bluuebunny/crossref_metadata_2025_split huggingface dataset:
Classification of iPSC-Derived Cultures Using Convolutional Neural Networks to Identify Single Differentiated Neurons for Isolation or Measurement
Authors: Patel Purva , Mohammed Ali Lina K , Kaushik Uma , Wright Mallory G , Green Kaylee P , Waligorski Jason E , Kremitzki Colin L , Bachman Graham W , Elia Serena N , Buchser William J 
Published: December 2023

AbstractUnderstanding neurodegenerative disease pathology depends on a close examination of neurons and their processes. However, image-based single-cell analyses of neurons often require laborious and time-consuming manual classification tasks. Here, we present a machine learning approach leveraging convolutional neural network (CNN) classifiers that have the capability to accurately identify various classes of neuronal images, including single neurons. We developed the Single Neuron Identification Model 20-Class (SNIM20) which was trained on a dataset of induced pluripotent stem cell (iPSC)-derived motor neurons, containing over 12,000 images from 20 distinct classes. SNIM20 is built in TensorFlow and trained on images of differentiated iPSC cultures stained for nuclei and microtubules. This classifier demonstrated high predictive accuracy (AUC = 0.99) for distinguishing single neurons. Additionally, the 2-stage training framework can be used more broadly for cellular classification tasks. A variation was successfully trained on images of a human osteosarcoma cell line (U2OS) for single-cell classification (AUC = 0.99). While this framework was primarily designed for single-cell microraft-based identification and capture, it also works with cells in standard plate formats. We additionally explore the impact of specific fluorescent channels and brightfield images, class groupings, and transfer learning on the quality of the classification. This framework can both assist in high throughput neuronal or cellular identification and be used to train a custom classifier for the user’s needs.
Virus-like DNA tracers for characterizing wastewater-based pathogen monitoring systems
Authors: Gopal Anjali , Machtinger Ari N. , Wang Brian , Rice Daniel P. , Bradshaw William J. , McLaren Michael R. , Esvelt Kevin M. 
Published: December 2023

AbstractWastewater-based pathogen monitoring has recently become a ubiquitous method for tracking the abundance and evolution of pathogens in a community or port of entry. But accurate inference of disease incidence from wastewater remains challenging, in large part due to noise and bias arising from wastewater transport and measurement. We developed a new system of tracer particles designed to enhance wastewater monitoring of viral pathogens. These tracers, which consist of synthetic DNA barcodes packaged into non-infectious viral capsids, can be deposited at known amounts and times into the sewer system and measured in wastewater samples to assess features such as assay sensitivity, and the decay and delay in viral signal arising from a shedding event. Here we describe the design, construction, and initial characterization of a 25-plex tracer library. Our tracer library supports simultaneous measurement of up to 5 distinct tracers by qPCR and up to 25 distinct tracers by amplicon or metagenomic sequencing. We demonstrate experimentally that the tracers are biologically inert and exhibit good stability and qPCR-assay performance in wastewater. These features collectively suggest that barcoded, virus-like tracers have the required properties for high-accuracy, high-resolution characterization of wastewater monitoring systems.
Genetic Mapping of Monocyte Fate Decisions Following Myocardial Infarction
Authors: Koenig Andrew L , Kadyrov Farid F , Amrute Junedh M , Yang Steven , Weinheimer Carla J , Nigro Jessica M , Kovacs Attila , Smith Gabriella , Lavine Kory J 
Published: December 2023

AbstractInflammation contributes to the pathogenesis of myocardial infarction and heart failure and represents a viable therapeutic target. Monocytes and their progeny are highly abundant and display incredible functional diversity, serving as key determinants of myocardial inflammation and tissue repair. Much remains to be learned regarding mechanisms and signaling events that instruct monocyte fate decisions. We devised a genetic lineage tracing strategy usingCcr2crERT2Rosa26LSL-tdTomatomice in combination with single cell RNA-sequencing to map the differentiation trajectories of monocytes that infiltrate the heart after reperfused myocardial infarction. Monocytes are recruited to the heart early after injury and give rise to transcriptionally distinct and spatially restricted macrophage and dendritic cell-like subsets that are specified prior to extravasation and chronically persist within the myocardium. Pseudotime analysis predicted two differentiation trajectories of monocyte-derived macrophages that are partitioned into the border and infarct zones, respectively. Among these trajectories, we show that macrophages expressing a type I IFN responsive signature are an intermediate population that gives rise to MHC-IIhimacrophages, are localized within the border zone, and promote myocardial protection. Collectively, these data uncover new complexities of monocyte differentiation in the infarcted heart and suggest that modulating monocyte fate decisions may have clinical implications.
Metabolic cost for isometric force scales nonlinearly and predicts how humans distribute forces across limbs
Authors: Muralidhar Sriram Sekaripuram , Marin Nadja , Melick Colin , Alwan Aya , Wang Zhengcan , Baldwin Ross , Walcott Sam , Srinivasan Manoj 
Published: December 2023

AbstractMuscles consume metabolic energy for force production and movement. A mathematical model of metabolic energy cost will be useful in predicting instantaneous costs during human exercise and in computing effort-minimizing movements via simulations. Previous in vivo data-derived models usually assumed either zero or linearly increasing cost with force, but a nonlinear relation could have significant metabolic or behavioural implications. Here, we show that metabolic cost scales nonlinearly with joint torque with an exponent of about 1.64, using calorimetric measurements of isometric squats. We then demonstrate that this metabolic nonlinearity is reflected in human behaviour: minimizing this nonlinear cost predicts how humans share forces between limbs in additional experiments involving arms and legs. This shows the utility of the nonlinear energy cost in predictive models and its generalizability across limbs. Finally, we show mathematical evidence that the same nonlinear metabolic objective may underlie force sharing at the muscle level.
Tissue of origin detection for cancer tumor using low-depth cfDNA samples through combination of tumor-specific methylation atlas and genome-wide methylation density in graph convolutional neural networks
Authors: Nguyen Trong Hieu , Doan Nhu Nhat Tan , Tran Trung Hieu , Huynh Le Anh Khoa , Doan Phuoc Loc , Nguyen Thi Hue Hanh , Nguyen Van Thien Chi , Nguyen Giang Thi Huong , Nguyen Hoai-Nghia , Giang Hoa , Tran Le Son , Phan Minh Duy 
Published: December 2023

AbstractBackgroundCell free DNA (cfDNA)-based assays hold great potential in detecting early cancer signals yet determining the tissue-of-origin (TOO) for cancer signals remains a challenging task. Here, we investigated the contribution of a methylation atlas to TOO detection in low depth cfDNA samples.MethodsWe constructed a tumor-specific methylation atlas (TSMA) using whole-genome bisulfite sequencing (WGBS) data from five types of tumor tissues (breast, colorectal, gastric, liver and lung cancer) and paired white blood cells (WBC). TSMA was used with a non-negative least square matrix factorization (NNLS) deconvolution algorithm to identify the abundance of tumor tissue types in a WGBS sample. We showed that TSMA worked well with tumor tissue but struggled with cfDNA samples due to the overwhelming amount of WBC-derived DNA. To construct a model for TOO, we adopted the multi-modal strategy and used as inputs the combination of deconvolution scores from TSMA with other features of cfDNA.ResultsOur final model comprised of a graph convolutional neural network using deconvolution scores and genome-wide methylation density features, which achieved an accuracy of 69% in a held-out validation dataset of 239 low-depth cfDNA samples.ConclusionsIn conclusion, we have demonstrated that our TSMA in combination with other cfDNA features can improve TOO detection in low-depth cfDNA samples.
Systematic screens for fertility genes essential for malaria parasite transmission reveal conserved aspects of sex in a divergent eukaryote
Authors: Sayers Claire , Pandey Vikash , Balakrishnan Arjun , Michie Katharine , Svedberg Dennis , Hunziker Mirjam , Calvo Mercedes Pardo , Choudhary Jyoti , Berntsson Ronnie , Billker Oliver 
Published: December 2023

SUMMARYSexual reproduction in malaria parasites is essential for their transmission to mosquitoes. It also offers a divergent eukaryote model to understand the evolution of sex. Through a panel of genetic screens, where each sex ofPlasmodium bergheiwas mutagenised separately with barcoded vectors, we identify 401 sex and transmission-related gene functions and define roles for hundreds of unstudied fertility genes as putative targets for transmission blocking interventions. The functional data provide a deeper understanding of female metabolic reprogramming, meiosis and the axoneme. We identify a protein complex of a SUN domain protein, SUN1, and a moonlighting putative allantoicase, ALLC1, that is essential for male fertility by linking the microtubule organising centre to the nuclear envelope and enabling mitotic spindle formation during male gametogenesis. Both proteins have orthologs in mouse testis, and the data point to an ancient role for atypical SUN domain proteins in fertility. Altogether, our data provide an unbiased picture of the molecular processes that underpin malaria parasite transmission but also highlight ancestral aspects of sex that have evolved close to the last eukaryotic common ancestor.
Dining in the daylight: Nocturnal rhinoceros beetles extend feeding periods on host trees with reduced sap exudation
Authors: Kanda Asahi , Shibata Ryo , Ueno Takahiro , Yamashita Namifu , Kojima Wataru 
Published: December 2023

AbstractWhile the Japanese rhinoceros beetleTrypoxylus dichotomustypically feeds on the sap of the oakQuercus acutissimaand the crape myrtleLagerstroemia subcostataduring the night, it exhibits feeding activity both during the day and night when it utilizes the ash treeFraxinus griffithii. However, the mechanisms underlying the variations in temporal activity patterns remain unknown. We compared feeding rates (measured as body mass increments) and sap exudation rates amongF. griffithii, Q. acutissima, andL. subcostata. We found that beetles feeding onL. subcostataandQ. acutissimaexhibited significantly higher feeding rates than those feeding onF. griffithii. No significant differences in feeding rates were observed betweenL. subcostataandQ. acutissima. The sap exudation rate was significantly higher forQ. acutissimathan forF. griffithii. However, there were no significant differences in the sap exudation rates betweenF. griffithiiandL. subcostataor betweenQ. acutissimaandL. subcostata. These findings suggest that lower feeding rates onF. griffithiiprolong the feeding duration, resulting in daytime activity. While the low sap exudation inL. subcostataseems inconsistent with high feeding rates on this host, this apparent contradiction could be related to the extended duration of sap exudation.
Taking flight with food: investigating the determinants of user acceptance toward drone-based food delivery services in India
Authors: Kumar Sachin , Singh Bhagwan , Kumar Vinod , Chaudhuri Ranjan , Chatterjee Sheshadri , Vrontis Demetris 
Published: December 2023

PurposeThe present study intends to discover and analyze the determinants of users' intention to use (ITU) drone-based online food delivery (OFD) services. The study mainly focuses on the drone-based food delivery system in India and its implications.Design/methodology/approachThis study has used the purposive sampling method. With the support of the technology acceptance model (TAM) and the theory of planned behavior (TPB), a theoretical model was developed conceptually. Later, the model was validated using the partial least square-structure equation modeling (PLS-SEM) technique with consideration of 324 responses mainly from university students in Delhi- National Capital Region (NCR).FindingsThe findings reveal that all the determinants are positively and significantly related to ITU, except for perceived behavioral control that does not influence the consumer’s ITU drone-based OFD services. The study also shows that how food delivery system through drone can revolutionize the entire food delivery system in India.Research limitations/implicationsThe present study has developed a unique model that can be used by practitioners, future researchers in this field and policymakers in government departments. The present study is limited to Delhi-NCR in India, and thus, there is an issue of generalizability in the present study.Practical implicationsThis study has examined the future of food delivery system through drone-based system. Thus, the leaders in the food industry will be better positioned to understand consumers' intentions to use OFD services using drones and be able to make more informed decisions about investment in drone technology in their respective organizations.Originality/valueThe present study has combined both the technology adoption model and the TPB and developed a theoretical model. The study enriches the literature on drone-based OFD services. Since users' acceptance of OFD services using drones is an under-researched area, the present study will make a meaningful contribution to bring the body of literature in this domain.
Gender inequalities in unpaid public work: Retention, stratification and segmentation in the volunteer leadership of charities in England and Wales
Authors: Clifford David 
Published: December 2023

AbstractWhile gender inequalities in employment (paid public work) and domestic and reproductive labour (unpaid private work) are a prominent focus within the sociological literature, gender inequalities in volunteering (unpaid public work) have received much less scholarly attention. We analyse a unique longitudinal dataset of volunteer leaders, that follows through time every individual to have served as a board member (trustee) for a charity in England and Wales between 2010 and 2023, to make three foundational contributions to our understanding of gender inequalities in unpaid public work. First, the salience of vertical gender stratification and horizontal gender segmentation in trusteeship shows that gendered inequalities in work extend to public work in general—encompassing unpaid public work, and not only paid public work. In terms of gender segmentation, we find that women are over‐represented as trustees in a small number of fields of charitable activity but under‐represented across the majority of fields. In terms of gender stratification, we find that women are under‐represented on the boards of the largest charities; under‐represented as chairs of trustee boards; and particularly under‐represented as chairs of the largest charities. Second, the dynamics underlying gendered differences in unpaid public work, which show higher rates of resignation for women trustees, resonate with research on paid employment which emphasises the importance of attrition to an understanding of how gendered inequalities in work are reproduced. This means that increasing the retention of women, not only the recruitment of women, becomes central to the policy agenda. Third, we show that there has been a decline in gender stratification and gender segmentation in trusteeship since 2010. This decline over time in gendered inequalities in unpaid public work provides an interesting counterpoint to influential research documenting a ‘stall’ in the reduction of gendered inequalities in paid employment.
Searching for desirable bodies: How recruiters value physically exertive extracurricular activities for graduate hiring at elite professional firms in China
Authors: Ren Ran 
Published: December 2023

AbstractThe field of research in evaluating and applying Bourdieu's theories has seen growing interests in studying how the formation and effect of cultural capital vary in different contexts and fields. While existing studies have increasingly focussed on evaluating the role of cultural capital in creating educational inequalities in the Chinese context, little is known about how activities and taste are valued in the Chinese labour market. Drawing on semi‐structured interviews with 73 recruiters in elite professional firms in China, this article presents a study on how recruiters interpret physically exertive extracurricular activities (ECAs) for graduate hiring. It shows that these ECAs were valorised for assessing individual qualities and competences in job interviews, while other cultural activities, leisure or tastes carried little value. The notion of the body appeared central to this valorisation, conferring symbolic value onto physical exertive ECAs. The value of these activities was twofold, serving to convey candidates' possession of physical and embodied capital, which resonated to the normative dimension of elite professional firms. Recruiters thus used these activities to seek new professional bodies consumable for demanding professional work and resonating with the normative discourses of professionalism. This study provides more nuanced understandings of cultural capital in a non‐Western context and the role of ECAs in elite hiring. It also contributes to the development of physical and embodied capital by integrating perspective that links the body with labour process and professional control.
Impact of isolated and unattractive crops on honeybee foraging: A case study using radio frequency identification and hybrid carrot seed crops
Authors: Warren Ryan J. , Colin Théotime , Quarrell Stephen R. , Barron Andrew B. , Allen Geoff R. 
Published: December 2023

Abstract
Hybrid vegetable varieties have become essential for global agricultural production, offering key advantages for yield, quality and disease resistance. The production of hybrid seeds is however limited by pollination challenges, with these systems commonly associated with unattractive and low‐quality floral resources, isolated growing environments and frequent insecticide applications.
Here, we utilise commercial carrot seed crops to investigate the impact of hybrid pollination on the behaviour of the honey bee (Apis mellifera).
Six full‐strength bee colonies were equipped with solar powered radio frequency identification systems and over 900 tagged bees per season. These colonies were deployed to commercial hybrid seed crops over two consecutive seasons. The colonies were allocated to either an on‐crop or off‐crop group. Individual bees were autonomously monitored for the pollination period to assess key parameters such as survival, age at foraging and the number and duration of orientation and foraging trips.
Hybrid carrots were found to have a significant impact on bee foraging behaviour. Bees situated on the carrot crop undertook less frequent yet longer foraging trips, resulting in less total time outside of the colony compared to off‐crop bees. However, bees placed in carrot fields survived to an older age, orientated successfully, became foragers later and collected more pollen by weight, despite only 2% originating from carrot. We hope that the improved behavioural understanding can be utilised to enhance both pollinator health and hybrid seed production globally.
The exploitation of women: Narrative of oppressed women in movies
Authors: Alam Iftekhar , Lakshmi Seetha 
Published: December 2023

AbstractThe status of women in Indian society has been paradoxical emanating from a deeply embedded socially construed gender‐based exploitation owing to historical and sociological reasons. Moreover, the intersectionality of gender and caste has made them one of the marginalized social groups who experience discrimination, exclusion, and exploitation. Plethora of Bollywood movies, and regional cinema narrate the humiliation and exploitation of women in various spheres of their life. Some of the recent Bollywood and regional cinema has successfully attempted to highlight the gender‐based exploitation and exclusion. Therefore, drawing upon an Amazon web series ‘Dahad’ and a movie ‘Kathal‐a jackfruit mystery’ the paper tries to explore the struggle, exploitation, discrimination, aspiration, and assertion of women against existing social oppression. Taking the inferences from these two movies, the paper endeavors to seek the answer to the following questions: What are the nature and pattern of gender and caste‐based humiliation of women? How gender and caste intersect in their humiliation and social exclusion? How are women making their own struggle against gender oppression and exploitation in society? What is the tactic they use to negotiate gender discrimination? How are they asserting against gender‐based discrimination? How are they asserting their ‘agency’ in patriarchal and hierarchical society? What aspire and motivate them to fight for their dignity?
Staple food and possible famine food in Han Dynasty Guanzhong: Archeobotanical and stable isotopic perspectives
Authors: Tao Dawei , Zou Huilin , Chen Qinlong , Zhang Guowen , Guo Yongqi 
Published: December 2023

AbstractAgricultural yield fluctuations caused by environmental and social factors in ancient China have been well recorded in extensive ancient documents; however, comparatively little is known archaeologically. This study revealed the consumption and utilization of staple cereal and possible famine food by Han Dynasty inhabitants in the Guanzhong area based on archeobotanical evidence, including plant macro‐remains and phytoliths uncovered from pottery granaries and isotopic evidence from human bone collagen from Miaojiazhai cemetery. This preliminary multidisciplinary research with clear archaeological contexts provides archaeological evidence to reveal the food diversification and indicate that the possible occurrence and coping strategies to mitigate fluctuations in agricultural yields in Han Dynasty Guanzhong and broaden the understanding of the Han Dynasty agricultural economies and society.