bluuebunny/crossref_metadata_2025_split huggingface dataset:
Quantifying Interpretation Reproducibility in Vision Transformer Models with TAVAC
Authors: Zhao Yue , Agyemang Dylan , Liu Yang , Mahoney Matt , Li Sheng 
Published: January 2024

AbstractThe use of deep learning algorithms to extract meaningful diagnostic features from biomedical images holds the promise to improve patient care given the expansion of digital pathology. Among these deep learning models, Vision Transformer (ViT) models have been demonstrated to capture long-range spatial relationships with more robust prediction power for image classification tasks than regular convolutional neural network (CNN) models, and also better model interpretability. Model interpretation is important for understanding and elucidating how a deep learning model makes predictions, especially for developing transparent models for digital pathology. However, like other deep learning algorithms, with limited annotated biomedical imaging datasets, ViT models are prone to poor performance due to overfitting, which can lead to false predictions due to random noise. Overfitting affects model interpretation when predictions are made out of random noise. To address this issue, we introduce a novel metric – Training Attention and Validation Attention Consistency (TAVAC) – for evaluating ViT model degree of overfitting on imaging datasets and quantifying the reproducibility of interpretation. Specifically, the model interpretation is performed by comparing the high-attention regions in the image between training and testing. We test the method on four publicly available image classification datasets and two independent breast cancer histological image datasets. All overfitted models exhibited significantly lower TAVAC scores than the good-fit models. The TAVAC score quantitatively measures the level of generalization of model interpretation on a fine-grained level for small groups of cells in each H&E image, which cannot be provided by traditional performance evaluation metrics like prediction accuracy. Furthermore, the application of TAVAC extends beyond medical diagnostic AI models; it enhances the monitoring of model interpretative reproducibility at pixel-resolution in basic research, to reveal critical spatial patterns and cellular structures essential to understanding biological processes and disease mechanisms. TAVAC sets a new standard for evaluating the performance of deep learning model interpretation and provides a method for determining the significance of high-attention regions detected from the attention map of the biomedical images.
From dust to seed: a lunar chickpea story
Authors: Atkin Jessica A. , Santos Sara Oliveira 
Published: January 2024

ABSTRACTFood sustainability is one of the most significant barriers to long-term space travel. Providing resources from Earth is not cost-efficient, and resupply missions are not viable to meet the needs of long-term life in deep space conditions. Plants in space can provide a source of nutrition and oxygen, reducing the reliance on packaged foods, reducing resupply needs, and extending the duration of missions. Using lunar regolith simulant, we employ a novel methodology to create a sustainable and productive growth medium to support the cultivation of horticultural crops on the Moon. Implementing microbial soil regeneration mechanisms derived from Earth, we leverage the interaction between Arbuscular Mycorrhizal Fungi (AMF) and Vermicompost (VC) to create a fertile LRS matrix. These amendments can sequester toxic contaminants, improve soil structure, and increase plant stress tolerance. We demonstrate the ability to produce chickpea (Cicer arietinum) in lunar regolith simulant augmented with AMF and VC under climate-controlled conditions. We cultivated chickpea to seed in a mixture containing 75% Lunar Regolith Simulant. Preliminary results suggest that higher LRS contents induce heightened stress responses. However, plants grown in 100% LRS inoculated with arbuscular mycorrhizal fungi demonstrated an average two-week survival extension compared to non-inoculated plants. This study provides, for the first time, a baseline for chickpea germination in varying mixtures of LRS and VC and will inform future studies as humanity goes back to the Moon.
PWAS Hub: Exploring Gene-Based Associations of Common Complex Diseases
Authors: Kelman Guy , Zucker Roei , Brandes Nadav , Linial Michal 
Published: January 2024

AbstractPWAS (Proteome-Wide Association Study) is an innovative genetic association approach that complements widely-used methods like GWAS (Genome-Wide Association Study). The PWAS platform involves consecutive phases. Initially, machine learning modeling and probabilistic considerations quantified the impact of genetic variants on protein-coding genes’ biochemical functions. Secondly, aggregating the variants per gene for each individual determines a gene-damaging score. Finally, standard statistical tests are activated in the case-control setting to yield statistically significant genes per phenotype. The PWAS Hub offers a user-friendly interface for an in-depth exploration of gene-disease associations from the UK Biobank (UKB). Results from PWAS cover 99 common diseases and conditions, each with over 10,000 diagnosed individuals per phenotype. Users can explore genes associated with these diseases, with separate analyses conducted for males and females. The PWAS Hub lists statistically significant genes associated with common diseases. It also indicates whether the analyzed damaged gene is associated with an increased or decreased risk. For each phenotype, the analyses account for sex-based genetic effects, inheritance modes (dominant and recessive), and the pleiotropic nature of associated genes. The PWAS Hub showcases its usefulness by navigating through such proteomic-genetic application for asthma. Graphical tools facilitate comparing genetic effects between the results of PWAS and coding GWAS, aiding in understanding the sex-specific genetic impact on common diseases. This adaptable platform is attractive for clinicians, researchers, and individuals interested in delving into gene-disease associations and sex-specific genetic effects. The PWAS Hub is accessible athttp://pwas.huji.ac.il.
Real-Time Ratiometric pH Imaging of Macrophage Lysosomes Using the Novel pH-sensitive Probe ApHID
Authors: Solé-Domènech Santiago , Singh Pradeep Kumar , Warren J. David , Maxfield Frederick R. 
Published: January 2024

SUMMARYLysosomes actively regulate their lumenal pH, which is necessary for optimal enzymatic activity. Endocytic processes are involved in many diseases, including Alzheimer’s disease, in which sub-optimal lysosomal function has been reported. To measure acidification, pH-sensitive probes can be delivered to endosomes and lysosomes using labeled dextran polymers or proteins. However, many commercially available probes have limited sensitivity in the acidic range of lysosomes, and their fluorescence is subject to photobleaching. Herein, we describe the preparation, characterization, and use of a novel pH-sensitive probe,ApHID, a green-emitting dye with a pKa near 5, increasing brightness with acidity, and resistance to oxidation and photobleaching. We used ApHID ratiometric imaging to measure lysosomal pH in macrophages, yielding nearly identical results when compared with fluorescein and Oregon Green. Overall,ApHIDcircumvents limitations presented by most commercially available pH-sensitive probes, and can be useful in demanding imaging applications such as intravital imaging of tissues.
Genomic diversity and antimicrobial resistance in clinicalKlebsiella pneumoniaeisolates from tertiary hospitals in Southern Ghana
Authors: Mills Richael O. , Dadzie Isaac , Le-Viet Thanh , Baker David J. , Addy Humphrey P. K. , Akwetey Samuel A. , Donkoh Irene E. , Quansah Elvis , Semanshia Prince S. , Morgan Jennifer , Mensah Abraham , Adade Nana E. , Ampah Emmanuel O. , Owusu Emmanuel , Mwintige Philimon , Amoako Eric O. , Spadar Anton , Holt Kathryn E. , Foster-Nyarko Ebenezer 
Published: January 2024

AbstractComprehensive data on the genomic epidemiology of hospital-associatedKlebsiella pneumoniaein Ghana is scarce. This study sequenced 103 clinicalK. pneumoniaeisolates from five tertiary hospitals in Southern Ghana, predominantly from paediatric patients under five years (67/103, 65%), with the majority collected from urine (32/103, 31%) and blood (25/103, 24%) cultures. We employed Pathogenwatch for genotyping via Kaptive (K/O antigens) and Kleborate (antimicrobial resistance and hypervirulence) and determined clonal relationships using core-genome multilocus sequence typing (cgMLST). Among the 44 distinct sequence types (STs) detected, ST133 was the most common, comprising 23% of isolates (n=23/103). We discovered 27 different capsular (K) locus antigens and seven lipopolysaccharide (O) types; KL116 (28/103, 27%) and O1 (66/103, 64%) were the most prevalent. Single-linkage clustering highlighted the global spread of multidrug-resistant clones such as ST15, ST307, ST17, ST11, ST101, and ST48, with minimal allele differences (1-5) from publicly available genomes worldwide. Conversely, several isolates (n=17) constituted novel clonal groups and lacked close relatives among publicly available genomes, displaying unique genetic diversity within our study population. A significant proportion of isolates (88/103, 85%) carried resistance genes for three or more antibiotic classes, with theblaCTXM-15gene present in 78% (n=80/103). Carbapenem resistance, predominantly due toblaOXA-181andblaNDM-1genes, was found in 10% (n=10/103) of the isolates. Yersiniabactin was the predominant acquired virulence trait, identified in 70% (n=72/103) of the isolates. Our findings reveal a complex genomic landscape ofK. pneumoniaein Southern Ghana, underscoring the critical need for ongoing genomic surveillance to manage the substantial burden of antimicrobial resistance.
Submicroscopic malaria parasitemia and migration: the hidden weight carried by pregnant women
Authors: Docquier L , Taelman C , Delforge M , Martin C. 
Published: January 2024

AbstractIntroductionSubmicroscopic malaria parasitemia is a known phenomenon for years, however there are currently not enough existing data to set guidelines for diagnosis and treatment. Due to multiple reasons, pregnant women arrived recently from endemic areas seem to be particularly at risk of submicroscopic malaria parasitemia, which can only be diagnosed by molecular techniques. This study aims to determine the prevalence of submicroscopic malaria parasitemia in pregnant women coming from endemic areas and to pin down its potential consequences on maternal and birth outcomes.MethodsA prospective study on pregnant women that recently arrived from endemic areas for malaria was conducted in the Obstetrics Department of CHU Saint-Pierre (Brussels). SeveralP. falciparumdetection techniques were performed for each participant on 2 maternal (pre and postnatal) and 1 cord blood samples, using both conventional tests and loop-mediated isothermal amplification (LAMP). Placentas were also analyzed to search for placental malaria. Birth outcomes were collected. Patients with and without submicroscopic malaria parasitemia were compared.ResultsMaternal and umbilical blood samples were collected in 96 enrolled patients and analyzed by conventional tests and loop mediated isothermal amplification. Among the enrolled patients, 5 (5.2%) had submicroscopic malaria parasitemia. Patients with submicroscopic malaria parasitemia had left their endemic area more recently (p <0.05), had higher reticulocyte counts in both maternal prenatal blood (p <0.02) and cord blood (p <0.02) and had higher lactate dehydrogenase level in cord blood (p <0.05). No impact of submicroscopic malaria parasitemia on birth weight and term of birth was detected.ConclusionThe prevalence of submicroscopic malaria parasitemia in pregnant women arriving in non-endemic countries is non negligible. More data need to be collected to assess the consequences of submicroscopic malaria parasitemia on maternal and birth outcomes.
Clinical value of plasma ALZpath pTau217 immunoassay for assessing mild cognitive impairment
Authors: Lehmann Sylvain , Schraen-Maschke Susanna , Vidal Jean-Sébastien , Delaby Constance , Buée Luc , Blanc Frédéric , Paquet Claire , Allinquant Bernadette , Bombois Stéphanie , Gabelle Audrey , Hanon Olivier 
Published: January 2024

AbstractObjectivesWe sought to compare two of the most promising plasma biomarkers for Alzheimer disease (AD): pTau181 and pTau217.MethodspTau181 and pTau217 were quantified using, Quanterix and ALZpath, SIMOA assays in the well characterized prospective multicentre BALTAZAR cohort of mild cognitive impairment (MCI) participants.ResultsAmong MCI participants, 55% were Aβ+ and 29% developed dementia due to AD. pTau181 and pTau217 were higher in the Aβ+ population with fold-change of 1.5 and 2.7 respectively. MCI that converted to AD also had higher levels than non-converters, with hazard ratios of 1.38 (1.26-1.51) for pTau181 compared to 8.22 (5.45-12.39) for pTau217. The AUC for predicting Aβ+ was 0.783 (95%CI: 0.721-0.836; cut-point 2.75 pg/mL) for pTau181 and 0.914 (95%CI: 0.868-0.948; cut-point 0.44 pg/mL) for pTau217. The high predictive power of pTau217 was not improved by adding age, sex, and APOEε4 status, in a logistic model. Age, APOEε4 and renal dysfunction were associated with pTau levels, but the clinical performance of pTau217 was only marginally altered by these factors. Using a two cut-point approach, a 95% positive predictive value for Aβ+ corresponded to pTau217 > 0.8 pg/mL and a 95% negative predictive value at <0.23 pg/mL. At these two cut-points, the percentages of MCI conversion were 56.8% and 9.7% respectively, while the annual rates of decline in MMSE were −2.32 versus −0.65.ConclusionsPlasma pTau217 and pTau181 both correlate with AD, but the fold-change in pTau217 make it better to diagnose cerebral amyloidosis, and predict cognitive decline and conversion to AD dementia.
Data-driven personalised recommendations for eczema treatment using a Bayesian model of severity dynamics
Authors: Hurault Guillem , Stalder Jean François , Aroman Markéta Saint , Tanaka Reiko J. 
Published: January 2024

ABSTRACTAtopic dermatitis (AD) is a chronic inflammatory skin disease. AD has heterogeneous phenotypes, making it challenging to predict treatment effects for each patient and to generate personalised treatment recommendations. Here we aim to develop a computational model that predicts the evolution of AD severity and generates treatment recommendations for individual patients. We modelled the temporal evolution of eczema severity by applying a previously developed computational framework (EczemaPred) to the daily record of Patient-Oriented SCORing Atopic Dermatitis (PO-SCORAD) collected from 16 AD patients over 12 weeks in an observational study. We also leveraged historical data from 337 AD patients to kickstart the model training and reach more robust conclusions. We estimated the effects of topical corticosteroids and emollients on the next day’s PO-SCORAD, and generated personalised treatment recommendations using Bayesian decision analysis on whether treatment should be applied to improve PO-SCORAD on the next day for each of the 16 patients. We calibrated daily PO-SCORAD recorded by patients with monthly SCORAD assessed by clinical staff to improve the data quality. This study demonstrated a proof-of-concept for generating personalised treatment recommendations for AD using a Bayesian model that integrates multiple sources of information, including PO-SCORAD, SCORAD, and treatment usage.
Glucose metabolism and Radiodensity of Abdominal Adipose Tissue: A 5-year longitudinal study in a large PET cohort
Authors: Pak Kyoungjune , Santavirta Severi , Shin Seunghyeon , Nam Hyun-Yeol , De Maeyer Sven , Nummenmaa Lauri 
Published: January 2024

ABSTRACTObjective18F-Fluorodeoxyglucose positron emission tomography/computed tomography (PET/CT) allows the noninvasive assessment of glucose metabolism and radiodensity of visceral adipose tissue (VAT) and subcutaneous adipose tissue (SAT).Research design and methodsWe retrospectively analyzed data from 435 healthy males (mean 42.8 years) who underwent health check-up program twice at baseline and 5-year follow-up. The mean standardized uptake value (SUV) was measured from SAT and VAT and was divided with liver SUV. The mean Hounsfield unit (HU) of SAT and VAT was measured from CT scans. The effects of clinical variable clusters on SUVR were investigated using Bayesian hierarchical modelling. Four clusters were established for predicting SUVR; 1) metabolic cluster (BMI, waist-to-hip ratio, fat percentage, muscle percentage*-1, HOMA-IR), 2) blood pressure (systolic, diastolic), 3) glucose (fasting plasma glucose level, HbA1c), and 4) C-reactive protein.ResultsAll the clinical variables except for C-reactive protein changed during the 5-year follow-up. SUVR and HU of VAT were increased during the 5-year follow-up, however, those of SAT were not changed. SUVR and HU were positively correlated in both VAT and SAT. SAT SUVR and VAT SUVR were negatively associated with metabolic cluster.ConclusionAgeing led to increased glucose metabolism and radiodensity in VAT, not in SAT. VAT may reflect the ageing process more directly than SAT. Glucose metabolism was higher and radiodensity was lower in VAT than in SAT, probably due to the difference in gene expression and lipid-density. Both glucose metabolism and radiodensity of VAT and SAT reflect the metabolic status.
Bacterial quorum sensing controls carbon metabolism to optimize growth in changing environmental conditions
Authors: Simpson Chelsea A. , Celentano Zach , McKinlay James B. , Nadell Carey D. , van Kessel Julia C. 
Published: January 2024

AbstractBacteria sense population density via the cell-cell communication system called quorum sensing (QS). Some QS-regulated phenotypes (e.g., secreted enzymes, chelators), are public goods exploitable by cells that stop producing them. We uncovered a phenomenon in whichVibriocells optimize expression of the methionine and tetrahydrofolate (THF) synthesis genes via QS. Strains that are genetically ‘locked’ at high cell density grow slowly in minimal glucose media and suppressor mutants accumulate via inactivating-mutations inmetF(methylenetetrahydrofolate reductase) andluxR(the master QS transcriptional regulator). Methionine/THF synthesis genes are repressed at low cell density when glucose is plentiful and are de-repressed by LuxR at high cell density as glucose becomes limiting. In mixed cultures, QS mutant strains initially co-exist with wild-type, but as glucose is depleted, wild-type outcompetes the QS mutants. Thus, QS regulation of methionine/THF synthesis is a fitness benefit that links private and public goods within the QS regulon, preventing accumulation of QS-defective mutants.
Solar neutrino constraints on light mediators through coherent elastic neutrino-nucleus scattering
Authors: Demirci M. , Mustamin M. F. 
Published: January 2024

We investigate new physics with light-neutral mediators through coherent elastic neutrino-nucleus scattering (CEνNS) at low energies. These mediators, with a mass of less than 1 GeV, are common properties for extensions of the Standard Model (SM). We consider general scalar, vector, and tensor interactions allowed by Lorentz invariance and involve universal light mediators accordingly. In addition, we study an additional vector gauge boson with an associated U(1)′ gauge group for a variety of models including U(1)B−L, U(1)B−3Le, U(1)B−3Lμ, and U(1)B−3Lτ. These models differ in the fermion charges, which determine their contributions within the CEνNS process. The effects of each model are investigated by embedding them in the SM process using solar neutrino flux. We derive new limits on the coupling-mass plane of these models from the latest CDEX-10 data. We also present projected sensitivities involving the future experimental developments for each model. Our results provide more stringent constraints in some regions, compared to previous works. Furthermore, the projected sensitivities yield an improvement of up to one order of magnitude.

Published by the American Physical Society
2024
The search for training and skill improvement of seasonal workers in tourism
Authors: Fasone Vincenzo , Pedrini Giulio , Scuderi Raffaele 
Published: January 2024

PurposeThe paper aims at assessing the role of the different stages of the employment process in gauging workers' willingness to upskill themselves at the end of a seasonal employment contract by investing in further training.Design/methodology/approachThe paper analyses data from a dedicated survey administered to a sample of seasonal employees. Through a regression analysis it explores the different stages of the employment process (job search, selection on the job activities), making a distinction between monetary and nonmonetary components of the investment in training.FindingsResults show that all stages matter, but they do not have the same importance. Ex-ante motivations and work experience, notably the level of perceived workload and organizational commitment, are the main factors affecting workers' willingness to acquire industry-specific skills through training.Originality/valueSo far, the literature has extensively dealt with the poor levels of training in seasonal employers, but it did not analyse worker’s willingness to invest in training over the different stages of the worker experience. This paper fills this gap by separately testing the relative importance of such stages and identifying the most important phases of the employment process.
Studying research in balanced scorecard over the years in performance management systems: a bibliometric analysis
Authors: Jaiswal Vishakha , Thaker Keyur 
Published: January 2024

PurposeSince the introduction of balanced scorecard by Kaplan and Norton in 1992, it garnered considerable research and practice attention across disciplines. Using bibliometric analysis, this study examines trends in balanced scorecard research in last 20 years and identifies future areas of research.Design/methodology/approachThe Web of Science database was used to extract research papers from the 2003 to 2023 period with “Balanced Scorecard” as topic. The final sample consisted of 445 articles. Trends and patterns were analyzed using bibliometric analysis through research profiling and thematic analysis.FindingsThe findings reveal that BSC, spanning across disciplines, including business and operations, has enriched the theory and practice of BSC research. Analytical and survey methods were more prevalent than primary studies. Scholars from the USA and the UK have made noteworthy contributions to balanced scorecard research. Emerging themes include integrating human resources, sustainability, subjectivity in performance evaluation and non-financial performance indicators in BSC for better strategic decision-making.Practical implicationsThe study would inspire researchers to generate new research questions and hypotheses and help in identifying gaps in the current knowledge base and areas where further investigation is needed. Managers would gain useful insights into performance management by studying the BSC research evolution to find a fit for modern-day industry needs.Originality/valueThe authors’ contribution fills the void by providing useful account of extent research over last 20 years using bibliometric analysis and motivate future research directions.