bluuebunny/crossref_metadata_2025 huggingface dataset:
Quantifying embodiment towards building better robots based on muscle-driven models
Authors: Chandiramani Vijay , Conn Andrew T. , Hauser Helmut
Published: November 2023

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

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

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

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

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

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

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

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 < 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

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

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

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

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

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.
Criminalizing Human Rights
Authors: Alston Philip
Published: November 2023

The priorities reflected in the overarching system that includes the regimes dealing with international human rights law, international humanitarian law, and international criminal law are currently undergoing a gradual but highly significant transformation. The cause is a growing preoccupation with ‘atrocity crimes’ in each of the three fields, along with the imposition of criminal sanctions in response to an ever increasing range of violations, the recasting of other violations as crimes (ecocide), and the urge to describe a great many situations as involving genocide. These developments have diminished the attention given to non-criminal violations and to techniques other than prosecution, and facilitated continuing neglect of the structural dimensions underpinning violations. In the foreign policies of key western states, sanctions against individuals now attract more attention than other human rights responses. The risk is that these trends will entrench an atrocity-centred normative hierarchy, empower judges and criminal lawyers at the expense of social movements, shine a spotlight on individual rather than collective responsibility, reinforce problematic North-South dynamics, and distort resource allocations at the international level.
Adapting a model of cervical carcinogenesis to self-identified Black women to evaluate racial disparities in the United States
Authors: Spencer Jennifer C , Burger Emily A , Campos Nicole G , Regan Mary Caroline , Sy Stephen , Kim Jane J
Published: November 2023

Background

Self-identified Black women in the United States have higher cervical cancer incidence and mortality than the general population, but these differences have not been clearly attributed across described cancer care inequities.

Methods

A previously established microsimulation model of cervical cancer was adapted to reflect demographic, screening, and survival data for Black US women and compared with a model reflecting data for all US women. Each model input with stratified data (all-cause mortality, hysterectomy rates, screening frequency, screening modality, follow-up, and cancer survival) was sequentially replaced with Black-race specific data to arrive at a fully specified model reflecting Black women. At each step, we estimated the relative contribution of inputs to observed disparities.

Results

Estimated (hysterectomy-adjusted) cervical cancer incidence was 8.6 per 100 000 in the all-race model vs 10.8 per 100 000 in the Black-race model (relative risk [RR] = 1.24, range = 1.23-1.27). Estimated all-race cervical cancer mortality was 2.9 per 100 000 vs 5.5 per 100 000 in the Black-race model (RR = 1.92, range = 1.85-2.00). We found the largest contributors of incidence disparities were follow-up from positive screening results (47.3% of the total disparity) and screening frequency (32.7%). For mortality disparities, the largest contributor was cancer survival differences (70.1%) followed by screening follow-up (12.7%).

Conclusion

To reduce disparities in cervical cancer incidence and mortality, it is important to understand and address differences in care access and quality across the continuum of care. Focusing on the practices and policies that drive differences in treatment and follow-up from cervical abnormalities may have the highest impact.
Relation of Aerobic Activity to Cognition and Well-being in Chronic Mild Traumatic Brain Injury: A LIMBIC-CENC Study
Authors: Wright Brennan M , Zhang Chong , Fisher Renae R , Karmarkar Amol M , Bjork James M , Pugh Mary Jo , Hodges Cooper B , Martindale Sarah L , Wilde Elisabeth A , Kenney Kimbra , McDonald Scott D , Scheibel Randall S , Newsome Mary R , Cook Lawrence J , Walker William C
Published: November 2023

Introduction

Because chronic difficulties with cognition and well-being are common after mild traumatic brain injury (mTBI) and aerobic physical activity and exercise (PAE) is a potential treatment and mitigation strategy, we sought to determine their relationship in a large sample with remote mTBI.

Materials and Methods

The Long-Term Impact of Military-Relevant Brain Injury Consortium–Chronic Effects of Neurotrauma Consortium prospective longitudinal study is a national multicenter observational study of combat-exposed service members and veterans. Study participants with positive mTBI histories (n = 1,087) were classified as “inactive” (23%), “insufficiently active” (46%), “active” (19%), or “highly active” (13%) based on the aerobic PAE level. The design was a cross-sectional analysis with multivariable regression. PAE was reported on the Behavioral Risk Factor Surveillance System. Preselected primary outcomes were seven well-validated cognitive performance tests of executive function, learning, and memory: The California Verbal Learning Test—Second Edition Long-Delay Free Recall and Total Recall, Brief Visuospatial Memory Test—Revised Total Recall, Trail-Making Test—Part B, and NIH Toolbox for the Assessment of Neurological Behavior and Function Cognition Battery Picture Sequence Memory, Flanker, and Dimensional Change Card Sort tests. Preselected secondary outcomes were standardized self-report questionnaires of cognitive functioning, life satisfaction, and well-being.

Results

Across the aerobic activity groups, cognitive performance tests were not significantly different. Life satisfaction and overall health status scores were higher for those engaging in regular aerobic activity. Exploratory analyses also showed better working memory and verbal fluency with higher aerobic activity levels.

Conclusions

An association between the aerobic activity level and the preselected primary cognitive performance outcome was not demonstrated using this study sample and methods. However, higher aerobic activity levels were associated with better subjective well-being. This supports a clinical recommendation for regular aerobic exercise among persons with chronic or remote mTBI. Future longitudinal analyses of the exercise–cognition relationship in chronic mTBI populations are recommended.
Strain Response of an Anatomically Accurate Nonhuman Primate Finite Element Brain Model Under Sagittal Loading
Authors: Rooks Tyler F , Chancey Valeta Carol , Baisden Jamie L , Yoganandan Narayan
Published: November 2023

Introduction

Prevention and treatment of traumatic brain injuries is critical to preserving soldier brain health. Laboratory studies are commonly used to reproduce injuries, understand injury mechanisms, and develop tolerance limits; however, this approach has limitations for studying brain injury, which requires a physiological response. The nonhuman primate (NHP) has been used as an effective model for investigating brain injury for many years. Prior research using the NHP provides a valuable resource to leverage using modern analysis and modeling techniques to improve our understanding of brain injury. The objectives of the present study are to develop an anatomically accurate finite element model of the NHP and determine regional brain responses using previously collected NHP data.

Materials and Methods

The finite element model was developed using a neuroimaging-based anatomical atlas of the rhesus macaque that includes both cortical and subcortical structures. Head kinematic data from 10 sagittal NHP experiments, four +Gx (rearward) and six −Gx (frontal), were used to test model stability and obtain brain strain responses from multiple severities and vectors.

Results

For +Gx tests, the whole-brain cumulative strain damage measure exceeding a strain threshold of 0.15 (CSDM15) ranged from 0.28 to 0.89, and 95th percentile of the whole-brain maximum principal strain (MPS95) ranged from 0.21 to 0.59. For −Gx tests, whole-brain CSDM15 ranged from 0.02 to 0.66, and whole-brain MPS95 ranged from 0.08 to 0.39.

Conclusions

Recognizing that NHPs are the closest surrogate to humans combined with the limitations of conducting brain injury research in the laboratory, a detailed anatomically accurate finite element model of an NHP was developed and exercised using previously collected data from the Naval Biodynamics Laboratory. The presently developed model can be used to conduct additional analyses to act as pilot data for the design of newer experiments with statistical power because of the sensitivity and resources needed to conduct experiments with NHPs.
Bright, photostable and long-circulating NIR-II nanoparticles for whole-process monitoring and evaluation of renal transplantation
Authors: Zhang Rongyuan , Shen Ping , Xiong Yu , Wu Tianjing , Wang Gang , Wang Yucheng , Zhang Liping , Yang Han , He Wei , Du Jian , Wei Xuedong , Zhang Siwei , Qiu Zijie , Zhang Weijie , Zhao Zheng , Tang Ben Zhong
Published: November 2023

Kidney transplantation is the gold standard for the treatment of end-stage renal diseases (ESRDs). However, the scarcity of donor kidneys has caused more and more ESRD patients to be stuck on the waiting list for transplant surgery. Improving the survival rate for renal grafts is an alternative solution to the shortage of donor kidneys. Therefore, real-time monitoring of the surgical process is crucial to the success of kidney transplantation, but efficient methods and techniques are lacking. Herein, a fluorescence technology based on bright, photostable and long-circulating aggregation-induced emission (AIE) active NIR-II nano-contrast agent DIPT-ICF nanoparticles for the whole-process monitoring and evaluation of renal transplantation has been reported. In the aggregated state, DIPT-ICF exhibits superior photophysical properties compared with the commercial dyes IR-26 and IR-1061. Besides, the long-circulating characteristic of the AIE nano-contrast agent helps to achieve renal angiography in kidney retrieval surgery, donor kidney quality evaluation, diagnosing vascular and ureteral complications, and assessment of renal graft reperfusion beyond renovascular reconstruction, which considerably outperforms the clinically approved indocyanine green (ICG).
Risk Factors for Recurrence of Community-Onset Urinary Tract Infections Caused by Extended-Spectrum Cephalosporin-Resistant Enterobacterales
Authors: Zhang Helen L , Perez Reinaldo , Krishnan Jay , Lautenbach Ebbing , Anderson Deverick J
Published: November 2023

Background

Extended-spectrum cephalosporin-resistant Enterobacterales (ESCrE) are an increasingly important cause of community-onset urinary tract infections (UTIs), including recurrent infections. We evaluated risk factors for recurrence among patients with community-onset ESCrE UTI.

Methods

This retrospective cohort study included adults with community-onset ESCrE UTI in the Duke University Health System from April 2018 through December 2021. ESCrE UTI recurrence by the same species was assessed 14–180 days (ie, 6 months) after completion of antibiotic treatment. We evaluated the relationships between candidate risk factors and time to recurrence using Cox proportional hazards regression models.

Results

Among 1347 patients with community-onset ESCrE UTI, 202 (15.0%) experienced recurrent infection during the 6-month follow-up period. Independent risk factors for recurrence included neurogenic bladder (adjusted hazard ratio [aHR], 1.8 [95% confidence interval {CI}, 1.2–2.6]; P = .005), prior history of UTI (aHR, 2.4 [95% CI, 1.7–3.3]; P < .001), and fluoroquinolone nonsusceptibility of the index UTI (aHR, 1.5 [95% CI, 1.1–2.1]; P = .02). Klebsiella pneumoniae infection was associated with recurrence in univariate analysis (HR, 1.6 [95% CI, 1.1–2.1]; P = .007) but not multivariate analysis (aHR, 1.4 [95% CI, 1.0–1.9]; P = .06). Inappropriate initial or definitive antibiotic therapy was not predictive of ESCrE UTI recurrence.

Conclusions

Recurrence of community-onset ESCrE UTI was common and associated with several patient and pathogen-level risk factors. Future studies should evaluate microbial risk factors for recurrence and improve the management of ESCrE UTI.
Introduction and Framework
Authors: Jejeebhoy Shireen J
Published: November 2023

Women’s access to education has been recognized as a fundamental right, and increasing their access is among the goals of most developing countries. The benefits of educating women are manifold, ranging from improved productivity, income, and economic development on the national level to a better quality of life on the individual level, notably a healthier and better nourished population and greater autonomy among women. Moreover, educating women is important for all kinds of demographic behaviour, affecting mortality, health, fertility, and contraception.1 In almost every setting, regardless of region, culture, or level of development, well-educated women are observed to have fewer children than do uneducated women.
Women’s Education, Family-Size Preferences, and the Structure of Demand
Authors: Jejeebhoy Shireen J
Published: November 2023

Five main points emerge regarding the relationship of women’s education to their family-size preferences. Women’s education has a moderate and consistently inverse effect on desired family size; By and large, a small amount of education does not markedly change family-size desires; an upper primary or secondary education is required to set off changes in demand; The strength of the relationship changes over time, although how it changes depends on the context: it becomes stronger over time in countries at early stages of the fertility transition and weaker in countries at later stages; Thresholds appear to fall in high-income countries as compared with low- and middle-income ones; however, the patterns by levels of female literacy and gender disparity in literacy tend to be irregular; After economic status and other covariates are controlled, about half of the gross effect of women’s education on family-size desires remains. What is especially striking in several multivariate studies is the persistence of thresholds: the net effect of education is far more likely to be strong among women with secondary and higher educations than among those with primary schooling.
Rhomboid protease RHBDL4/RHBDD1 cleaves SREBP-1c at endoplasmic reticulum monitoring and regulating fatty acids
Authors: Han Song-Iee , Nakakuki Masanori , Nakagawa Yoshimi , Wang Yunong , Araki Masaya , Yamamoto Yuta , Tokiwa Hiroaki , Takeda Hiroyuki , Mizunoe Yuhei , Motomura Kaori , Ohno Hiroshi , Kainoh Kenta , Murayama Yuki , Aita Yuichi , Takeuchi Yoshinori , Osaki Yoshinori , Miyamoto Takafumi , Sekiya Motohiro , Matsuzaka Takashi , Yahagi Naoya , Sone Hirohito , Daitoku Hiroaki , Sato Ryuichiro , Kawano Hiroyuki , Shimano Hitoshi
Published: November 2023

The endoplasmic reticulum (ER)–embedded transcription factors, sterol regulatory element-binding proteins (SREBPs), master regulators of lipid biosynthesis, are transported to the Golgi for proteolytic activation to tune cellular cholesterol levels and regulate lipogenesis. However, mechanisms by which the cell responds to the levels of saturated or unsaturated fatty acids remain underexplored. Here, we show that RHBDL4/RHBDD1, a rhomboid family protease, directly cleaves SREBP-1c at the ER. The p97/VCP, AAA-ATPase complex then acts as an auxiliary segregase to extract the remaining ER-embedded fragment of SREBP-1c. Importantly, the enzymatic activity of RHBDL4 is enhanced by saturated fatty acids (SFAs) but inhibited by polyunsaturated fatty acids (PUFAs). Genetic deletion of RHBDL4 in mice fed on a Western diet enriched in SFAs and cholesterol prevented SREBP-1c from inducing genes for lipogenesis, particularly for synthesis and incorporation of PUFAs, and secretion of lipoproteins. The RHBDL4-SREBP-1c pathway reveals a regulatory system for monitoring fatty acid composition and maintaining cellular lipid homeostasis.
A quantum-enhanced support vector machine for galaxy classification
Authors: Hassanshahi Mohammad Hassan , Jastrzebski Marcin , Malik Sarah , Lahav Ofer
Published: November 2023

Galaxy morphology, a key tracer of the evolution of a galaxy’s physical structure, has motivated extensive research on machine learning techniques for efficient and accurate galaxy classification. The emergence of quantum computers has generated optimism about the potential for significantly improving the accuracy of such classifications by leveraging the large dimensionality of quantum Hilbert space. This paper presents a quantum-enhanced support vector machine (SVM) algorithm for classifying galaxies based on their morphology. The algorithm requires the computation of a kernel matrix, a task that is performed on a simulated quantum computer using a quantum circuit conjectured to be intractable on classical computers. The result shows similar performance between classical and quantum-enhanced SVM algorithms. For a training size of 40k, the receiver operating characteristic curve for differentiating ellipticals and spirals has an under-curve area of 0.946 ± 0.005 for both classical and quantum-enhanced algorithms. Additionally, we demonstrate for a small data set that the performance of a noise-mitigated quantum SVM algorithm on a quantum device is in agreement with simulation. Finally, a necessary condition for achieving a potential quantum advantage is presented. This investigation is among the very first applications of quantum machine learning in astronomy and highlights their potential for further application in this field.
Anti-inflammatory and antioxidant activities assessment of an aqueous extract of Ceiba pentandra (L.) Gaertn (Malvaceae)
Authors: Silué Gniènèfèrètien Nounaféri Awa , Belemlilga Mohamed Bonewendé , Djadji Ayoman Thierry Lenoir , Traoré Kadiatou Tata , Boly Gilchrist Abdoul Laurent , Koala Moumouni , Ouédraogo Noufou , Traoré Aristide , Kouakou-Siransy Gisèle
Published: November 2023

Objective

In traditional folk medicine, Ceiba pentandra has been used for its anti-diabetic and anti-infective effects. This study investigates the anti-inflammatory and antioxidant activities of the aqueous extract of the plant’s leaves.

Methods

The anti-oedematous tests with carrageenan and lipoxygenase inhibition assay were carried out concerning anti-inflammatory studies. DPPH free radical scavenging, ferric-reducing antioxidant power, ABTS+ free radical scavenging assay, and lipid peroxide determination were investigated for antioxidant activities.

Key findings

As a result, C. pentandra extract inhibited edema between 3 and 5 h in the order of 83.07% and 94.09% at 200 kg. b.w. and lipoxygenase enzyme with a percentage of 87.11 ± 3.02%. This study used the lipid peroxidation level as a marker. The results of the lipid peroxidation test show a percentage inhibition of 49.60%, close to Trolox 48.11%, and present a good antioxidant activity compare with the free radical scavenging assay.

Conclusions

The aqueous decoction of C. pentandra leaves has demonstrated anti-inflammatory solid activities as well as lipid peroxidation due to the presence of phytochemical groups of interest such as sterols, polyphenols, quinones, catechin tannins, flavonoids, and saponins.
Reflections on a journey as sleep researcher and geriatric psychiatrist
Authors: Reynolds Charles F
Published: November 2023

After first recalling the origins of my interest in sleep and dreams at UVa (1969) and my MD thesis at Yale on sleep in mood disorders (1973), I will describe my service to the field of sleep disorders medicine, through various roles in the American Sleep Disorders Association, the Institute of Medicine, the National Institute of Mental Health, and the DSM-5 Task Force of the American Psychiatric Association. I will then present the broad themes of my contributions to psychiatric sleep research, focusing on the neurobiology of sleep as a dimension of the risk and protective architecture for depression in older adults, as a bridge to diagnostic and treatment issues in later-life depression, and to clinical and translational neuroscience addressing the intersections of sleep, aging, and mind/brain health. Throughout this narrative, I highlight many relationships with mentors and mentees. All of my scientific activity has been team-based, providing the social matrix for the physician–scientist I have become.

This paper is part of the Living Legends in Sleep Research series, which is sponsored by Idorsia Pharmaceuticals and Jazz Pharmaceuticals.
Investigating the replacement of carboxylates with carboxamides to modulate the safety and efficacy of platinum(II) thioether cyanide scavengers
Authors: Behymer Matthew M , Mo Huaping , Fujii Naoaki , Suresh Vallabh , Arzumanian Ari S , Chan Adriano , Nath Anjali K , McCain Robyn , MacRae Calum A , Peterson Randall , Boss Gerry R , Davisson Vincent Jo , Knipp Gregory T
Published: November 2023

Cyanide represents a persistent threat for accidental or malicious misuse due to easy conversion into a toxic gas and access to large quantities through several industries. The high safety index of hydroxocobalamin is a cornerstone quality as a cyanide scavenger. Unfortunately, intravenous infusion of hydroxocobalamin limits the utility in a mass casualty setting. We previously reported platinum(II) [Pt(II)] complexes with trans-directing sulfur ligands as an efficacious alternative to hydroxocobalamin when delivered by a bolus intramuscular (IM) injection in mice and rabbits. Thus, to enable Pt(II) as an alternative to hydroxocobalamin, a high safety factor is needed. The objective is to maintain efficacy and mitigate the risk of nephrotoxicity. Platinum amino acid complexes with the ability to form 5- or 6-membered rings and possessing either carboxylates or carboxamides are evaluated in vitro for cyanide scavenging. In vivo efficacy was evaluated in the zebrafish and mice cyanide exposure models. In addition, Pt(II) complex toxicity and pharmacokinetics were evaluated in a cyanide naive Sprague Dawley model. Doses for toxicity are escalated to 5× from the efficacious dose in mice using a body surface area adjustment. The results show the carboxamide ligands display a time and pH dependence on cyanide scavenging in vitro and efficacy in vivo. Additionally, exchanging the carboxylate for carboxamide showed reduced indications of renal injury. A pharmacokinetic analysis of the larger bidentate complexes displayed rapid absorption by IM administration and having similar plasma exposure. These findings point to the importance of pH and ligand structures for methionine carboxamide complexes with Pt(II).
Known phyla dominate the Tara Oceans RNA virome
Authors: Edgar Robert
Published: November 2023

A recent study proposed five new RNA virus phyla, two of which, ‘Taraviricota’ and ‘Arctiviricota’, were stated to be ‘dominant in the oceans’. However, the study’s assignments classify 28,353 putative RdRp-containing contigs to known phyla but only 886 (2.8%) to the five proposed new phyla combined. I re-mapped the reads to the contigs, finding that known phyla also account for a large majority (93.8%) of reads according to the study’s classifications, and that contigs originally assigned to ‘Arctiviricota’ accounted for only a tiny fraction (0.01%) of reads from Arctic Ocean samples. Performing my own virus identification and classifications, I found that 99.95 per cent of reads could be assigned to known phyla. The most abundant species was Beihai picorna-like virus 34 (15% of reads), and the most abundant order-like cluster was classified as Picornavirales (45% of reads). Sequences in the claimed new phylum ‘Pomiviricota’ were placed inside a phylogenetic tree for established order Durnavirales with 100 per cent confidence. Moreover, two contigs assigned to the proposed phylum ‘Taraviricota’ were found to have high-identity alignments to dinoflagellate proteins, tentatively identifying this group of RdRp-like sequences as deriving from non-viral transcripts. Together, these results comprehensively contradict the claim that new phyla dominate the data.
Molecular phylogeny, biogeography, and species delimitation of segmented spider genus Liphistius (Araneae: Liphistiidae) in Thailand
Authors: Sivayyapram Varat , Kunsete Chawakorn , Xu Xin , Smith Deborah R , Traiyasut Prapun , Deowanish Sureerat , Li Daiqin , Warrit Natapot
Published: November 2023

Mesothelae, or primitively segmented trapdoor spiders, form the most basal clade among living spiders. In Southeast Asia, Liphistius is the only genus recognized in the extant family Liphistiidae. Liphistius taxonomy and species identification are based largely on characters of the genitalia; however, the female genitalia show high intraspecific variation, males are rarely collected, and the phylogenetic relationships among the 69 described Liphistius species are unresolved. Here, we focused on the Liphistius of Thailand, including 37 described and numerous undescribed species in four species groups. We generated sequences from five loci (COI, 16S, H3, 28S, and ITS2) for 162 specimens from 52 sites in Thailand and Myanmar to reconstruct phylogenetic relationships, infer historical biogeography, and delimit species. The five-locus data set resolved nearly all species and species group relationships and was mostly congruent with morphology-based classifications. Ancestral area reconstruction suggested that Liphistius originated in Sibumasu (Siam–Burma–Malaysia–Sumatra) and diversified into several species groups, four (birmanicus, bristowei, linang, and trang) of which are found in Thailand. Speciation within Liphistius occurred in the area corresponding to their current distribution. All delimitation methods tested (ASAP, GMYC, PTP, STACEY and BFD) delimited specimens from discrete locations as separate species; variation in the number of species proposed (ranging from 53 to 72) stemmed from variation in delimitation of sympatric cryptic species.