bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Evaluation of Acute Myeloid Leukaemia (AML) Blood Cell Detection Models Using Different YOLO Approaches
Authors: Naing Kaung Myat , Kittichai Veerayuth , Tongloy Teerawat , Chuwongin Santhad , Boonsang Siridech 
Published: August 2021

AbstractThis study proposes to evaluate the performance of Acute Myeloid Leukaemia (AML) blast cell detection models in microscopic examination images for faster diagnosis and disease monitoring. One of the popular deep learning algorithms such as You Only Look Once (YOLO) developed for object detection is the successful state-of-the-art algorithms in real-time object detection systems. We employ four versions of the YOLO algorithm: YOLOv3, YOLOv3-Tiny, YOLOv2 and YOLOv2-Tiny for detection of 15-class of AML blood cells in examination images. We also acquired the publicly available dataset from The Cancer Imaging Archive (TCIA), which consists of 18,365 expert-labelled single-cell images. Data augmentation techniques are additionally applied to enhance and balance the training images in the dataset. The overall results indicated that four types of YOLO approach have outstanding performances of more than 92% in precision and sensitivity. In comparison, YOLOv3 has more reliable performance than the other three approaches. Consistently, the AUC values for the four YOLO models are 0.969 (YOLOv3), 0.967 (YOLOv3-Tiny), 0.963 (YOLOv2), and 0.948 (YOLOv2-Tiny). Furthermore, we compare the best model’s performance between approaches that use the entire training dataset without using data augmentation techniques and image division with data augmentation techniques. Remarkably, by using 33.51 percent of the training data in model training, the prediction outcomes from the model that used image partitioning with data augmentation were similar to those obtained using the complete training dataset. This work potentially provides a beneficial digital rapid tool in the screening and evaluation of numerous haematological disorders.
Slightly different metabolomic profiles are associated with high or low weights duck foie gras
Authors: Lo Bara , Marty-Gasset Nathalie , Manse Hélène , Canlet Cécile , Domitile Renaud , Rémignon Hervé 
Published: August 2021

AbstractUnderstanding the evolution of fatty liver metabolism of ducks is a recurrent issue for researchers and industry. Indeed, the increase in weight during the overfeeding period leads to an important change in the liver metabolism. However, liver weight is highly variable at the end of overfeeding within a batch of animals reared, force-fed and slaughtered in the same way. For this study, we performed a proton nuclear magnetic resonance (1H-NMR) analysis on two classes of fatty liver samples, called low-weight liver (weight between 550 and 599 g) and high-weight liver (weight above 700 g). The aim of this study was to identify the differences in metabolism between two classes of liver weight (low and high). Firstly, the results showed that increased liver weight is associated with higher glucose uptake leading to greater lipid synthesis. Secondly, this increase is probably also due to a decline in the level of export of triglycerides and cholesterol from the liver by maintaining them at high hepatic concentration levels. Finally, the increase in liver weight could lead to a significant decrease in the efficiency of aerobic energy metabolism associated with a significant increase in the level of oxidative stress.
Test-retest reproducibility of in vivo oscillating gradient and microscopic anisotropy diffusion MRI in mice at 9.4 Tesla
Authors: Rahman Naila , Xu Kathy , Omer Mohammad , Budde Matthew D. , Brown Arthur , Baron Corey A. 
Published: August 2021

ABSTRACTBackground and PurposeMicrostructure imaging with advanced diffusion MRI (dMRI) techniques have shown increased sensitivity and specificity to microstructural changes in various disease and injury models. Oscillating gradient spin echo (OGSE) dMRI, implemented by varying the oscillating gradient frequency, and microscopic anisotropy (µA) dMRI, implemented via tensor valued diffusion encoding, may provide additional insight by increasing sensitivity to smaller spatial scales and disentangling fiber orientation dispersion from true microstructural changes, respectively. The aims of this study were to characterize the test-retest reproducibility of in vivo OGSE and µA dMRI metrics in the mouse brain at 9.4 Tesla and provide estimates of required sample sizes for future investigations.MethodsEight adult C57Bl/6 mice were scanned twice (5 days apart). Each imaging session consisted of multifrequency OGSE and µA dMRI protocols. Metrics investigated included µA, isotropic and anisotropic kurtosis, and the diffusion dispersion rate (Λ), which explores the power-law frequency dependence of mean diffusivity. The dMRI metric maps were analyzed with mean region-of-interest (ROI) and whole brain voxel-wise analysis. Bland-Altman plots and coefficients of variation (CV) were used to assess the reproducibility of OGSE and µA metrics. Furthermore, we estimated sample sizes required to detect a variety of effect sizes.ResultsBland-Altman plots showed negligible biases between test and retest sessions. ROI-based CVs revealed high reproducibility for both µA (CVs < 8 %) and Λ (CVs < 15 %). Voxel-wise CV maps revealed high reproducibility for µA (CVs ∼ 10 %), but low reproducibility for OGSE metrics (CVs ∼ 50 %).ConclusionMost of the µA dMRI metrics are reproducible in both ROI-based and voxel-wise analysis, while the OGSE dMRI metrics are only reproducible in ROI-based analysis. µA and Λ may provide sensitivity to subtle microstructural changes (4 - 8 %) with feasible sample sizes (10 – 15).
Harmonisation of multi-site MRS data with ComBat
Authors: Bell Tiffany K. , Godfrey Kate J. , Ware Ashley L. , Yeates Keith Owen , Harris Ashley D. 
Published: August 2021

ABSTRACTMagnetic resonance spectroscopy (MRS) is a non-invasive neuroimaging technique used to measure brain chemistry in vivo and has been used to study the healthy brain as well as neuropathology in numerous neurological disorders. The number of multi-site studies using MRS are increasing; however, non-biological variability introduced during data collection across multiple sites, such as differences in scanner vendors and site-specific acquisition implementations for MRS, can obscure detection of biological effects of interest. ComBat is a data harmonisation technique that can remove non-biological sources of variance in multisite studies. It has been validated for use with structural and functional MRI metrics but not for MRS metabolites. This study investigated the validity of using ComBat to harmonize MRS metabolites for vendor and site differences. Analyses were performed using data acquired across 20 sites and included edited MRS for GABA+ (N=218) and macromolecule-suppressed GABA data (N=209), as well as standard PRESS data to quantify NAA, creatine, choline, and glutamate (N=195). ComBat harmonisation successfully mitigated vendor and site differences for all metabolites of interest. Moreover, significant associations were detected between sex and choline levels and between age and glutamate and GABA+ levels that were not detectable prior to harmonisation, confirming the importance of removing site and vendor effects in multi-site data. In conclusion, ComBat harmonisation can be successfully applied to MRS data in multi-site MRS studies.HighlightsMulti-site MRS data contains sources of non-biological variance that can mask biological effects of interest.ComBat data harmonisation successfully removes variance contributed by scanner and site differences.Removal of this variance revealed biological effects that were previously not detected.ComBat harmonisation can be successfully applied to MRS data in multi-site MRS studies
GlycoSHIELD: a versatile pipeline to assess glycan impact on protein structures
Authors: Gecht Michael , von Bülow Sören , Penet Camille , Hummer Gerhard , Hanus Cyril , Sikora Mateusz 
Published: August 2021

AbstractMore than 75% of surface and secreted proteins are modified by covalent addition of complex sugars through N- and O-glycosylation. Unlike proteins, glycans do not typically adopt specific secondary structures and remain very mobile, influencing protein dynamics and interactions with other molecules. Glycan conformational freedom impairs complete structural elucidation of glycoproteins. Computer simulations may be used to model glycan structure and dynamics. However, such simulations typically require thousands of computing hours on specialized supercomputers, thus limiting routine use. Here, we describe a reductionist method that can be implemented on personal computers to graft ensembles of realistic glycan conformers onto static protein structures in a matter of minutes. Using this open-source pipeline, we reconstructed the full glycan cover of SARS-CoV-2 Spike protein (S-protein) and a human GABAA receptor. Focusing on S-protein, we show that GlycoSHIELD recapitulates key features of extended simulations of the glycosylated protein, including epitope masking, and provides new mechanistic insights on N-glycan impact on protein structural dynamics.
Towards a genome sequence for every animal: where are we now?
Authors: Hotaling Scott , Kelley Joanna L. , Frandsen Paul B. 
Published: August 2021

AbstractIn less than 25 years, the field of animal genome science has transformed from a discipline seeking its first glimpses into genome sequences across the Tree of Life to a global enterprise with ambitions to sequence genomes for all of Earth’s eukaryotic diversity (1). As the field rapidly moves forward, it is important to take stock of the progress that has been made to best inform the discipline’s future. In this Perspective, we provide a contemporary, quantitative overview of animal genome sequencing. We identified the best available genome assemblies on GenBank, the world’s most extensive genetic database, for 3,278 unique animal species across 24 phyla. We assessed taxonomic representation, assembly quality, and annotation status for major clades. We show that while tremendous taxonomic progress has occurred, stark disparities in genomic representation exist, highlighted by a systemic overrepresentation of vertebrates and underrepresentation of arthropods. In terms of assembly quality, long-read sequencing has dramatically improved contiguity, whereas gene annotations are available for just 34.3% of taxa. Furthermore, we show that animal genome science has diversified in recent years with an ever-expanding pool of researchers participating. However, the field still appears to be dominated by institutions in the Global North, which have been listed as the submitting institution for 77% of all assemblies. We conclude by offering recommendations for how we can collectively improve genomic resource availability and value while also broadening global representation.Significance statementThe field of animal genome science is rapidly developing, and efforts are underway to sequence genomes for all of Earth’s eukaryotic biodiversity. Here, we provide an overview of animal genome sequencing, with emphases on taxonomic representation, assembly quality, and geographic representation. We show that while a staggering 3,278 unique animal species have had their genomes sequenced, massive disparities exist in terms of the taxonomic groups receiving attention, the quality of the resources being produced, and the institutions driving the field. We highlight areas where improvements can be made, notably by continuing to increase the quality of genome assemblies, including by improving metadata and voucher specimen associations, and actively developing meaningful collaborations between researchers form the Global North and South.
University-wide chronotyping shows late-type students have lower grades, shorter sleep, poorer well-being, lower self-regulation, and more absenteeism
Authors: Yeo Sing Chen , Tan Jacinda , Lai Clin K.Y. , Lim Samantha , Chandramoghan Yuvan , Fung Fun Man , Chen Patricia , Strauman Timothy J. , Gooley Joshua J. 
Published: August 2021

AbstractA person’s preferred timing of nocturnal sleep (chronotype) has important implications for cognitive performance. Students who prefer to sleep late may have a selective learning disadvantage for morning classes due to inadequate sleep and circadian desynchrony. Here, (1) we tested whether late-type students perform worse only for morning classes, and (2) we investigated factors that may contribute to their poorer academic achievement. Chronotype was determined objectively in 33,645 university students (early,n=3,965; intermediate,n=23,787; late,n=5,893) by analyzing the diurnal distribution of their logins on the university’s Learning Management System (LMS). Late-type students had lower grades than their peers for courses held at all different times of day, and during semesters when they had no morning classes. Actigraphy studies (n=261) confirmed LMS-derived chronotype was associated with students’ sleep patterns. Nocturnal sleep on school days was shortest in late-type students because they went to bed the latest and woke up early compared with non-school days. Surveys showed that late-type students had lower self-rated health and mood (n=357), and lower metacognitive self-regulation (n=752). Wi-Fi connection data for classrooms (n=17,356) revealed that late-type students had lower lecture attendance than their peers for classes held in both the morning and the afternoon. Our findings suggest that multiple factors converge to impair learning in late-type students. Shifting classes later can improve sleep and circadian synchrony in late-type students but is unlikely to eliminate the performance gap. Interventions that focus on improving students’ well-being and learning strategies may be important for addressing the late-type academic disadvantage.
A Herpes Simplex Virus Type-1-derived influenza vaccine induces balanced adaptive immune responses and protects mice from lethal influenza virus challenge
Authors: Rider Paul J.F. , Dulin Harrison , Uche Ifeanyi K. , McGee Michael C. , Breitenstein Blake , Tan Gene S. , Huang Weishan , Kousoulas Konstantin G. , Hai Rong 
Published: August 2021

AbstractInfluenza virus is a major respiratory viral pathogen responsible for the deaths of hundreds of thousands worldwide each year. Current vaccines provide protection primarily by inducing strain-specific antibody responses with the requirement of a match between vaccine strains and circulating strains. It has been suggested that anti-influenza T-cell responses, in addition to antibody responses may provide the broadest protection against different flu strains. Therefore, to address this urgent need, it is desirable to develop a vaccine candidate with an ability to induce balanced adaptive immunity including cell mediated immune responses. A live viral vector technology should exhibit safety, immunogenicity, effectiveness in the presence of pre-existing immunity, and the ability to induce mucosal immune responses. Here, we used VC2, an established Herpes Simplex Virus type 1 vaccine vector, to express the influenza HA protein. We show that this virus is capable of generating potent and specific anti-influenza humoral and cell-mediated immune responses. We further show that a single vaccination with the VC2-derived influenza vaccine protects mice from lethal challenge with influenza virus. Our data support the continued development of VC2-derived influenza vaccines for protection of human populations from both seasonal and pandemic strains of influenza. Finally, our results support the potential of VC2-derived vaccines as a platform for the rapid development of vaccines against emerging and established pathogens, particularly respiratory pathogens.
Distinct Roles of Dopamine D1 and D2 Receptor-expressing Neurons in the Nucleus Accumbens for a Strategy Dependent Decision Making
Authors: Nishioka Tadaaki , Macpherson Tom , Hamaguchi Kosuke , Hikida Takatoshi 
Published: August 2021

SUMMARYTo optimize decision making, animals need to execute not only a strategy to choose a good option but sometimes also one to avoid a bad option. A psychological study indicates that positive and negative information is processed in a different manner in the brain. The nucleus accumbens (NAc) contains two different types of neurons, dopamine D1 and D2 receptor-expressing neurons which are implicated in reward-based decision making and aversive learning. However, little is known about the neural mechanisms by which D1 or D2 receptor-expressing neurons in the NAc contribute to the execution of the strategy to choose a good option or one to avoid a bad option under decision making. Here, we have developed two novel visual discrimination tasks for mice to assess the strategy to choose a good option and one to avoid a bad option. By chemogenetically suppressing the subpopulation of the NAc neurons, we have shown that dopamine D2 receptor-expressing neurons in the NAc selectively contribute to the strategy to avoid a bad option under reward-based decision making. Furthermore, our optogenetic and calcium imaging experiments indicate that dopamine D2 receptor-expressing neurons are activated by error choices and the activation following an error plays an important role in optimizing the strategy in the next trial. Our findings suggest that the activation of D2 receptor-expressing neurons by error choices through learning enables animals to execute the appropriate strategy.
Robust model reference adaptive backstepping sliding-mode control for quadrotor attitude with disturbance observer
Authors: Ahmed Nigar , Chen Mou 
Published: August 2021

PurposeThe purpose of this research paper is to design a disturbance observer-based control based on the robust model reference adaptive backstepping sliding-mode control for attitude quadrotor model subject to uncertainties and disturbances.Design/methodology/approachTo estimate and reject the disturbance, a disturbance observer is designed for the exogenous disturbances with perturbation while a control criterion is developed for the tracking of desired output. To achieve the control performance, backstepping and sliding-mode control techniques are patched together to obtain robust chattering-free controller. Furthermore, a model reference adaptive control criterion is also combined with the design of robust control for the estimation and rejection of uncertainties and unmodeled dynamics of the attitude quadrotor.FindingsThe findings of this research work includes the design of a disturbance observer-based control for uncertain attitude quadrotor system with the ability of achieving tracking control objective in the presence of nonlinear exogenous disturbance with and without perturbation.Practical implicationsIn practice, the quadrotor flight is opposed by different kinds of the disturbances. In addition, being an underactuated system, it is difficult to obtain an accurate mathematical model of quadrotor for the control design. Thus, a quadrotor model with uncertainties and disturbances is inevitable. Hence, it is necessary to design a control system with the ability to achieve the control objectives in the presence of uncertainties and disturbances.Originality/valueDesigning the control methods for quadrotor control without uncertainties and disturbances is a common practice. However, investigating the uncertain quadrotor plant in the presence of nonlinear disturbances is rarely taken into consideration for the control design. Hence, this paper presents a control algorithm to address the issues of the uncertainties and disturbances as well as investigate a control algorithm to achieve tracking performance.
Popular music in the youth culture of Hong Kong: the social functions of indie music
Authors: Lau Stella Sai-Chun 
Published: August 2021

PurposeThe key concepts to be explored in this article include the blurring boundary between “indie” and “pop”; the significance of digital media in contemporary music industry and the distinctive socio-political nature of indie music in Hong Kong. To a large extent, it discusses the social functions of music – a subject discussed by Simon Frith (2007), a leading scholar in popular music studies.Design/methodology/approachIn order to expound on some observations of the connections between music cultures and socio-political development in Hong Kong, a selection of musical works by indie musicians will be looked into closely.FindingsA focus of discussion will be given to the difference between mainstream Cantopop and indie music in a way that the latter mentions socio-political matters overtly while the former downplays sensitive political issues, particularly in the post-colonial era after the handover of Hong Kong to mainland China in 1997.Originality/valueOriginality of research can be evidenced by the author's textual analysis of the musical styles and lyrics produced by various local indie artists' musical works through primary sources.
Statistical analysis of wind resource and energy potential assessment of Sanghar site, Sindh Pakistan
Authors: Hulio Zahid Hussain , Wei Jiang , Khan Ghulam Mujtaba 
Published: August 2021

Purpose
The purpose of this paper is to assess the wind resource and energy potential of the Sanghar site for minimizing the dependence on fossil fuels and improving the environment.

Design/methodology/approach
The Sanghar site wind shear coefficient and turbulence intensity factor are investigated for a period of a year. The two-parameter k and c Weibull distribution function is used to analyze the wind speed of the Sanghar site. The standard deviation, coefficient of variation, wind power density and energy density; and capacity factor was assessed for a period of a year. The economic assessment of energy/kWh is investigated for the selection of appropriate wind turbines.

Findings
The mean wind shear of the Sanghar site was found to be 0.2509. The mean wind speed was found to be 4.766, 5.534 and 6.121 at 20, 40 and 60 m above the ground level. The mean value of the k parameter was observed to be 2.433, 2.777 and 2.862 at 20, 40 and 60 m for a period of a year. The Weibull c m/s parameter was found to be 5.377, 6.245 and 6.906 m/s at 20, 40 and 60 m. The major portion of values of standard deviation was found to be in between 0.1 to 2.00 at 20, 40 and 60 m. The mean wind power density values were observed to be 88.33, 93.5 and 110.16 W/m2 at 20, 40 and 60 m; respectively, for a period of a year. The mean coefficient of variation was found to be 0.1478, 0.1205 and 0.1033 at 20, 40 and 60 m; respectively. The mean energy density was found to be 476.75, 683.08 and 866.33 kWh/m2 at 20, 40 and 60 m; respectively. The mean capacity factor for different wind turbines was ranged between 18 to 24.83 for a period of a year. The economic assessment showed that wind turbine B has the minimum cost (US$) 0.0484/kWh.

Practical implications
The assessment provides the solution to sustainable energy generation which reduces the consumption of fuel and the effect of fluctuating price of fuel in the world market on local consumers.

Social implications
Wind energy may have social implications including environmentally friendly, consistent supply of energy during the peak summer season, less unit per cost, etc.

Originality/value
The Sanghar site is new and assessed for the first time in this research work. The Sanghar site is suitable for installing utility wind turbines for energy generation at the lowest cost.