based airborne approach.
Cell type-specific DNA methylome signatures reveal epigenetic mechanisms for neuronal diversity and neurodevelopmental disorder
Authors: Jin Yulin , Su Kenong , Kong Ha Eun , Ma Wenjing , Wang Zhiqin , Li Yujing , Li Ronghua , Allen Emily G , Wu Hao , Jin Peng 
Published: August 2022

Abstract
DNA methylation plays a critical function in establishing and maintaining cell identity in brain. Disruption of DNA methylation-related processes leads to diverse neurological disorders. However, the role of DNA methylation characteristics in neuronal diversity remains underexplored. Here, we report detailed context-specific DNA methylation maps for GABAergic, glutamatergic (Glu) and Purkinje neurons, together with matched transcriptome profiles. Genome-wide mCH levels are distinguishable, while the mCG levels are similar among the three cell types. Substantial CG-differentially methylated regions (DMRs) are also seen, with Glu neurons experiencing substantial hypomethylation events. The relationship between mCG levels and gene expression displays cell type-specific patterns, while genic CH methylation exhibits a negative effect on transcriptional abundance. We found that cell type-specific CG-DMRs are informative in terms of represented neuronal function. Furthermore, we observed that the identified Glu-specific hypo-DMRs have a high level of consistency with the chromatin accessibility of excitatory neurons and the regions enriched for histone modifications (H3K27ac and H3K4me1) of active enhancers, suggesting their regulatory potential. Hypomethylation regions specific to each cell type are predicted to bind neuron type-specific transcription factors. Finally, we show that the DNA methylation changes in a mouse model of Rett syndrome, a neurodevelopmental disorder caused by the de novo mutations in MECP2, are cell type- and brain region-specific. Our results suggest that cell type-specific DNA methylation signatures are associated with the functional characteristics of the neuronal subtypes. The presented results emphasize the importance of DNA methylation-mediated epigenetic regulation in neuronal diversity and disease.
Do We All Walk the Walk? A Comparison of Walking Behaviors across Tetrapods
Authors: Struble M K , Gibb A C 
Published: August 2022

SynopsisA “walking” gait has been identified in a range of vertebrate species with different body plans, habitats, and life histories. With increased application of this broad umbrella term, it has become necessary to assess the physical characteristics, analytical approaches, definitions, and diction used to describe walks. To do this, we reviewed studies of slow-speed locomotion across a range of vertebrates to refine the parameters used to define walking, evaluate analytical techniques, and propose approaches to maximize consistency across subdisciplines of zoology. We summarize nine key parameters used to characterize walking behaviors in mammals, birds, reptiles, amphibians, and fish. After identifying consistent patterns across groups, we propose a comprehensive definition for a walking gait. A walk is a form of locomotion where the majority of the forward propulsion of the animal comes from forces generated by the appendages interacting with the ground. During a walk, an appendage must be out of phase with the opposing limb in the same girdle and there is always at least one limb acting as ground-support (no suspension phase). Additionally, walking occurs at dimensionless speeds &lt;1 v* and the average duty factor of the limbs is always &gt;0.5. Relative to other gaits used by the same species, the stance duration of a walk is long, the cycle frequency is low, and the cycle distance is small. Unfortunately, some of these biomechanical parameters, while effectively describing walks, may also characterize other, non-walking gaits. Inconsistent methodology likely contributes to difficulties in comparing data across many groups of animals; consistent application of data collection and analytical techniques in research methodology can improve these comparisons. Finally, we note that the kinetics of quadrupedal movements are still poorly understood and much work remains to be done to understand the movements of small, ecothermic tetrapods.
High performance evaluation of a PV/T hybrid system connected with a thermal store unit holding paraffin wax
Authors: Abbas Ehsan F , Tahseen Tahseen A , Madlol N A , Sulaiman Hulya S , Al-bonsrulah Hussein A Z , Raja Vijayanandh , Al-Bahrani Mohammed 
Published: August 2022

Abstract
The photovoltaic/thermal (PV/T) hybrid system combines a PV panel with a thermal collector to generate both electricity and heat energy. Several research have been conducted globally since the 1970s to increase its efficiency utilising various methodologies. One type of enhancing approach employed in this industry is phase-change materials. The current study combined a paraffin wax thermal storage unit with a typical PV/T hybrid collector (WPVT) and compared its performance with that of another comparable collector without a thermal store unit (TPVT). Both collectors were tested under actual weather circumstances from January to April 2021, with two water flow rates of 0.7 and 1.2 LPM. To analyse the rate of improvement in the PV/T system by adding a paraffin wax store unit, energy and exergy were simulated. During the trial period, the WPVT system provided the maximum efficiency flow rate of 1.2 LPM. It obtained around 60% efficiency, which was around 1.4 times that of TPVT. Furthermore, the modelling results indicated that the WPVT system’s maximum overall and exergy efficiencies were projected to be around 74.44 and 12%, respectively.
Characterization of sabatolimab, a novel immunotherapy with immuno-myeloid activity directed against TIM-3 receptor
Authors: Schwartz Stephanie , Patel Nidhi , Longmire Tyler , Jayaraman Pushpa , Jiang Xiaomo , Lu Hongbo , Baker Lisa , Velez Janelle , Ramesh Radha , Wavreille Anne-Sophie , Verneret Melanie , Fan Hong , Hu Tiancen , Xu Fangmin , Taraszka John , Pelletier Marc , Miyashiro Joy , Rinne Mikael , Dranoff Glenn , Sabatos-Peyton Catherine , Cremasco Viviana 
Published: August 2022

AbstractObjectivesSabatolimab is a humanized monoclonal antibody (hIgG4, S228P) directed against human T-cell immunoglobulin domain and mucin domain-3 (TIM-3). Herein, we describe the development and characterization of sabatolimab.MethodsSabatolimab was tested for binding to its target TIM-3 and blocking properties. The functional effects of sabatolimab were tested in T-cell killing and myeloid cell cytokine assays. Antibody-mediated cell phagocytosis (ADCP) by sabatolimab was also assessed.ResultsSabatolimab was shown to (i) enhance T-cell killing and inflammatory cytokine production by dendritic cells (DCs); (ii) facilitate the phagocytic uptake of TIM-3-expressing target cells; and (iii) block the interaction between TIM-3 and its ligands PtdSer/galectin-9.ConclusionTaken together, our results support both direct anti-leukemic effects and immune-mediated modulation by sabatolimab, reinforcing the notion that sabatolimab represents a novel immunotherapy with immuno-myeloid activity, holding promise for the treatment of myeloid cell neoplasms.