bluuebunny/crossref_metadata_2025 huggingface dataset:
Ethical Dilemmas of the COVID-19 Pandemic
Authors: Nichol Ariadne A. , Burgart Alyssa
Published: August 2024

The COVID-19 pandemic highlights numerous public health ethical dilemmas. During the long public health emergency, knowledge, prevention, and treatment options for COVID-19 are evolving, creating novel challenges which in turn give rise to new issues that require ethical deliberation. In this chapter, learners explore three of these critical dilemmas: approaching the allocation of scarce resources, addressing vaccine hesitancy, and evaluating healthcare workers’ duty to treat. Each of these dilemmas provides an occasion to apply foundational ethical principles in the provision of healthcare during a public health emergency. The authors discuss approaches to creating a public health emergency response plan, recognizing values embedded in a limited resource allocation framework, defining distributive justice, and identifying vulnerable groups and protected classes under the law.
Bloom’s Taxonomy
Authors: Juve Amy Miller , Zisblatt Lara
Published: August 2024

Bloom’s taxonomy is one of the most widely used educational taxonomies to date. The cognitive domain is the most well-known and developed domain of the three in the taxonomy. It is used to support the acquisition and utilization of knowledge and provides a useful framework to aid in the development of educational objectives, curriculum, and assessment tools. While the cognitive domain can be used to support learning in a broad array of educational settings with learners ranging in skill from novice to expert, caution should be taken to assure learning is not structured as a purely linear experience and that learning activities are identified based on learner competence and not years of experience.
The Pros and Cons of the Socratic Method
Authors: Moser Karen A. , Khan Jawaria
Published: August 2024

The Socratic method is frequently cited as a technique used in health sciences education, but it is difficult to define. When considered as part of a broader spectrum of inquiry-based didactic techniques, several fundamental principles emerge. Systematic questions posed by educators can identify knowledge gaps and promote discovery of new ideas and connections during group discussion. Successful use of the Socratic method requires a psychologically safe environment, learners who are willing to reveal their thought processes and risk giving a wrong answer, and a willingness by all team members to be changed by the shared experience. There is no role for questions intended to humiliate or shame learners in an effective inquiry-based learning environment. Finally, the process of asking and answering questions can help faculty share their own knowledge gaps and model strategies for self-directed learning that are needed for continuous development as a health science professional. Incorporating all of these basic principles can make inquiry-based learning a rewarding educational experience for teachers and learners alike.
Assessment of Learners
Authors: O’Connor Meghan , Richards Boyd
Published: August 2024

56.This chapter explores the concepts of learner assessment and evaluation by presenting a case in which a medical student participates in a year-long clinical experience with a preceptor. Using various data points and direct observation, the student is given both formative and summative assessments throughout the learning experience, providing them with information needed to guide their learning and improve their clinical skills. As the case progresses, questions are posed to help identify key concepts in learner assessment and explore the interconnectivity between assessment, evaluation, feedback, and grading. The information presented will help educators identify and develop effective assessment strategies that support learner development and growth.
The Utility of Deliberate Practice During and After Medical Training
Authors: Goldfarb Tally , Ambardekar Aditee , Kimatian Stephen
Published: August 2024

Achievement of expertise in healthcare contributes to excellent patient care, job satisfaction, and longevity of career. Medical training is simply not long enough for healthcare professionals to fully develop mastery in their trade. Initially used to describe expertise in other fields, Ericsson’s research in the development of expertise provides a useful framework for healthcare professionals both in training and after. Paired with important concepts in adult learning, intentional and focused practice has utility in skill acquisition, remediation of the challenged learner, maintenance of skill and expertise, and lifelong learning. Simple, regular practice alone is not sufficient. Deliberate practice is highly structured and labor-intensive and requires learner motivation, personalized learning plans, formative feedback, and preferably a coach or mentor. This chapter discusses the utility of deliberate practice at various stages of the career. Rapid-cycle deliberate practice has been shown to be useful in low-incidence but clinically significant and high-risk events. Beneficial during training and beyond, deliberate practice supports continued mastery and lifelong learning, which is essential to the provision of excellent patient care and a long and productive career.
Identity, Professionalism, and Education via Social Media in Medicine
Authors: Sienna Julianna , Chan Teresa M.
Published: August 2024

Social media has infiltrated health professions education and represents an exciting opportunity to create and foster dynamic communities for the rapid distribution of knowledge, research collaboration, health advocacy, and inspiring and spreading health innovation. This chapter serves as a primer for health professionals to learn about how the power of social media can be harnessed by health professionals, with particular attention paid to how it can enhance education and advance careers. The chapter defines digital identify formation, describes strategies for social media teaching and learning, and lists the benefits and risks of engaging audiences through social media. The authors also explore professional and ethical challenges to developing the digital self.
Human Factors Affecting Critically Ill Patients
Authors: Lee Deborah , Wilt Jeffrey
Published: August 2024

Significant medical errors resulting in increased patient harm and mortality can occur from decisions made by individual providers based on their healthcare organization’s standards. Developing standardized care in medicine reduces the potential for errors in patient care, but this challenges the provider in making independent clinical judgments about each patient based on their presentation. Human factors such as fatigue, situational awareness, psychological stress, and physical stress can result in unreliable delivery of best practice. Increased awareness of human factors is the first step to minimizing error. Human factor analysis can also provide a helpful framework for determining barriers in reliable delivery of care and steps for improving patient safety.
Electronic Distractions in Healthcare
Authors: Ehrenfeld Jesse M.
Published: August 2024

Across all healthcare settings, there are a growing number of opportunities for electronic distraction and interruptions in patient care. Common sources of electronic distraction include personal electronic devices (e.g., smartphones and tablets), communication tools (e.g., pagers), computer workstations, the electronic health record itself, and medical equipment (e.g., infusion pumps). While noise and distractions have been studied in a variety of settings, there is growing concern about the particular effects and impact of electronic distraction and interruptions on cognitive processing, task performance, and patient outcomes. It is therefore important to understand the sources of electronic distraction, their impact, and potential mitigation strategies.
Parkinson’s Disease
Authors: Diederich Nico J. , Goetz Christopher G.
Published: August 2024

Parkinson’s disease (PD) is a neurodegenerative disease characterized by bradykinesia, tremor, and rigidity, all due to basal gangliar dopaminergic deficits. Behavioral and autonomic non-motor symptoms accompany the core motor syndrome. The precise pathophysiology of PD is incompletely understood, and the hypothesis of an ascending proteinopathy cannot explain the temporal parallelism of motor and non-motor syndromes. The authors reconsider PD from an evolutionary perspective, noting that PD occurs only in humans. At the anatomical level, the vulnerable dysfunctioning nuclei of PD are evolutionarily old and overburdened by human telencephalization. While taking over new tasks and enduring continuous, energy requiring, challenges due to human longevity, the structural composition of these archaic areas has remained largely unchanged over millions of years. At the functional level, reflex, immediate reactions to environmental stimuli are primarily affected. An evolutionary focus on PD encourages exploration of involved circuitries and transmitters beyond the best-explored dopaminergic deficits.
Addiction
Authors: Sullivan Roger , Hagen Edward
Published: August 2024

In this chapter, the authors draw on insights from evolutionary ecology to point out that “drugs,” in the form of plant secondary metabolites (PSMs), are ubiquitous in natural environments and are utilized by plants as a toxic chemical defense against plant eaters. This evolved dynamic emphasizes punishment rather than reward—plants deploy PSMs to poison their predators, which in turn do their best to avoid chemical defenses or to find ways to use them to their own advantage. The authors argue that the punishment dynamic ubiquitous in nature has also affected people, both in the present and in the evolutionary past. They explore the implications of a “punishment model” for conventional perspectives of drug abuse and addiction, particularly in regard to neurobiological reward models. They conclude that a “punishment” perspective contradicts fundamental assumptions about drug use and addiction but offers several novel avenues for future research.
Are Evolutionary Concepts Helpful in Designing Preventive Strategies for Brain Diseases?
Authors: Levy Gilberto , Levin Bruce
Published: August 2024

This chapter describes how two evolutionary concepts, selection shadow and evolutionary mismatch, as integrated into an overarching causation framework, may naturally lead to preventive strategies for brain diseases. According to the evolutionary theory of aging, the force of natural selection acting on age-specific genetic effects declines with increasing adult age. The age at which natural selection becomes all but ineffective to eliminate deleterious mutations marks the onset of selection shadow. Evolutionary mismatch, in turn, results from the discordance between the human genetic makeup, which was selected in past environments, and the environment of modern life. Through the evolution-based model of causation, it is possible to conceptualize how selection shadow and evolutionary mismatch are related to the preventive strategies of postponed aging, involving a modification of the fundamental processes of aging, and evolutionary health promotion, involving prevention research and potentially health recommendations based on evolutionary principles.
Concluding Remarks and Future Directions
Authors: Brüne Martin , Diederich Nico J. , Goetz Christopher G. , Amunts Katrin
Published: August 2024

The present multi-authored volume covers a lot of ground in regard of healthy brain function and mechanisms of break down from an evolutionary point of view. We view this volume as a compendium of relevant and archetypal examples of the role of evolutionary science to a modern discussion of health and brain disease. Our major premise stressed throughout the book is that the brain, even though meticulously adapted to the environmental conditions of our evolutionary past, is vulnerable to dysfunction and disease. This vulnerability is, in part, related to “modern” lifestyles, which include (in industrialised countries) an over-supply of energy, lack of physical activity, and heightened exposure to stress, foremost social stress. An essential conclusion from the contributions to this volume is that, in spite of differences in onset and manifestation, the medical fields of neurology and psychiatry are much more intimately linked to one another than is currently taught at medical schools. It is the hope of the editors that the present book can help build bridges between the two disciplines in the interest of medical science.
Introduction
Authors: Besag Frank M. C. , Vasey Michael
Published: August 2024

It could be argued that perhaps one of the greatest advances in the management of epilepsy, alongside the growth of genetics, antiseizure medication, and surgical options, has been the recognition of the importance of the coexisting cognitive, psychological and psychiatric, and psychosocial conditions. This book brings together leaders in the field to provide an overview of the current evidence and thinking in this area.
The impact of surgery on comorbidities in epilepsy
Authors: Vakharia Vejay N. , Brownstone Robert M.
Published: August 2024

One-third of people fail to achieve long-term seizure remission with antiseizure medications. In these individuals, if the epileptogenic zone can be identified and removed or disconnected, epilepsy surgery may result in long-term seizure remission. The neurological, neuropsychological, and neuropsychiatric morbidities associated with surgery are dependent on the brain regions involved in the epileptogenesis. This chapter reviews comorbidities of surgery for epilepsy, focusing primarily on the most common type of surgery: resections for temporal lobe epilepsy. It also briefly considers surgery for other types of epilepsy (frontal, insular, parietal, or occipital lobe epilepsy), which are rarer entities and carry their own unique challenges. The chapter discusses the effects on seizure outcomes, and focuses on comorbidities, both negative and positive, including effects on visual fields, memory, language, cognitive function, neuropsychiatric function, and quality of life. Overall, epilepsy surgery can be highly effective for drug-refractory epilepsy, with modern neurosurgical techniques continuing to improve seizure remission rates while reducing neurological complications.
Epilepsy, employment, and work
Authors: Brown Ian
Published: August 2024

Epilepsy and worklessness are related as unemployment is up to twice as high in individuals with epilepsy. This chapter explores why this situation exists and what factors drive this unemployment rate. The reasons are multifactorial and can be related to both extrinsic and intrinsic factors, which are discussed with the best remedial solutions. The greatest obstacle to work is pharmacoresistant epilepsy where seizure control is poor or erratic although this in itself can be related to a number of interrelated factors, some of which have remedial solutions. The potential stigma of epilepsy is also examined in detail and how nomenclature affects opinion. Individuals may also (paradoxically) discriminate against themselves. The various barriers to employment are classified and each is discussed in turn. This chapter also discusses the employee who develops epilepsy in the course of their employment, employing individuals who declare epilepsy, and sensible restrictions and when these can be lifted.
Harris' Developmental Neuropsychiatry: The Interface with Cognitive and Social Neuroscience
Authors: Harris James C. , Coyle Joseph T.
Published: August 2024

Harris' Developmental Neuropsychiatry is an update of the First Edition, which introduced the integration of developmental neuroscience into the understanding of the pathophysiology and treatment of children with neuropsychiatric conditions. It opens with a comprehensive review of methods of assessment including behavior rating scales and neuropsychological testing moving from the scientific underpinnings to clinical application. The developmental aspects of components of cognition including attention, emotion, language, memory and consciousness are reviewed. It addresses how current brain imaging techniques have transformed our ability to link specific cognitive/emotional states to brain structure and function in health and disease. Historically, discussion of social and emotional development did not generally include the role of the brain. The Harris textbook commits significant space to connecting attachment, social development and temperament to normal brain maturation and pathologies associated with genetic disorders and environmental risk factors. The textbook closes by reviewing the diagnosis and treatment of several childhood neuropsychiatric disorders that can now be viewed through a lens informed by the prior basic chapters. The late James Harris, MD was a pioneer in bringing the brain into Child and Adolescent Psychiatry, and this textbook demonstrates how radically the advances in neuroscience and genetics have transformed the field and improved the care of this vulnerable population.
Deep learning and direct sequencing of labeled RNA captures transcriptome dynamics
Authors: Martinek Vlastimil , Martin Jessica , Belair Cedric , Payea Matthew J , Malla Sulochan , Alexiou Panagiotis , Maragkakis Manolis
Published: August 2024

In eukaryotes, genes produce a variety of distinct RNA isoforms, each with potentially unique protein products, coding potential or regulatory signals such as poly(A) tail and nucleotide modifications. Assessing the kinetics of RNA isoform metabolism, such as transcription and decay rates, is essential for unraveling gene regulation. However, it is currently impeded by lack of methods that can differentiate between individual isoforms. Here, we introduce RNAkinet, a deep convolutional and recurrent neural network, to detect nascent RNA molecules following metabolic labeling with the nucleoside analog 5-ethynyl uridine and long-read, direct RNA sequencing with nanopores. RNAkinet processes electrical signals from nanopore sequencing directly and distinguishes nascent from pre-existing RNA molecules. Our results show that RNAkinet prediction performance generalizes in various cell types and organisms and can be used to quantify RNA isoform half-lives. RNAkinet is expected to enable the identification of the kinetic parameters of RNA isoforms and to facilitate studies of RNA metabolism and the regulatory elements that influence it.
Interference detection in radio astronomy: applying Shapiro–Wilks normality test, spectral entropy, and spectral relative entropy
Authors: Cao Zhicheng , Schmid Natalia A , Bandura Kevin , Lorimer Duncan R , Dameron Morgan , Crockett Katelyn , Grubick Clayton , Schmid Andreas , Zheng Shaonan
Published: August 2024

Radio-frequency interference (RFI) is becoming an increasingly significant problem for most radio telescopes. Working with Green Bank Telescope data from PSR J1730+0747 in the form of complex-valued channelized voltages and their respective high-resolution power spectral densities, we evaluate a variety of statistical measures to characterize RFI. As a baseline for performance comparison, we use median absolute deviation (MAD) in complex channelized voltage data and spectral kurtosis (SK) in power spectral density data to characterize and filter out RFI. From a new perspective, we implement the Shapiro–Wilks (SW) test for normality and two information theoretical measures, spectral entropy (SE) and spectral relative entropy (SRE), and apply them to mitigate RFI. The baseline RFI mitigation algorithms are compared against our novel RFI detection algorithms to determine how effective and robust the performance is. Except for MAD, we find significant improvements in signal-to-noise ratio through the application of SE, symmetrical SRE, asymmetrical SRE, SK, and SW. These algorithms also do a good job of characterizing broad-band RFI. Time- and frequency-variable RFI signals are best detected by SK and SW tests.
Evaluating the Severity Spectrum: A Hierarchical Analysis of Complications During Hip Fracture Admission Associated With Mortality
Authors: Pettit Christopher J. , Herbosa Carolyn F. , Ganta Abhishek , Rivero Steven , Tejwani Nirmal , Leucht Philipp , Konda Sanjit R. , Egol Kenneth A.
Published: August 2024

OBJECTIVES:

To determine which in-hospital complications after the operative treatment of hip fractures are associated with increased in-patient, 30-day, and 1-year mortality.

METHODS:

Design:

Retrospective study.

Setting:

A single academic medical center and a Level 1 Trauma Center.

Patient Selection Criteria:

All patients who were operatively treated for hip fractures (Orthopaedic Trauma Association/AO 31A, 31B and Vancouver A, B, and C periprosthetic fractures) at a single center between October, 2014, and June, 2023.

Outcome Measures and Comparisons:

Occurrence of an in-hospital complication was recorded. Cohorts were based on mortality time points (during admission, 30 days, and 1 year) and compared with patients who were alive at those time points to determine which in-hospital complications were most associated with mortality. Correlation analysis was performed between patients who died and those who were alive at each time point.

RESULTS:

A total of 3134 patients (average age of 79.6 years, range 18–104 years and 66.6% women) met inclusion for this study. The overall mortality rate during admission, 30 days, and 1 year was found to be 1.6%, 3.9%, and 11.1%, respectively. Sepsis was the complication most associated with increased in-hospital mortality (odds ratio [OR] 7.79, 95% confidence interval [CI], 3.22–18.82, P < 0.001) compared with other in-hospital complications. Compared with other in-hospital complications, stroke was the complication most associated with 30-day mortality (OR 7.95, 95% CI, 1.82–34.68, P < 0.001). Myocardial infarction was the complication most associated with 1-year mortality (OR 2.86, 95% CI, 1.21–6.77, P = 0.017) compared with other in-hospital complications.

CONCLUSIONS:

Postoperative sepsis, stroke, and myocardial infraction were the 3 complications most associated with mortality during admission, 30-day mortality, and 1-year mortality, respectively, during the operative treatment of hip fractures.

LEVEL OF EVIDENCE:

Prognostic Level III. See Instructions for Authors for a complete description of levels of evidence.
Analyzing leukemia content on social media: a comprehensive cross-sectional examination of Instagram and YouTube
Authors: Varma Meghal , Syed Aina M. , Patel Visarg J. , Mediboina Anjali
Published: August 2024

Introduction:

Leukemia is a hematologic malignancy characterized by the uncontrolled proliferation of abnormal white blood cells. Patients with childhood leukemia may turn to social media for emotional support and information. This study aimed to identify the quality, reliability, understandability, and actionability of posts related to leukemia on YouTube and Instagram.

Methods:

Apify, a web scraping tool was used to gather relevant posts. The top 100 posts in each hashtag “leukemia,” “childhoodcancer,” “childhoodcancerawareness,” “leukemiaawareness” on Instagram, and the top 60 videos on YouTube for the term “leukemia” were scraped on 24 September 2023, resulting in the collection of 361 Instagram and 58 YouTube videos. All posts and videos in English and related to leukemia were included in the analysis, and thus, a total of 231 Instagram posts and 56 YouTube videos were evaluated, guided by the strengthening the reporting of cohort studies in surgery guidelines and utilized standardized tools [Global Quality Scale (GQS), modified DISCERN, and Patient Education Materials Assessment Tool for Audiovisual Materials (PEMAT-A/V)]. Data analysis was done in R Studio (4.3.1.); Kruskal–Wallis test was used to determine statistical significance.

Results:

YouTube videos demonstrated commendable standards with moderate quality and reliability (GQS 3.1, modified DISCERN 2.9, PEMAT-A/V understandability averaged 89%, and actionability averaged 50%). The impact of the uploader type on content quality and reliability was insignificant on both platforms. However, a notable correlation between YouTube video duration and quality scores underscored the potential influence of content length on information presentation. Instagram posts exhibited comparatively lower scores (GQS 2, modified DISCERN 1.8, PEMAT-A/V understandability averaged 56%, and actionability averaged 15%), indicating a need for enhanced content quality. Personal narratives emphasized the significant role of lived experiences in shaping content.

Conclusion:

Despite high understandability, actionable content, particularly on Instagram, necessitated improvement, revealing a potential gap in disseminating practical information. While personal narratives contributed significantly, lower reliability scores highlighted inherent challenges, underscoring the pivotal role of healthcare provider engagement and content validation.
Evaluating cancer rehabilitation services: Insight from Australia and New Zealand
Authors: Song Krystal , Jena Swatee , Alexander Tara , Lee Su Yi , Amatya Bhasker , Faux Steven G. , Khan Fary
Published: August 2024

Background:

Despite evidence supporting the benefits of rehabilitation for cancer survivors, the nature of cancer rehabilitation programs is inadequately described in Australia and New Zealand. This study provides insight into current service delivery and challenges for healthcare systems in implementation of cancer rehabilitation programs.

Methods:

A cross-sectional survey of directors of public and private rehabilitation services in hospital and ambulatory settings across Australia and New Zealand using the Australasian Rehabilitation Outcomes Centre (AROC) registry evaluated the current delivery of cancer rehabilitation programs, health professional workforce, core care components delivered, barriers and facilitators to service delivery, and unit/organisation-wide cancer rehabilitation activities. Descriptive statistics analyzed quantitative data, and qualitative analyses interpreted item responses.

Results:

Of the 300 services, 102 (34%) participants completed the survey. Most services provide non-dedicated cancer rehabilitation programs (n=63), led by rehabilitation physicians, followed by allied health. The common tumour streams referred included central nervous system (67%, n=56), haematological (59%, n=49), prostate (58%, n=48), and lung cancers (58%, n=48). Patients were frequently referred during post-treatment (87%, n=72) and treatment phases (66%, n=55). Core program components were multimodal exercises, fatigue management strategies, and management of medical complications and medications. The main barriers and facilitators toward the uptake of cancer rehabilitation programs were identified. Key activities in education, research, advocacy, and clinical practice improvement were also highlighted.

Conclusions:

The survey identified key barriers and facilitators for the implementation of cancer rehabilitation programs. Collaborative efforts of relevant stakeholders, clinicians, consumers, and policymakers need to address barriers to broader implementation of cancer rehabilitation services.
Association between HIV and cytomegalovirus and neurocognitive outcomes among children with HIV
Authors: Neary Jillian , Chebet Daisy , Benki-Nugent Sarah , Moraa Hellen , Richardson Barbra A. , Njuguna Irene , Langat Agnes , Ngugi Evelyn , Lehman Dara A. , Slyker Jennifer , Wamalwa Dalton , John-Stewart Grace
Published: August 2024

Objectives:

Children with HIV may experience adverse neurocognitive outcomes despite antiretroviral therapy (ART). Cytomegalovirus (CMV) is common in children with HIV. Among children on ART, we examined the influences of early HIV viral load and CMV DNA on neurocognition.

Design:

We determined the association between pre-ART viral load, cumulative viral load, and CMV viremia and neurocognition using data from a cohort study.

Methods:

Children who initiated ART before 12 months of age were enrolled from 2007 to 2010 in Nairobi, Kenya. Blood was collected at enrollment and every 6 months thereafter. Four neurocognitive assessments with 12 domains were conducted when children were a median age of 7 years. Primary outcomes included cognitive ability, executive function, attention, and motor z scores. Generalized linear models were used to determine associations between HIV viral load (pre-ART and cumulative; N = 38) and peak CMV DNA (by 24 months of age; N = 20) and neurocognitive outcomes.

Results:

In adjusted models, higher peak CMV viremia by 24 months of age was associated with lower cognitive ability and motor z scores. Higher pre-ART HIV viral load was associated with lower executive function z scores. Among secondary outcomes, higher pre-ART viral load was associated with lower mean nonverbal and metacognition z scores.

Conclusion:

Higher pre-ART viral load and CMV DNA in infancy were associated with lower executive function, nonverbal and metacognition scores and cognitive ability and motor scores in childhood, respectively. These findings suggest long-term benefits of early HIV viral suppression and CMV control on neurocognition.
Gilvirhabdus luticola gen. nov., sp. nov., a mesophilic and halophilic bacterium isolated from tidal flat sediment
Authors: Jayan Jaincy N. , Kim Hee-Su , Srinivasan Sathiyaraj , Kim Hyung-Seop , Yu Jae-Yon , Lee Sang-Seob
Published: August 2024

Two novel bacteria, MJ-SS3T and MJ-SS4, were isolated from tidal flat sediment sampled in Gochang, Republic of Korea. The isolates were Gram-stain-negative, aerobic, non-motile, rod-shaped, yellow-coloured, oxidase-positive, and catalase-positive. Strains MJ-SS3T and MJ-SS4 grew at 20–37 °C (optimum, 30 °C), at pH 6–8 (optimum, pH 7.0) and in the presence of 0–7 % (w/v) NaCl (optimum, 2.0 % NaCl). Strains MJ-SS3T and MJ-SS4 showed 99.9 % 16S rRNA gene sequence similarity. Phylogenetic analysis based on genome and 16S rRNA gene sequences indicated that strains MJ-SS3T and MJ-SS4 were affiliated with the family Flavobacteriaceae and most closely related to Formosa maritima 1494T (95.3 %), Hanstruepera flava NBU2984T (95.2 %), Yeosuana marina JLT21T (95.2 %), Meridianimaribacter flavus NH57NT (95.1 %), and Geojedonia litorea YCS-16T (95.1 %). The major respiratory quinone was menaquinone-6. The major identified polar lipids were phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine, and amino lipids. The major cellular fatty acids of strain MJ-SS3T were iso-C15 : 1 G (24.6 %), iso-C15 : 0 (21.6 %), and iso-C17 : 0 3-OH (15.8 %). The genome length of strain MJ-SS3T is 3.1 Mbp (DNA G+C content, 32.5 mol%) and it has 2822 coding and 59 tRNA genes. The average amino acid identity and average nucleotide identity values, as well as biochemical, phylogenetic, and physiological characteristics, strongly supported the genotypic and phenotypic differentiation of strains MJ-SS3T and MJ-SS4 from other members of the family Flavobacteriaceae. Hence, strains MJ-SS3T and MJ-SS4 are considered to represent a novel species of a new genus in the family Flavobacteriaceae, for which the Gilvirhabdus luticola gen. nov., sp. nov. is proposed. The type strain is MJ-SS3T (=KCTC 102114T=KEMB 20189T=JCM 36595T), with reference strain MJ-SS4 (=KCTC 102115=KEMB 20190).
BioLP-bench: Measuring understanding of biological lab protocols by large language models
Authors: Ivanov Igor
Published: August 2024

Language models rapidly become more capable in many domains, including biology. Both AI developers and policy makers [1] [2] [3] are in need of benchmarks that evaluate their proficiency in conducting biological research. However, there are only a handful of such benchmarks[4, 5], and all of them have their limitations. This paper introduces the Biological Lab Protocol benchmark (BioLP-bench) that evaluates the ability of language models to find and correct mistakes in a diverse set of laboratory protocols commonly used in biological research.

To evaluate understanding of the protocols by AI models, we introduced in these protocols numerous mistakes that would still allow them to function correctly. After that we introduced in each protocol a single mistake that would cause it to fail. We then presented these modified protocols to an LLM, prompting it to identify the mistake that would cause it to fail, and measured the accuracy of a model in identifying such mistakes across many test cases. Only OpenAI o1-preview scored similarly to the performance of human experts, while other language models demonstrated substantially worse performance, and in most cases couldn’t correctly identify the mistake.

Code and dataset are published athttps://github.com/baceolus/BioLP-bench
GENETIC VARIABILITY AND ASSOCIATION OF TRAITS IN COMMON BEAN (Phaseolus vulgarisL.)GENOTYPES IN SEKOTA, NORTH WESTERN ETHIOPIA
Authors: Assefa Abebe , Worku Dereje , Bantayhu Muluken , Asres Fentaw
Published: August 2024

Common bean (Phaseolus vulgaris L.) is one of the most important pulse crops in Ethiopia, contributing to income generation and food security. Information on the genetic variability and trait associations of common bean in the Sekota district of north Western Ethiopia is inadequate. This study was initiated with the objective to assess variability, heritability and trait association among 64 common bean genotypes for quantitative traits using 8x8 simple lattice design at Aybra main research site 2023 under rain fed conditions. Analysis of variance was performed using SAS software and the ANOVA revealed highly significant variations among genotypes for all the traits considered in the study. The yield ranged from 1633.1 to 3702.10 kg ha-1with a mean of 2542.53 kg ha-1. There was a yield advantage of 24.56 to 55.89% over the checks. A moderate genotypic coefficient of variation coupled with high heritability and high genetic advance as a percentage of the mean was obtained for plant height, branches per plant, hundred seed weight, seed yield, and harvest index. Branches per plant, aboveground biomass and harvest index had significant positive correlations and direct effects on seed yield at the genotypic and phenotypic levels while days to maturity had a significant negative correlation and indirect effect with seed yield at the genotypic. The maximum inter cluster distance was found between clusters VII and 8 (D2=351.39), followed by clusters V and VIII (D2=331.23). The first five principal component axes accounted for 74.3% of the total variation, with eigenvalues greater than unity. The number of days to maturity, plant height, number of pods per plant, number seeds per pod, seed yield, and harvest index were the traits that contributed most of the variation in the first PCs. Generally, the presence of variability, and strong positive association of traits among the genotypes were observed in the traits under study. Therefore, selection based on agronomic performance and hybridization based on cluster distance could be possible for the improvement of common bean in the study area.
An Affordable and Customizable Arduino-based Thermo-controller for Thermal Ecology Experiments
Authors: Hawk Cassidy , Iverson Erik , Havird Justin
Published: August 2024

Insight into organismal physiology, evolutionary ecology, and climate change susceptibility all rely on high-quality and easily-obtainable thermal tolerance information. A variety of methods exist for measuring thermal tolerance, and thermal tolerance metrics are highly influenced by small differences in methodology. To promote consistency, reproducibility, and accessibility, we present here instructions for building an Arduino-based thermo-controller for raising, lowering, and holding temperature in a variety of experimental conditions. The setup is affordable (∼$100), highly customizable, and highly consistent in the outcomes it produces. We include data from real thermal trials demonstrating the ability of the system to meet, hold, and reproduce desired ramping rates and hold temperatures.
Pipeline for Assessing Tumor Immune Status Using Superplex Immunostaining and Spatial Immune Interaction Analysis
Authors: Xiao Chaoxin , Zhou Ruihan , Chen Qin , Hou Wanting , Li Xiaoying , Wang Yulin , Liu Lu , Wang Huanhuan , Yao Xiaohong , Xu Tongtong , Cao Fujun , Yin Banglei , Yan Ouying , Jiang Lili , Wang Wei , Cao Dan , Zhao Chengjian
Published: August 2024

The characteristics of the tumor microenvironment (TME) are closely linked to tumor progression and treatment response. The TME comprises various cell types, their spatial distribution, cell-cell interactions, and their organization into cellular niches or neighborhoods. To capture this complexity, several spatial profiling technologies have been developed. However, challenges such as low throughput, high costs, and complicated data analysis have limited their widespread use in immune research. In this study, we introduce the Cyclic-multiplex TSA (CmTSA) staining platform, a high-throughput superplex staining technology based on tyramide signal amplification (TSA) immunostaining combined with an efficient fluorophore recycling method. The CmTSA platform allows for the labeling of 30-60 antigens across multiple parallel formalin-fixed paraffin-embedded (FFPE) slides. Furthermore, the automated CmTSA workflow requires only standard histological equipment and conventional immunohistochemistry (IHC) primary antibodies (Abs), significantly reducing costs. While the superplex images produced contain extensive multidimensional information, extracting the spatial features of the TME from raw pixel data can be challenging. To address this, we present a computer vision-based analysis pipeline, which begins with deep learning-based algorithms to segment individual cells and identify cell types based on defined annotation rules. It then evaluates the spatial distribution tendencies of each cell type, the interaction intensity between paired cells, and the multicellular functional niches. This comprehensive approach enables researchers to visualize and quantify the types, states, and levels of immune activities within the TME effectively, advancing tumor immunology research and precision immune medicine.
Developing and characterising decellularized extracellular matrix hydrogels to bio-fabricate female reproductive tissues
Authors: Ribes Martinez E. , Franko Y. , Franko R. , Ferronato G.A. , Viana A.E.S. , Windenbach E , Stoeckl J. B. , Frohlich T. , Ferraz M.A.M.M.
Published: August 2024

This study investigated the development and characterization of decellularized extracellular matrix (dECM) hydrogels tailored for the bio-fabrication of female reproductive tissues, specifically targeting cortex, endometrium, medulla, and oviduct tissues. We aimed to evaluate the cytocompatibility, biomechanical properties, and overall efficacy of these dECMs in promoting cell viability, proliferation, and differentiation. Our findings revealed that these dECMs exhibited high biocompatibility with embryo development and cell viability, supporting micro vascularization and cellular differentiation without the need for external growth factors. These hydrogels displayed biomechanical properties that closely mimicked native tissues, which was vital for maintaining their functional integrity and supporting cellular activities. The printability assessments showed that dECMs, particularly those from cortex tissues, achieved high precision in replicating the intended structures, though challenges such as low porosity remained. The bioprinted constructs demonstrated robust cell growth, with over 97% viability observed by day 7, indicating their suitability for cell culture. This work represented a significant advancement in reproductive tissue bio-fabrication, demonstrating the potential of dECM-based hydrogels in creating structurally and functionally viable tissue constructs. By tailoring each dECM to match the unique biomechanical properties of different tissues, we paved the way for more effective and reliable applications in reproductive medicine and tissue engineering.

Highlights

Developed decellularized extracellular matrix (dECM) bio-inks for bio-fabrication of female reproductive tissues.

Demonstrated high biocompatibility with embryo development and cell viability.

Achieved accurate bioprinting, maintaining structural integrity.

Promoted micro vascularization and cell differentiation without added growth factors.
Stay or go? Outcomes of lower limb arthroplasty in patients travelling away from home for surgery: A cross-sectional analysis of the AOANJRR comparing patient residence and hospital remoteness
Authors: Scholes Corey , Holder Carl , Vertullo Christopher , Broadhead Matthew
Published: August 2024

Purpose

The relationship between remoteness of patient residence and post-surgical outcomes, such as early implant revision, has yet to be examined. The aim of this study was to assess whether the incidence of all-cause revision at up to 2 years following primary hip or knee total joint arthroplasty varies with the remoteness of a person’s place of residence at the time of the primary procedure.

Methods

An analysis was performed of data from the Australian Orthopaedic Association National Joint Replacement Registry (AOANJRR) from 1 Sept 1999 to 31 Dec 2022. The Modified Monash Model (2015) of remoteness classification was used to categorise patient residence and hospital location into metro-regional (MM 1-2) and rural-remote (MM 3-7). All-cause revision within the two-year period after surgery for primary total knee arthroplasty (TKA) and primary total hip arthroplasty (THA) for osteoarthritis as the primary diagnosis was selected as the primary outcome. A directed-acyclic graph approach was used to prioritise covariates for inclusion in a Cox proportional hazards regression model. Cumulative percent revision (CPR) rates with 95% confidence intervals was reported with hazard ratios between subgroups of residential and hospital remoteness.

Results

The two-year CPR for primary TKA ranged from 1.8% (95% CI 1.7 - 1.9) to 2.2% (95% CI 1.8 - 2.7). Patients residing in rural-remote areas who travelled to a metro-regional hospital displayed a significantly higher rate of revision following TKA compared to patients that were treated at a rural-remote hospital (HR: 1.11, 95% CI 1.05 - 1.18, P = 0.001) within two-year follow-up of the primary procedure. Patients residing in rural-remote areas that stayed in these areas for their operation displayed a significantly reduced revision rate compared to metro-regional patients that stayed in-area for their joint replacement (HR=0.90, 95%CI 0.85 - 0.95, P <0.001). Infection was the dominant reason for TKA revision for patients in the follow-up period. No discernible differences in revision risk were observed between patient and hospital combinations for primary total hip replacement.

Conclusions

Travel distance, but not remoteness of a patient’s place of residence may be associated with cumulative risk of early revision (within 2 years) of primary TKA, particularly in regional/remote patients travelling out of area, but not for patients undergoing THA. Further work linking service utilisation prior to a revision procedure is required to clarify whether differences in revision between remoteness and travel distances are due to variability in the clinical threshold for offering revision arthroplasty between regional and metropolitan surgeons or improved outcomes of the primary procedure.
Multi-trait and multi-ancestry genetic analysis of comorbid lung diseases and traits improves genetic discovery and polygenic risk prediction
Authors: He Yixuan , Lu Wenhan , Jee Yon Ho , Wang Ying , Tsuo Kristin , Qian David C. , Diao James A. , Huang Hailiang , Patel Chirag J. , Byun Jinyoung , Pasaniuc Bogdan , Atkinson Elizabeth G. , Amos Christopher I. , Moll Matthew , Cho Michael H. , Martin Alicia R.
Published: August 2024

While respiratory diseases such as COPD and asthma share many risk factors, most studies investigate them in insolation and in predominantly European ancestry populations. Here, we conducted the most powerful multi-trait and -ancestry genetic analysis of respiratory diseases and auxiliary traits to date. Our approach improves the power of genetic discovery across traits and ancestries, identifying 44 novel loci associated with lung function in individuals of East Asian ancestry. Using these results, we developed PRSxtra (cross TRait and Ancestry), a multi-trait and -ancestry polygenic risk score approach that leverages shared components of heritable risk via pleiotropic effects. PRSxtra significantly improved the prediction of asthma, COPD, and lung cancer compared to trait- and ancestry-matched PRS in a multi-ancestry cohort from the All of Us Research Program, especially in diverse populations. PRSxtra identified individuals in the top decile with over four-fold odds of asthma and COPD compared to the first decile. Our results present a new framework for multi-trait and -ancestry studies of respiratory diseases to improve genetic discovery and polygenic prediction.
Repetitive neonatal pain increases spinal cord DNA methylation of the µ-opioid receptor
Authors: Baudat Mathilde , Joosten Elbert A.J , Simons Sinno H.P. , van den Hove Daniël L.A. , Riemens Renzo J.M.
Published: August 2024

Repetitive neonatal painful procedures experienced in the neonatal intensive care unit (NICU) are known to alter the development of the nociceptive system and have long-lasting consequences, notably lower post-operative µ-opioid receptor levels in the spinal cord. Given the influence of the NICU on the epigenome, the present study hypothesized that neonatal procedural pain alters the DNA methylation status of the opioid receptor mu 1 encoding gene (Mor-1) in the spinal cord and dorsal root ganglions (DRGs). To this end, the needle prick model of repetitive neonatal pain was used, and methylation ofMor-1promotor was assessed in the spinal cord and the DRG using bisulfite pyrosequencing. Our findings demonstrated that neonatal procedural pain increased spinal cordMor-1promotor DNA methylation in the ipsilateral side as compared to the contralateral side, an effect that was not observed in the control animals, nor in the DRG. We also identified a behaviorally-associated CpG site following neonatal needle pricks. This study is the first to highlight a localized and noxious-stimuli-dependent effect of repetitive neonatal procedural pain onMor-1promotor methylation and emphasizes the need to explore the effects of repetitive neonatal procedural pain on the epigenome.

Impact

This study reveals that repetitive neonatal procedural pain increases DNA methylation of the Mor-1 promoter in the spinal cord of neonatal rats.

This is the first study to identify an effect of neonatal procedural pain on DNA methylation, emphasizing the critical need for further investigation into the epigenetic consequences of neonatal procedural pain.

These insights could lead to better management and treatment strategies to mitigate the long-term impacts of early pain exposure on neurodevelopment and behavior.