bluuebunny/crossref_metadata_2025_split huggingface dataset:
Multimodal learning in clinical proteomics: enhancing antimicrobial resistance prediction models with chemical information
Authors: Visonà Giovanni , Duroux Diane , Miranda Lucas , Sükei Emese , Li Yiran , Borgwardt Karsten , Oliver Carlos 
Published: November 2023

Abstract

Motivation
Large-scale clinical proteomics datasets of infectious pathogens, combined with antimicrobial resistance outcomes, have recently opened the door for machine learning models which aim to improve clinical treatment by predicting resistance early. However, existing prediction frameworks typically train a separate model for each antimicrobial and species in order to predict a pathogen’s resistance outcome, resulting in missed opportunities for chemical knowledge transfer and generalizability.

Results
We demonstrate the effectiveness of multimodal learning over proteomic and chemical features by exploring two clinically relevant tasks for our proposed deep learning models: drug recommendation and generalized resistance prediction. By adopting this multi-view representation of the pathogenic samples and leveraging the scale of the available datasets, our models outperformed the previous single-drug and single-species predictive models by statistically significant margins. We extensively validated the multi-drug setting, highlighting the challenges in generalizing beyond the training data distribution, and quantitatively demonstrate how suitable representations of antimicrobial drugs constitute a crucial tool in the development of clinically relevant predictive models.

Availability and implementation
The code used to produce the results presented in this article is available at https://github.com/BorgwardtLab/MultimodalAMR.
Hybkit: a Python API and command-line toolkit for hybrid sequence data from chimeric RNA methods
Authors: Stribling Daniel , Gay Lauren A , Renne Rolf 
Published: November 2023

Abstract

Summary
Experimental methods using microRNA/target ligation have recently provided significant insights into microRNA functioning through generation of chimeric (hybrid) RNA sequences. Here, we introduce Hybkit, a Python3 API, and command-line toolkit for analysis of hybrid sequence data in the “hyb” file format to enable customizable evaluation and annotation of hybrid characteristics. The Hybkit API includes a suite of python objects for developing custom analyses of hybrid data as well as miRNA-specific analysis methods, built-in plotting of analysis results, and incorporation of predicted miRNA/target interactions in Vienna format.

Availability and implementation
Hybkit is provided free and open source under the GNU GPL license at github.com/RenneLab/hybkit and archived on Zenodo (doi.org/10.5281/zenodo.7834299). Hybkit distributions are also provided via PyPI (pypi.org/project/hybkit), Conda (bioconda.github.io/recipes/hybkit/README.html), and Docker (quay.io/repository/biocontainers/hybkit).
Microcosmos explorers: foldscope workshop for science outreach in Mexican schools
Authors: López Clinton Samantha 
Published: November 2023

Abstract
Foldscopes are ultra-low-cost paper microscopes invented by Manu Prakash and Jim Cybulski at Stanford University. They are about as light as a pencil and waterproof, all whilst offering similar optic quality to traditional microscopes. Foldscopes do not require electricity or glass slides to be used, which increases the possibilities of their use in education and outreach activities with children or people with disabilities. In 2019, thanks to a material grant of 100 foldscopes from One World Science and additional purchased foldscopes, I designed and implemented a science workshop called Exploradores del Microcosmos, or Explorers of Microcosmos in English. The aim of the workshop was to help make microscopy more accessible, in particular at underfunded schools, and stimulate active learning about ecosystems and evolution in the participants. Within this article, I describe the workshop and relay my personal insights and reflections on its execution across multiple schools and groups in Mexico.
Validation of epidermal AMBRA1 and loricrin (AMBLor) as a prognostic biomarker for nonulcerated American Joint Committee on Cancer stage I/II cutaneous melanoma
Authors: Ewen Tom , Husain Akhtar , Stefanos Niki , Barrett Paul , Jones Claire , Ness Tom , Long Anna , Horswell Stuart , Bosomworth Helen , Lowenstein Joe , Richardson Grant , Swan David , McConnell Ashleigh , Rose Aidan , Andrew Tom , Reynolds Nick , Malvehy Josep , Carrera Christina , Alos Llucia , Mailer Sonia , Helm Thomas , Ding Liang , Bogner Paul , Podlipnik Sebastian , Puig Susana , McArthur Grant A , Paragh Gyorgy , Labus Marie , Sloan Philip , Armstrong Jane L , Lovat Penny E 
Published: November 2023

Abstract

Background
Combined expression of the autophagy-regulatory protein AMBRA1 (activating molecule in Beclin1-regulated autophagy) and the terminal differentiation marker loricrin in the peritumoral epidermis of stage I melanomas can identify tumour subsets at low risk of ­metastasis.

Objectives
To validate the combined expression of peritumoral AMBRA1 and loricrin (AMBLor) as a prognostic biomarker able to identify both stage I and II melanomas at low risk of tumour recurrence.

Methods
Automated immunohistochemistry was used to analyse peritumoral AMBRA1 and loricrin expression in geographically distinct discovery (n = 540) and validation (n = 300) cohorts of nonulcerated American Joint Committee on Cancer (AJCC) stage I and II melanomas. AMBLor status was correlated with clinical outcomes in the discovery and validation cohorts separately and combined.

Results
Analysis of AMBLor in the discovery cohort revealed a recurrence-free survival (RFS) rate of 95.5% in the AMBLor low-risk group vs. 81.7% in the AMBLor at-risk group (multivariate log-rank, P &lt; 0.001) and a negative predictive value (NPV) of 96.0%. In the validation cohort, AMBLor analysis revealed a RFS rate of 97.6% in the AMBLor low-risk group vs. 78.3% in the at-risk group (multivariate log-rank, P &lt; 0.001) and a NPV of 97.6%. In a multivariate model considering AMBLor, Breslow thickness, age and sex, analysis of the combined discovery and validation cohorts showed that the estimated effect of AMBLor was statistically significant, with a hazard ratio of 3.469 (95% confidence interval 1.403–8.580, P = 0.007) and an overall NPV of 96.5%.

Conclusions
These data provide further evidence validating AMBLor as a prognostic biomarker to identify nonulcerated AJCC stage I and II melanoma tumours at low risk of disease recurrence.
Abolitionism and Ecosocial Work: Towards Equity, Liberation and Environmental Justice
Authors: Shackelford Amy , Rao Smitha , Krings Amy , Frances Kathryn 
Published: November 2023

Abstract
The ecosocial work approach incorporates the environment into social justice frameworks. It calls for holistic practices that centre Indigenous and Global South voices, transdisciplinarity, anti-oppressive strategies in micro–macro practice and sustainability. In this article, we argue that the integration of abolitionist theory and practice within ecosocial work—specifically the reduction or elimination of social work from carceral systems that harm the environment and marginalised people—will better equip social workers to meet these goals. To this end, we critically examine three sites of ongoing abolitionist struggle—militaries, prisons and disinvested communities—to demonstrate reimagined strategies for an environmentally just future. Our analysis reveals areas where the ecosocial approach and abolitionism intersect, and how one might inform the other. We conclude by calling for future research to integrate abolitionist ideas into ecosocial work research, education and practice. In integrating environmental justice and abolition, ecosocial work will be better positioned to critique and resist its location in racialised capitalist systems that perpetuate economic, environmental, racial and social injustices.
Online clinical tools to support the use of new plasma biomarker diagnostic technology in the assessment of Alzheimer’s disease: a narrative review
Authors: Hazan Jemma , Liu Kathy Y , Fox Nick C , Howard Robert 
Published: November 2023

Abstract
Recent advances in new diagnostic technologies for Alzheimer’s disease have improved the speed and precision of diagnosis. However, accessing the potential benefits of this technology poses challenges for clinicians, such as deciding whether it is clinically appropriate to order a diagnostic test, which specific test or tests to order and how to interpret test results and communicate these to the patient and their caregiver. Tools to support decision-making could provide additional structure and information to the clinical assessment process. These tools could be accessed online, and such ‘e-tools’ can provide an interactive interface to support patients and clinicians in the use of new diagnostic technologies for Alzheimer’s disease. We performed a narrative review of the literature to synthesize information available on this research topic. Relevant studies that provide an understanding of how these online tools could be used to optimize the clinical utility of diagnostic technology were identified. Based on these, we discuss the ways in which e-tools have been used to assist in the diagnosis of Alzheimer’s disease and propose recommendations for future research to aid further development.
Targeted drug delivery into glial scar using CAQK peptide in a mouse model of multiple sclerosis
Authors: Zare Leila , Rezaei Safoura , Esmaeili Elaheh , Khajeh Khosro , Javan Mohammad 
Published: November 2023

Abstract
In multiple sclerosis, lesions are formed in various areas of the CNS, which are characterized by reactive gliosis, immune cell infiltration, extracellular matrix changes and demyelination. CAQK peptide (peptide sequence: cysteine–alanine–glutamine–lysine) was previously introduced as a targeting peptide for the injured site of the brain. In the present study, we aimed to develop a multifunctional system using nanoparticles coated by CAQK peptide, to target the demyelinated lesions in animal model of multiple sclerosis. We investigated the binding of fluorescein amidite–labelled CAQK and fluorescein amidite–labelled CGGK (as control) on mouse brain sections. Then, the porous silicon nanoparticles were synthesized and coupled with fluorescein amidite–labelled CAQK. Five days after lysolecithin-induced demyelination, male mice were intravenously injected with methylprednisolone-loaded porous silicon nanoparticles conjugated to CAQK or the same amount of free methylprednisolone. Our results showed that fluorescein amidite–labelled CAQK recognizes demyelinated lesions in brain sections of animal brains injected with lysolecithin. In addition, intravenous application of methylprednisolone-loaded nanoparticle porous silicon conjugated to CAQK at a single dose of 0.24 mg reduced the levels of microglial activation and astrocyte reactivation in the lesions of mouse corpus callosum after 24 and 48 h. No significant effect was observed following the injection of the same dose of free methylprednisolone. CAQK seems a potential targeting peptide for delivering drugs or other biologically active chemicals/reagents to the CNS of patients with multiple sclerosis. Low-dose methylprednisolone in this targeted drug delivery system showed significant beneficial effect.
Mindfulness meditation enhances interbrain synchrony of adolescents when experiencing different emotions simultaneously
Authors: Deng Xinmei , Lin Mingping , Li Xiaoling 
Published: November 2023

Abstract
Mindfulness is considered to benefit social behavior and interpersonal communication. However, the underlying neural mechanism has not been fully examined. This study aimed to explore how mindfulness practice affected the interbrain synchrony within adolescent peer dyads when sharing emotional experience together by using the electroencephalograph hyperscanning approach. Thirty adolescent dyads were randomly assigned to a mindfulness group or a non-mindfulness group. Mindfulness group performed a 20-min mindfulness exercise. Non-mindfulness group were instructed to rest. Simultaneously, electroencephalograph was recorded when they completed a picture-processing task. Phase-locking-value in the gamma band was used to calculate adolescent dyads’ brain-to-brain synchrony. Results showed that greater interbrain synchrony in the frontal region was observed when viewing different emotional stimuli together after the mindfulness than before the mindfulness in the mindfulness group. However, there was no significant difference in the interbrain synchrony in the non-mindfulness group. Moreover, greater interbrain synchrony was observed in the mindfulness group than in the non-mindfulness group after mindfulness or rest in the frontal region. However, there was no significant difference between the mindfulness and non-mindfulness group before mindfulness or rest. The findings are discussed in light of the broader theoretical questions of how mindfulness may promote interpersonal functioning from a psychophysiological perspective.
Protection Conferred by COVID-19 Vaccination, Prior SARS-CoV-2 Infection, or Hybrid Immunity Against Omicron-Associated Severe Outcomes Among Community-Dwelling Adults
Authors: Lee Nelson , Nguyen Lena , Austin Peter C , Brown Kevin A , Grewal Ramandip , Buchan Sarah A , Nasreen Sharifa , Gubbay Jonathan , Schwartz Kevin L , Tadrous Mina , Wilson Kumanan , Wilson Sarah E , Kwong Jeffrey C 
Published: November 2023

Abstract

Introduction
We assessed protection from coronavirus disease 2019 (COVID-19) vaccines and/or prior severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection against Omicron-associated severe outcomes during successive sublineage-predominant periods.

Methods
We used a test-negative design to estimate protection by vaccines and/or prior infection against hospitalization/death among community-dwelling, polymerase chain reaction (PCR)-tested adults aged ≥50 years in Ontario, Canada, between 2 January 2022 and 30 June 2023. Multivariable logistic regression was used to estimate the relative change in the odds of hospitalization/death with each vaccine dose (2–5) and/or prior PCR-confirmed SARS-CoV-2 infection (compared with unvaccinated, uninfected subjects) up to 15 months since the last vaccination or infection.

Results
We included 18 526 cases with Omicron-associated severe outcomes and 90 778 test-negative controls. Vaccine protection was high during BA.1/BA.2 predominance but was generally &lt;50% during periods of BA.4/BA.5 and BQ/XBB predominance without boosters. A third/fourth dose transiently increased protection during BA.4/BA.5 predominance (third-dose, 6-month: 68%, 95% confidence interval [CI] 63%–72%; fourth-dose, 6-month: 80%, 95% CI 77%–83%) but was lower and waned quickly during BQ/XBB predominance (third-dose, 6-month: 59%, 95% CI 48%–67%; 12-month: 49%, 95% CI 41%–56%; fourth-dose, 6-month: 62%, 95% CI 56%–68%, 12-months: 51%, 95% CI 41%–56%). Hybrid immunity conferred nearly 90% protection throughout BA.1/BA.2 and BA.4/BA.5 predominance but was reduced during BQ/XBB predominance (third-dose, 6-month: 60%, 95% CI 36%–75%; fourth-dose, 6-month: 63%, 95% CI 42%–76%). Protection was restored with a fifth dose (bivalent; 6-month: 91%, 95% CI 79%–96%). Prior infection alone did not confer lasting protection.

Conclusions
Protection from COVID-19 vaccines and/or prior SARS-CoV-2 infections against severe outcomes is reduced when immune-evasive variants/subvariants emerge and may also wane over time. Our findings support a variant-adapted booster vaccination strategy with periodic review.
Dynamics of stored lipids in fall migratory monarch butterflies (Danaus plexippus): Nectaring in northern Mexico allows recovery from droughts at higher latitudes
Authors: Hobson Keith A , Taylor Orley , Ramírez M Isabel , Carrera-Treviño Rogelio , Pleasants John , Bitzer Royce , Baum Kristen A , Mora Alvarez Blanca X , Kastens Jude , McNeil Jeremy N 
Published: November 2023

Abstract
The eastern population of the North American monarch butterfly (Danaus plexippus) overwinters from November through March in the high-altitude (3000 m+) forests of central Mexico during which time they rely largely on stored lipids. These are acquired during larval development and the conversion of sugars from floral nectar by adults. We sampled fall migrant monarchs from southern Canada through the migratory route to two overwintering sites in 2019 (n = 10 locations), 2020 (n = 8 locations) and 2021 (n = 7 locations). Moderate to extreme droughts along the migratory route were expected to result in low lipid levels in overwintering monarchs but our analysis of lipid levels of monarchs collected at overwintering sites indicated that in all years most had high levels of lipids prior to winter. Clearly, a significant proportion of lipids were consistently acquired in Mexico during the last portion of the migration. Drought conditions in Oklahoma, Texas and northern Mexico in 2019 resulted in the lowest levels of lipid mass and wing loading observed in that year but with higher levels at locations southward in Mexico to the overwintering sites. Compared with 2019, lipid levels increased during the 2020 and 2021 fall migrations but were again higher during the Mexican portion of the migration than for Oklahoma and Texas samples, emphasizing a recovery of lipids as monarchs advanced toward the overwintering locations. In all 3 years, body water was highest during the Canada—USA phase of migration but then declined during the nectar foraging phase in Mexico before recovering again at the overwintering sites. The increase in mass and lipids from those in Texas to the overwintering sites in Mexico indicates that nectar availability in Mexico can compensate for poor conditions experienced further north. Our work emphasizes the need to maintain the floral and therefore nectar resources that fuel both the migration and storage of lipids throughout the entire migratory route.
Physiological plasticity in elephants: highly dynamic glucocorticoids in African and Asian elephants
Authors: Pokharel Sanjeeta Sharma , Brown Janine L 
Published: November 2023

Abstract
Slowly reproducing and long-lived terrestrial mammals are often more at risk from challenges that influence fitness and survival. It is, therefore, important to understand how animals cope with such challenges and how coping mechanisms translate over generations and affect phenotypic plasticity. Rapidly escalating anthropogenic challenges may further diminish an animal’s ability to reinstate homeostasis. Research to advance insights on elephant stress physiology has predominantly focused on relative or comparative analyses of a major stress response marker, glucocorticoids (GCs), across different ecological, anthropogenic, and reproductive contexts. This paper presents an extensive review of published findings on Asian and African elephants from 1980 to 2023 (May) and reveals that stress responses, as measured by alterations in GCs in different sample matrices, often are highly dynamic and vary within and across individuals exposed to similar stimuli, and not always in a predictable fashion. Such dynamicity in physiological reactivity may be mediated by individual differences in personality traits or coping styles, ecological conditions, and technical factors that often are not considered in study designs. We describe probable causations under the ‘Physiological Dynamicity Model’, which considers context–experience–individuality effects. Highly variable adrenal responses may affect physiological plasticity with potential fitness and survival consequences. This review also addresses the significance of cautious interpretations of GCs data in the context of normal adaptive stress versus distress. We emphasize the need for long-term assessments of GCs that incorporate multiple markers of ‘stress’ and ‘well-being’ to decipher the probable fitness consequences of highly dynamic physiological adrenal responses in elephants. Ultimately, we propose that assessing GC responses to current and future challenges is one of the most valuable and informative conservation tools we have for guiding conservation strategies.
Capture and transport of white rhinoceroses (Ceratotherium simum) cause shifts in their fecal microbiota composition towards dysbiosis
Authors: Pohlin Friederike , Frei Carolin , Meyer Leith C R , Roch Franz-Ferdinand , Quijada Narciso M , Conrady Beate , Neubauer Viktoria , Hofmeyr Markus , Cooper Dave , Stalder Gabrielle , Wetzels Stefanie U 
Published: November 2023

Abstract
Translocations of Rhinocerotidae are commonly performed for conservation purposes but expose the animals to a variety of stressors (e.g. prolonged fasting, confinement, novel environment, etc.). Stress may change the composition of gut microbiota, which can impact animal health and welfare. White rhinoceroses in particular can develop anorexia, diarrhea and enterocolitis after translocation. The aim of this study was to investigate the associations of age, sex and translocation on the rhinoceros’ fecal bacterial microbiota composition. Fecal samples were collected from rhinoceroses at capture (n = 16) and after a &gt;30-hour road transport (n = 7). DNA was isolated from these samples and submitted for 16S rRNA V3-V4 phylotyping. Alpha diversity indices of the rhinoceros’ fecal microbiota composition of different age, sex and before and after transport were compared using non-parametric statistical tests and beta diversity indices using Permutational Multivariate Analysis Of Variance (PERMANOVA). Resulting P-values were alpha-corrected (Padj.). Alpha and beta diversity did not differ between rhinoceroses of different age and sex. However, there was a significant difference in beta diversity between fecal samples collected from adult animals at capture and after transport. The most abundant bacterial phyla in samples collected at capture were Firmicutes and Bacteroidetes (85.76%), represented by Lachnospiraceae, Ruminococcaceae and Prevotellaceae families. The phyla Proteobacteria (Padj. = 0.009) and Actinobacteria (Padj. = 0.012), amongst others, increased in relative abundance from capture to after transport encompassing potentially pathogenic bacterial families such as Enterobacteriaceae (Padj. = 0.018) and Pseudomonadaceae (Padj. = 0.022). Important commensals such as Spirochaetes (Padj. = 0.009), Fibrobacteres (Padj. = 0.018) and Lachnospiraceae (Padj. = 0.021) decreased in relative abundance. These results indicate that the stressors associated with capture and transport cause an imbalanced fecal microbiota composition in white rhinoceroses that may lead to potentially infectious intestinal disorders. This imbalance may result from recrudescence of normally innocuous pathogens, increased shedding of pathogens or increased vulnerability to new pathogens.