bluuebunny/crossref_metadata_2025_split huggingface dataset:
Antioxidant and Antimicrobial Activity of Essential oil Extracted from Trachyspermum Ammi (ajwain) Seeds: an In-vitro Study
Authors: Paliwal N. , Dwivedi M. K. , Shrivastava P. , Malviya V. , Malviya R. , Yadav A. 
Published: November 2023

AbstractThe food industry uses essential oils derived from natural sources as flavouring and preservatives. The purpose of this study is to investigate how temperature affects the essential oil extracted from Trachyspermum ammi, seeds which has the best antioxidant and antimicrobial properties, in order to find a green substitute for toxic chemically produced preservatives used in food and pharmaceutical chemistry. Trachyspermum ammi (ajwain seeds) seeds were hydrodistilled at various temperatures (60°C to 90°C). The amount of essential oil was found to decrease on increasing temperature (2.1ml, 1.5 ml and 1.0 ml at 70°C, 80°C, and 90°C respectively). Hence, 70°C was the ideal temperature for extracting the essential oil from ajwain seeds. 25 components were discovered in the essential oil extracted from ajwain seeds by GC-MS technique. The predominant ingredient was shown to be thymol (31.40%). The percentages of scavenger activity against hydrogen peroxide were 70.75%, 86.99%, and 95.28% for 70°C, 80°C, and 90°C respectively. Due to the presence of the largest concentration of thymol (67.66%), the results showed that essential oil extracted at 90°C demonstrated the highest level of antioxidant property. By using the disc diffusion method, the antimicrobial activity of an essential oil made from ajwain seeds was evaluated. MIC50 of standard essential oil of Trachyspermum ammi seeds against gram positive strain was observed 10 µL/mL of culture and 25µL/mL of culture was observed against gram negative bacteria. Essential oil extracted at 70°C showed antimicrobial activity by forming zones of inhibition with diameters including discs of 18.3 mm and 14.36 mm against S. aureus and E. coli, respectively. Essential oil extracted at 80°C produced zones of inhibition with diameters of 18.68 mm and 15.30 mm, respectively. In the case of essential oil extracted at 90°C, the zones of inhibition against S. aureus and E. coli had diameters of 18.690.3 mm and 15.38 mm, respectively. As a result, using Trachyspermum ammi essential oil as a food preservative and the temperature at which it is extracted are unaffected by an increase in extraction temperature. Hence, essential oil obtained from Trachyspermum ammi seeds can be used as green alternative of chemically synthesized toxic preservatives used in food and pharmaceutical chemistry.
Quantifying embodiment towards building better robots based on muscle-driven models
Authors: Chandiramani Vijay , Conn Andrew T. , Hauser Helmut 
Published: November 2023

Abstract
In recent years, researchers have investigated different methods to quantify embodiment for a variety of robotic systems including robotic arms, grippers and legged robots. This paper will discuss some of these methods, focusing on their potential contribution to designing robotic systems based on muscle-driven models. We start with the definition of embodiment based on the relational dynamics between the system and its environments by drawing upon the idea of mutual perturbation and structural coupling between the two. We will discuss how such an understanding can provide potential approaches to quantify embodiment. These includes two information-theoretic measures which are particularly suitable for muscle-driven models. The two methods are based on (i) comparing the controller and behaviour complexity and (ii) Conditional Mutual Information, which compares the difference in distribution of the action conditional on the actuated state and purely on its morphological properties. These methods were used on muscle-driven, biologically realistic hopping models to quantify embodiment at different stages of the hopping gait. The results clearly demonstrate the contribution of morphology of the muscle fibers at different points in the hopping cycle. Furthermore, these methods have been used in latter studies to measure the contribution of embodiment across different levels in a hierarchical control system of a neuro-musculoskeletal model and also to quantify the effects of information cost during various actions in a muscle-driven robotic system. We discuss the practical implications as well as limitations and the future work in the application of these quantification methods.
Imitation and reinforcement learning to control soft robots: a perspective
Authors: Nazeer Muhammad Sunny , Laschi Cecilia , Falotico Egidio 
Published: November 2023

Abstract
It would not be an over-stretch to appraise soft robotics as one of the most sizzling topic in this era, owing to its unparalleled performance in terms of exhibited deformability, soft-interaction and luscious dexterity. In spite of that, we see minimal applications of this class around us. We believe the reason roots in the gap between design and fabrication of the soft robots and the capability to control them. The remedy to this imbalance, we believe, is a necessity for a climacteric rise in the capability to control them. The control, however poses challenges due to virtually infinite degrees of freedom of soft robot design, in terms of modelling the behavior of the robot, modelling its interaction with the environment or the environment’s effect on the robot. These challenges provoke the preponderant need for solutions that either can work with the inaccurate models of the robot obtained or avoid it altogether. To answer what can be used with these limitations we present here two potential classes of algorithms from machine learning capable of performing well under just the listed conditions: reinforcement learning (RL) can provide a solution in the form of a policy to control a platform with sophisticated dynamics even when the presented environment to train said policy has questionable accuracy, while Imitation Learning (IL) trains a policy while avoiding the need of a model or its constituent parts altogether and a policy is learned based on the teachings of an expert.
Theoretical Framework for Human-Like Robotic Taste with Reference to Nutritional Needs
Authors: Sochacki Grzegorz , Abdulali Arsen , Cheke Lucy , Iida Fumiya 
Published: November 2023

Abstract
This paper contains a theoretical framework for an intelligent robot that can feed itself with organic matter and learns to like and want certain foods. Furthermore, being tied to the onboard generation of power, the robot’s learning is grounded to physical requirements that need to be met for continued robot operation. We posit a system wherein the electrical power is generated by a microbial fuel cell(MFC), and the food value can be assessed by measuring the current generated. Interestingly, the MFC requires feed similar in many parameters to food preferred by most people with respect to parameters like salinity or pH. This property is theorized to be a good start for teaching a robotic chef human preferences. We also propose a circuit that injects additional current, simulating social cues for some foods, and effectively resulting in learning an acquired taste.
Two notions of medium and their implications for intelligence
Authors: Nonaka Tetsushi 
Published: November 2023

Abstract
In biology, the term medium is defined as a substance that a biological system exists or grows in or that it travels through. In physics, the term medium is defined as a substance that propagates and transmits the energy from one location to another. These two notions of medium in biology and physics are distinct, yet in reality, their referents frequently coincide in the same material systems in the environment. The air, a medium for terrestrial animals in the sense defined in biology, is a medium that transmits light, mechanical waves, and diffuses molecules from the source in the sense defined in physics. A medium that surrounds each cell in the living body in the sense of biology, at the same time, is an excitable medium that propagates electrical events, mechanical stresses, and the variety of chemical molecules in the sense of physics. In this article, I discuss the implications of this coincidence of the two notions of medium in the real world for the evolution and development of intelligent systems.
hipFG: high-throughput harmonization and integration pipeline for functional genomics data
Authors: Cifello Jeffrey , Kuksa Pavel P , Saravanan Naveensri , Valladares Otto , Wang Li-San , Leung Yuk Yee 
Published: November 2023

Abstract

Summary
Preparing functional genomic (FG) data with diverse assay types and file formats for integration into analysis workflows that interpret genome-wide association and other studies is a significant and time-consuming challenge. Here we introduce hipFG (Harmonization and Integration Pipeline for Functional Genomics), an automatically customized pipeline for efficient and scalable normalization of heterogenous FG data collections into standardized, indexed, rapidly searchable analysis-ready datasets while accounting for FG datatypes (e.g. chromatin interactions, genomic intervals, quantitative trait loci).

Availability and implementation
hipFG is freely available at https://bitbucket.org/wanglab-upenn/hipFG. A Docker container is available at https://hub.docker.com/r/wanglab/hipfg.
FitMultiCell: simulating and parameterizing computational models of multi-scale and multi-cellular processes
Authors: Alamoudi Emad , Schälte Yannik , Müller Robert , Starruß Jörn , Bundgaard Nils , Graw Frederik , Brusch Lutz , Hasenauer Jan 
Published: November 2023

Abstract

Motivation
Biological tissues are dynamic and highly organized. Multi-scale models are helpful tools to analyse and understand the processes determining tissue dynamics. These models usually depend on parameters that need to be inferred from experimental data to achieve a quantitative understanding, to predict the response to perturbations, and to evaluate competing hypotheses. However, even advanced inference approaches such as approximate Bayesian computation (ABC) are difficult to apply due to the computational complexity of the simulation of multi-scale models. Thus, there is a need for a scalable pipeline for modeling, simulating, and parameterizing multi-scale models of multi-cellular processes.

Results
Here, we present FitMultiCell, a computationally efficient and user-friendly open-source pipeline that can handle the full workflow of modeling, simulating, and parameterizing for multi-scale models of multi-cellular processes. The pipeline is modular and integrates the modeling and simulation tool Morpheus and the statistical inference tool pyABC. The easy integration of high-performance infrastructure allows to scale to computationally expensive problems. The introduction of a novel standard for the formulation of parameter inference problems for multi-scale models additionally ensures reproducibility and reusability. By applying the pipeline to multiple biological problems, we demonstrate its broad applicability, which will benefit in particular image-based systems biology.

Availability and implementation
FitMultiCell is available open-source at https://gitlab.com/fitmulticell/fit.
AFRbase: a database of protein mutations responsible for antifungal resistance
Authors: Jain Aakriti , Singhal Neelja , Kumar Manish 
Published: November 2023

Abstract

Motivation
Fungal pathogens are known to cause life threatening invasive infections with rising global mortality rates. Besides, the indiscriminate use of antifungals in both clinics and agriculture has promoted antifungal drug resistance in the last decade. Fungi can show drug resistance by a variety of mechanisms. But primary driver in all these hitherto documented mechanisms is stable and heritable point mutations in the key proteins. Therefore, cataloguing mutations that can confer resistance is the first step toward understanding the mechanisms leading to the emergence of antifungal resistance.

Results
In the present, work we have described a database of all the mutations responsible for antifungal resistance. Named as antifungal resistance database (AFRbase), it is better than the existing databases of antifungal resistance namely, FunResDB and MARDy which have a limited scope and inadequate information. Data of AFRbase was collected using both text mining and manual curation. AFRbase provides a separate window for visualization of mutations in the 2D and 3D formats making it easy for researchers to analyze the mutation data and ensures interoperability with other standard molecular biology databases like NCBI and UniProtKB. We hope AFRbase can be useful to both clinicians and basic biomedical scientists as we envision it as an important resource for genotypic susceptibility testing of fungi and to study/predict the course of evolution of antifungal resistance. The current version of AFRbase contains manually curated 3691 unique mutations present in 29 proteins of 32 fungal species along with the information of drugs against which resistance is caused.

Availability and implementation
AFRbase is an open access database available at http://proteininformatics.org/mkumar/afrbase/.
Total adrenalectomy versus subtotal adrenalectomy for bilateral pheochromocytoma: meta-analysis
Authors: Schiavone Donatella , Ballo Mattia , Filardo Marco , Dughiero Silvia , Torresan Francesca , Rossi Gian Paolo , Iacobone Maurizio 
Published: November 2023

Abstract

Background
Bilateral pheochromocytomas are rare and often heritable. Total adrenalectomy leads to a definitive oncological cure, with subsequent definitive hypocortisolism. Subtotal adrenalectomy is a possible alternative. The aim of this study was to assess the effects of total adrenalectomy and subtotal adrenalectomy on bilateral pheochromocytoma in terms of post-surgical rate of recurrence, metastatic disease, and steroid dependence.

Methods
Systematic searches in the bibliographic databases PubMed, Embase, and Europe PMC were performed for 1945 to 1 June 2023. PRISMA guidelines were followed and the PICO strategy was applied to English-language studies comparing subtotal adrenalectomy with total adrenalectomy. A random-effects model was used to assess the different outcomes for studies with high heterogeneity. The Newcastle–Ottawa scale and the Risk Of Bias In Non-randomized Studies of Interventions (‘ROBINS-I’) tool were used to assess quality and risk of bias.

Results
From a total of 12 909 studies, 1202 patients (from 10 retrospective studies) were eligible for the meta-analysis. In six studies, including 1176 patients, the recurrence rate after subtotal adrenalectomy and total adrenalectomy was 14.1 versus 2.6 per cent respectively (OR 4.91, 95 per cent c.i. 1.30 to 18.54; P = 0.020; I2 72 per cent). In nine studies, including 1124 patients, the rate of post-surgical steroid dependence was 93.3 versus 11.6 per cent after total adrenalectomy and subtotal adrenalectomy respectively (OR 0.003, 95 per cent c.i. 0.0003 to 0.03; P &lt; 0.00001; I2 66 per cent). Based on two studies, including 719 patients, no differences were evident regarding the occurrence of post-surgery metastatic disease.

Conclusion
Subtotal adrenalectomy leads to less post-surgical primary adrenal insufficiency, but leads to a higher postoperative recurrence rate. Future prospective randomized studies, with clear eligibility criteria, are needed to confirm these results.
Understanding ethnic diversity in open dementia neuroimaging data sets
Authors: Heng Nicholas Yew Wei , Rittman Timothy 
Published: November 2023

Abstract
Ethnic differences in dementia are increasingly recognized in epidemiological measures and diagnostic biomarkers. Nonetheless, ethnic diversity remains limited in many study populations. Here, we provide insights into ethnic diversity in open-access neuroimaging dementia data sets. Data sets comprising dementia populations with available data on ethnicity were included. Statistical analyses of sample and effect sizes were based on the Cochrane Handbook. Nineteen databases were included, with 17 studies of healthy groups or a combination of diagnostic groups if breakdown was unavailable and 12 of mild cognitive impairment and dementia groups. Combining all studies on dementia patients, the largest ethnic group was Caucasian (20 547 participants), with the next most common being Afro-Caribbean (1958), followed by Asian (1211). The smallest effect size detectable within the Caucasian group was 0.03, compared to Afro-Caribbean (0.1) and Asian (0.13). Our findings quantify the lack of ethnic diversity in openly available dementia data sets. More representative data would facilitate the development and validation of biomarkers relevant across ethnicities.
Probiotic treatment with Bifidobacterium animalis subsp. lactis LKM512 + arginine improves cognitive flexibility in middle-aged mice
Authors: Joho Daisuke , Takahashi Masahira , Suzuki Takeru , Ikuta Kayo , Matsumoto Mitsuharu , Kakeyama Masaki 
Published: November 2023

Abstract
Cognitive flexibility, the ability of adapting to an ever-changing environment, declines with aging and impaired in early stages of dementia. Although recent studies have indicated there is a relationship between the intestinal microbiota and cognitive function, few studies have shown relationships between intestinal microbiota and cognitive flexibility because of limited behavioural tasks in mice. We recently established a novel cognitive flexibility task for mice using a touchscreen operant apparatus and found that probiotic treatment with a mixture of Bifidobacterium animalis subsp. lactis LKM512 and arginine improved cognitive flexibility in young adult mice. To confirm the effects of the probiotic treatment on cognitive flexibility and to determine whether it is effective even in older age, we here examined the effects of long-term treatment with Bifidobacterium animalis subsp. lactis LKM512 and arginine on cognitive flexibility in middle-aged mice. From 8 to 15 months of age, mice received LKM + Arg or vehicle (controls) orally three times per week and were subjected to the cognitive flexibility task at 13–15 months old. In one of indices of cognitive flexibility, both Bifidobacterium animalis subsp. lactis LKM512 and arginine-treated mice and vehicle-treated mice showed progressively improved performance by repeating reversal tasks, with a small trend that Bifidobacterium animalis subsp. lactis LKM512 and arginine-treated mice showed better learning performance through reversal phases. With respect to the other index of cognitive flexibility, Bifidobacterium animalis subsp. lactis LKM512 and arginine-treated mice showed significantly fewer error choices than control mice at the reversal phase, i.e. Bifidobacterium animalis subsp. lactis LKM512 and arginine improved the performance of behavioural sequencing acquired in the previous phase, which allowed Bifidobacterium animalis subsp. lactis LKM512 and arginine-treated mice to show an early onset of shift to reversal contingency. Taken together, long-term treatment with Bifidobacterium animalis subsp. lactis LKM512 and arginine was found to improve cognitive flexibility in middle-aged mice, indicating that probiotic treatment might contribute to prevention of age-related cognitive decline.
Conduction system pacing: overview, definitions, and nomenclature
Authors: Jastrzebski Marek , Dandamudi Gopi , Burri Haran , Ellenbogen Kenneth A 
Published: November 2023

Abstract
Pacing from the right ventricle is associated with an increased risk of development of congestive heart failure, increases in total and cardiac mortality, and a worsened quality of life. Conduction system pacing has become increasingly realized as an alternative to right ventricular apical pacing. Conduction system pacing from the His bundle and left bundle branch area has been shown to provide physiologic activation of the ventricle and may be an alternative to coronary sinus pacing. Conduction system pacing has been studied as an alternative for both bradycardia pacing and for heart failure pacing. In this review, we summarize the clinical results of conduction system pacing under a variety of different clinical settings. The anatomic targets of conduction system pacing are illustrated, and electrocardiographic correlates of pacing from different sites in the conduction system are defined. Ultimately, clinical trials comparing conduction system pacing with standard right ventricular apical pacing and cardiac resynchronization therapy pacing will help define its benefit and risks compared with existing techniques.
Uncovering the miRNA-mediated regulatory network involved in Ma bamboo (Dendrocalamus latiflorus) de novo shoot organogenesis
Authors: Wang Nannan , Wang Wenjia , Cheng Yang , Cai Changyang , Zhu Qiang 
Published: November 2023

Abstract
Bamboo is an important non-timber forest product and is well-known for its reluctance to regenerate. Recently we have established a de novo shoot organogenesis (DNSO) protocol in Ma bamboo (Dendrocalamus latiflorus) and revealed the transcriptomic dynamics during Ma bamboo regeneration, which suggested the potential roles of Ma bamboo microRNAs (DlamiRNAs) in this process. However, how DlamiRNAs regulate bamboo DNSO is poorly understood. Here we performed integrated analysis with sRNAome, degradome, and transcriptome sequencing by using samples covering the four stages of the bamboo DNSO process. A total of 727 DlamiRNAs showed differential expression during the bamboo DNSO process, and the core DlamiRNA–DlamRNA- mediated regulatory networks for bamboo DNSO were constructed. Based on the results, DlamiR156 was selected for further functional characterization of its potential roles in bamboo DNSO. Transgenic bamboos with increased DlamiR156 levels exhibited an enhancement in their regeneration efficiency. Conversely, when DlamiR156 levels were downregulated, the regeneration efficiencies of transgenic bamboos decreased. Our findings show that the DlamiRNA-mediated regulatory pathways are significant in the process of bamboo regeneration and will contribute to our understanding of the molecular mechanisms governing plant organogenesis in a more comprehensive manner.
Berry texture QTL and candidate gene analysis in grape (Vitis vinifera L.)
Authors: Lin Hong , Ma Li , Guo Qiuyu , Liu Cheng , Hou Yangming , Liu Zhendong , Zhao Yuhui , Jiang Changyue , Guo Xiuwu , Guo Yinshan 
Published: November 2023

Abstract
Berry texture is a noteworthy economic trait for grape; however, the genetic bases and the complex gene expression and regulatory mechanism for the diverse changes in berry texture are still poorly understood. In this study, the results suggest that it is difficult to obtain high-mesocarp firmness (MesF) and high-pericarp puncture hardness (PPH) grape cultivars with high pericarp brittleness (PerB). The high-density linkage map was constructed using whole-genome resequencing based on 151 F1 individuals originating from intraspecific hybridization between the firm-flesh cultivar ‘Red Globe’ and soft-flesh cultivar ‘Muscat Hamburg’. The total length of the consensus map was 1613.17 cM, with a mean genetic distance between adjacent bin markers of 0.59 cM. Twenty-seven quantitative trait loci (QTLs) for berry MesF, PPH, and PerB were identified in linkage groups (LGs) 1, 3, 4, 6, 8, 9, 10, 11, 14, 16, and 17, including twelve QTLs that were firstly detected in LGs 6, 11, and 14. Fourteen promising candidate genes were identified from the stable QTL regions in LGs 10, 11, 14, and 17. In particular, VvWARK2 and VvWARK8 refer to chromosome 17 and are two promising candidate genes for MesF and PPH, as the VvWARK8 gene may increase pectin residue binding with WARK for high berry firmness maintenance and the allele for VvWARK2 carrying the ‘CC’ and ‘GA’ genotypes at Chr17:1836764 and Chr17:1836770 may be associated with non-hard texture grape cultivars. In addition, real-time quantitative polymerase chain reaction (RT–qPCR) verification revealed that the promising candidate transcription factor genes VvMYB4-like, VvERF113, VvWRKY31, VvWRKY1, and VvNAC83 may regulate cell wall metabolism candidate gene expression for grape berry texture changes.