bluuebunny/crossref_metadata_2025 huggingface dataset:
Creating a computer assisted ICD coding system: performance metric choice and use of the ICD hierarchy
Authors: Marcou Quentin , Berti-Equille Laure , Novelli Noel
Published: January 2024

Objective: Machine learning methods hold the promise of leveraging available data and generating higher quality data while alleviating the data collection burden on healthcare professionals. International Classification of Diseases (ICD) diagnoses data, collected globally for billing and epidemiological purposes, represents a valuable source of structured information. However, ICD coding is a challenging task. While numerous previous studies reported promising results in automatic ICD classification, they often describe input data specific model architectures, that are heterogeneously evaluated with different performance metrics and ICD code subsets. This study aims to explore the evaluation and construction of more effective Computer Assisted Coding (CAC) systems using generic approaches, focusing on the use of ICD hierarchy, medication data and a feed forward neural network architecture. Methods: We conduct comprehensive experiments using the MIMIC-III clinical database, mapped to the OMOP data model. Our evaluations encompass various performance metrics, alongside investigations into multitask, hierarchical, and imbalanced learning for neural networks. Results: We introduce a novel metric, RE@R, tailored to the ICD coding task, which offers interpretable insights for healthcare informatics practitioners, aiding them in assessing the quality of assisted coding systems. Our findings highlight that selectively cherry-picking ICD codes diminish retrieval performance without performance improvement over the selected subset. We show that optimizing for metrics such as NDCG and AUPRC outperforms traditional F1-based metrics in ranking performance. We observe that Neural Network training on different ICD levels simultaneously offers minor benefits for ranking and significant runtime gains. However, our models do not derive benefits from hierarchical or class imbalance correction techniques for ICD code retrieval. Conclusion: This study offers valuable insights for researchers and healthcare practitioners interested in developing and evaluating CAC systems. Using a straightforward sequential neural network model, we confirm that medical prescriptions are a rich data source for CAC systems, providing competitive retrieval capabilities for a fraction of the computational load compared to text-based models. Our study underscores the importance of metric selection and challenges existing practices related to ICD code sub-setting for model training and evaluation.
Sleep moderates the effects of exercise on cognition in chronic stroke: secondary analysis of a randomized trial
Authors: Falck Ryan S. , Stein Ryan G. , Davis Jennifer C. , Eng Janice J. , Middleton Laura E. , Hall Peter A. , Liu-Ambrose Teresa
Published: January 2024

Background

Exercise (EX) or cognitive and social enrichment (ENRICH) are two promising strategies for promoting cognitive function post-stroke. Sleep may moderate the effects of these interventions on cogntion, whereby intervention effects may be more robust among individuals suffering from poor sleep. We examined whether sleep moderates the effects of EX or ENRICH on cognitive function in adults with chronic stroke.

Methods

Secondary analysis of a three-arm parallel, single-blinded, randomized clinical trial among community-dwelling adults aged 55+ years with chronic stroke (i.e., ≥12 months since stroke). Participants were randomized to 2x/week EX, ENRICH, or balance and tone control (BAT). At baseline, device-measured sleep duration and efficiency were measured using MotionWatch8 wrist-worn actigraphy; self-reported quality was measured by Pittsburgh Sleep Quality Index (PSQI). Participants were categorized at baseline as having good or poor: 1) device-measured duration; 2) device-measured efficiency; or 3) self-reported quality. The primary cognitive outcome was Alzheimer’s Disease Assessment Scale Plus (ADAS-Cog-Plus) measured at baseline, 6 months (end of intervention), and 12 months (6-month follow-up). Linear mixed models examined if baseline sleep categorizations (i.e., good/poor) moderated the effects of EX or ENRICH on ADAS-Cog-Plus.

Results

We enrolled 120 participants in the trial (EX=34; ENRICH=34; BAT=52). Baseline sleep categorization did not moderate the effect of ENRICH on ADAS-Cog-Plus; however, it moderated the effect of EX. EX participants with poor baseline sleep efficiency (estimated mean difference: −0.48; 95% CI:[−0.85, −0.10];p=0.010) or self-reported sleep quality (estimated mean difference: −0.38; 95% CI:[−0.70, −0.07];p=0.014) had significantly better ADAS-Cog-Plus performance at 6 months compared with BAT participants with poor sleep. There was no effect of EX on ADAS-Cog-Plus for participants with good baseline sleep.

Conclusion

The effects of EX on cognitive function in adults with chronic stroke is moderated by sleep, whereby poor sleepers benefit more.
Neuronal polyunsaturated fatty acids are protective in FTD/ALS
Authors: Giblin A , Cammack AJ , Blomberg N , Mikheenko A , Carcolé M , Coneys R , Zhou L , Mohammed Y , Olivier-Jimenez D , Atilano ML , Niccoli T , Coyne AN , van der Kant R , Lashley T , Giera M , Partridge L , Isaacs AM
Published: January 2024

We report a conserved transcriptomic signature of reduced fatty acid and lipid metabolism gene expression in human post-mortem ALS spinal cord and aDrosophilamodel of the most common genetic cause of FTD/ALS, a repeat expansion inC9orf72. To investigate lipid alterations, we performed lipidomics on C9FTD/ALS iPSC-neurons and post-mortem FTLD brain tissue. This revealed a common and specific reduction in phospholipid species containing polyunsaturated fatty acids (PUFAs). To determine whether this PUFA deficit contributes to neurodegeneration, we fed C9FTD/ALS flies PUFAs, which yielded a modest increase in survival. However, increasing PUFA levels specifically in neurons of theC9orf72flies, by overexpressing fatty acid desaturase enzymes, led to a substantial extension of lifespan. Neuronal overexpression of fatty acid desaturases also suppressed stressor induced neuronal death in C9FTD/ALS patient iPSC-neurons. These data implicate neuronal fatty acid saturation in the pathogenesis of FTD/ALS and suggest that interventions to increase PUFA levels specifically within neurons will be beneficial.
ProteinMPNN Recovers Complex Sequence Properties of Transmembrane β-barrels
Authors: Dolorfino Marissa , Samanta Rituparna , Vorobieva Anastassia
Published: January 2024

Recent deep-learning (DL) protein design methods have been successfully applied to a range of protein design problems, including thede novodesign of novel folds, protein binders, and enzymes. However, DL methods have yet to meet the challenge ofde novomembrane protein (MP) and the design of complex β-sheet folds. We performed a comprehensive benchmark of one DL protein sequence design method, ProteinMPNN, using transmembrane and water-soluble β-barrel folds as a model, and compared the performance of ProteinMPNN to the new membrane-specific Rosetta Franklin2023 energy function. We tested the effect of input backbone refinement on ProteinMPNN performance and found that given refined and well-defined inputs, ProteinMPNN more accurately captures global sequence properties despite complex folding biophysics. It generates more diverse TMB sequences than Franklin2023 in pore-facing positions. In addition, ProteinMPNN generated TMB sequences that passed state-of-the-art in silico filters for experimental validation, suggesting that the model could be used inde novodesign tasks of diverse nanopores for single-molecule sensing and sequencing. Lastly, our results indicate that the low success rate of ProteinMPNN for the design of β-sheet proteins stems from backbone input accuracy rather than software limitations.
Nonnative Fish in the Pearl River Delta: A Comprehensive Study on Their Salinity Adaptability and Potential Distribution Area in Brackish Water
Authors: Luo Du , Yang Dingtian , Li Yuefei , Li Jie
Published: January 2024

After extensive aquaculture, urbanization, and industrial development, the Pearl River Delta (PRD) has undergone profound environmental changes, with biological invasion emerging as a consequential anthropogenic byproduct, carrying significant implications for natural ecosystems, human health, and the economy. Despite these transformations, our understanding of nonnative fish species and their adaptability to the dynamic environmental conditions within the intricate river network of the PRD remains incomplete. To address this, we conducted a systematic survey of nonnative fish species in PRD waters through literature reviews. Then we analyzed the salinity adaptation of these fish, coupled with a spatial examination of salinity distribution, to comprehensively understand the potential invasion mechanisms of exotic fish in the region. Our findings identified 25 nonnative fish species in PRD waters, with three being translocated species within China and the remaining 22 being exotic introductions. Phylogenetically, these fish are broadly distributed among several orders, with Cichliformes, Perciformes, Cypriniformes, and Siluriformes emerging as the predominant orders. Despite most of the nonnative fish being freshwater species and exhibiting species-specific differences in salinity adaptability, they generally demonstrated an average salinity tolerance of 23.74 ppt, allowing them to adjust to brackish water. The diversity of species declined as the relative distance decreased from the upstream of the Pearl River Estuary (PRE) to its mouth in the sea (p < 0.01). Spatial analysis unveiled pronounced heterogeneity in salinity distribution, particularly in the east PRE of the LingDing Bay, featuring a sizable area with brackish water. Notably, under salinity intrusion circumstances, a gap region between salinity levels of 5.0 ppt and 15.0 ppt, spanning 3111.2 km2, emerged as a potential adaptation zone for nonnative fish. By emphasizing salinity as a key factor, our study may contribute to elucidating invasion mechanisms and enhancing the assessment of invasion risks in estuarine environments.
Digital Microbe: A Genome-Informed Data Integration Framework for Collaborative Research on Emerging Model Organisms
Authors: Veseli Iva , DeMers Michelle A. , Cooper Zachary S. , Schechter Matthew S. , Miller Samuel , Weber Laura , Smith Christa B. , Rodriguez Lidimarie T. , Schroer William F. , McIlvin Matthew R. , Lopez Paloma Z. , Saito Makoto , Dyhrman Sonya , Eren A. Murat , Moran Mary Ann , Braakman Rogier
Published: January 2024

The remarkable pace of genomic data generation is rapidly transforming our understanding of life at the micron scale. Yet this data stream also creates challenges for team science. A single microbe can have multiple versions of genome architecture, functional gene annotations, and gene identifiers; additionally, the lack of mechanisms for collating and preserving advances in this knowledge raises barriers to community coalescence around shared datasets. "Digital Microbes" are frameworks for interoperable and reproducible collaborative science through open source, community-curated data packages built on a (pan)genomic foundation. Housed within an integrative software environment, Digital Microbes ensure real-time alignment of research efforts for collaborative teams and facilitate novel scientific insights as new layers of data are added. Here we describe two Digital Microbes: 1) the heterotrophic marine bacterium Ruegeria pomeroyi DSS-3 with >100 transcriptomic datasets from lab and field studies, and 2) the pangenome of the cosmopolitan marine heterotroph Alteromonas containing 339 genomes. Examples demonstrate how an integrated framework collating public (pan)genome-informed data can generate novel and reproducible findings.
Substrate elasticity does not impact on DNA methylation changes during differentiation of pluripotent stem cells
Authors: Mabrouk Mohamed H. Elsafi , Zeevaert Kira , Henneke Ann-Christine , Maaßen Catharina , Wagner Wolfgang
Published: January 2024

Substrate elasticity may direct cell-fate decisions of stem cells. However, it is largely unclear how matrix stiffness impacts on differentiation of induced pluripotent stem cells (iPSCs) and if this is also reflected by epigenetic modifications. We have therefore cultured iPSCs on tissue culture plastic (TCP) and polydimethylsiloxane (PDMS) with different Young’s modulus (0.2 kPa, 16 kPa, or 64 kPa) to investigate the sequel on growth and differentiation towards endoderm, mesoderm, and ectoderm. Immunofluorescence and gene expression of canonical differentiation markers was hardly affected by the substrates. Notably, when we analyzed DNA methylation profiles of undifferentiated iPSCs or after three-lineage differentiation, we did not see any significant differences on the three different PDMS elasticities. Only when we compared DNA methylation profiles on PDMS-substratesversusTCP, we observed epigenetic differences, particularly upon mesodermal differentiation. Taken together, stiffness of PDMS-substrates did not impact on directed differentiation of iPSCs, whereas the moderate epigenetic differences on TCP might also be attributed to other chemical parameters.
Liming pasture soils in the Amazon region promotes low-affinity methane oxidation by type I and II methanotrophs
Authors: de Souza Leandro Fonseca , Nakamura Fernanda Mancini , Kroeger Marie , Alvarez Dasiel Obregon , de Moraes Moacir Tuzzin , Vicente Mariana Gomes , Moreira Marcelo Zacharias , Pellizari Vivian Helena , Tsai Siu Mui , Nüsslein Klaus
Published: January 2024

In the Amazon Forest region, cattle pastures are the main land use subsequent to deforestation. This land-use change affects the soil microbial community and methane fluxes, shifting the soil from a methane sink to a source. Soil physical and chemical attributes are changed due to slash-and-burn processes, including an increased soil pH after forest-to-pasture conversion. Without amendments, the pasture soils can become acidic again resulting in many cases in soil degradation. Liming is a standard management practice to increase soil pH while decreasing Al3+availability. Liming is important to recover these degraded lands and increase soil fertility, but its impact on soil methane cycling in tropical soils is unknown. Here we investigated the role of soil pH on methane uptake under high concentrations of the gas. The top layer of forest (pH 4.1) and adjacent pasture soils (pH 4.8) from the Eastern Amazon were subjected to liming treatment (final pH 5.8) and incubated with ∼10,000 ppm of13CH4for 24 days to label DNA with13C. Soil DNA was evaluated with Stable Isotopic Probing (SIP-DNA), methanotrophic abundance was quantified (pmoAgene), and high throughput sequencing of 16SrRNAwas performed. Liming increased the methane uptake in both forest (∼10%) and pasture (∼25%) soils. MethanotrophsMethylocaldum sp. (type I) and Beijerinckaceae (type II) were identified to actively incorporate carbon from methane in limed pasture soils. In limed forest soils,Nitrososphaeraceae,Lysobactersp., andAcidothermus sp. were identified as13C-enriched taxa. The enrichment of the archaeal familyNitrososphaeraceae, known as ammonia oxidizers, is correlated with an increase of ammonia monooxygenase genes, which code for an enzyme complex with wide substrate specificity that can also perform methane oxidation. In conclusion, liming Amazonian pasture soils not only contributes to the fertility and recovery of degraded areas but also has the potential to improve the oxidation of methane at high concentrations of this gas.
Plant kleptomaniacs: geographic genetic patterns in the amphi-apomicticRubusser.Glandulosi(Rosaceae) reveal complex reticulate evolution of Eurasian brambles
Authors: Sochor Michal , Šarhanová Petra , Duchoslav Martin , Konečná Michaela , Hroneš Michal , Trávníček Bohumil
Published: January 2024

Rubusser.Glandulosirepresents a unique model of geographic parthenogenesis on a homoploid (4x) level. We employed double digest restriction-site associated DNA sequencing (ddRADseq) in 587 individuals of differentRubustaxa and modelling of suitable climate to characterize evolutionary and phylogeographic patterns and shed light on the geographic differentiation of apomicts and sexuals. Six ancestral species were identified that contributed to the contemporary gene pool ofR.ser.Glandulosi. While sexuals were introgressed fromR. dolichocarpusandR. moschusin West Asia and fromR. ulmifoliusagg.,R. canescensandR. incanescensin Europe, apomicts were characterized by alleles ofR.subsect.Rubus. Gene flow between sexuals and apomicts was also detected, as well as occasional hybridization with other taxa. We hypothesize that sexuals survived the last glacial period in several large southern refugia, whereas apomicts were mostly restricted to southern France from whence they quickly recolonized Central and Western Europe. The secondary contact of sexuals and apomicts was probably the principal factor that established geographic parthenogenesis inR.ser.Glandulosi. Sexual populations are not impoverished in genetic diversity along their borderline with apomicts and maladaptive population genetic processes likely did not shape the geographic patterns.

Highlights

Geographic parthenogenesis inRubusser.Glandulosiis caused by secondary contact

Reticulate evolution in Eurasian brambles is more extensive than expected

At least six species contributed to the evolution ofRubusser.Glandulosi

Extinct ancestor’s gene pool is associated with apomixis

Abstract Figure

Graphical abstract
Protein Translation Can Fluidize Bacterial Cytoplasm
Authors: Bera Palash , Wasim Abdul , Bakshi Somenath , Mondal Jagannath
Published: January 2024

The cytoplasm of bacterial cells is densely packed with highly polydisperse macromolecules that exhibit glassy dynamics. Research has revealed that metabolic activities in living cells can counteract the glassy nature of these macromolecules, allowing the cell to maintain critical fluidity for its growth and function. While it has been proposed that the crowded cytoplasm is responsible for this glassy behavior, a detailed explanation for how cellular activity induces fluidization remains elusive. In this study, we introduce and validate a novel hypothesis through computer simulations: protein synthesis in living cells contributes to the metabolism-dependent fluidization of the cytoplasm. The main protein synthesis machinery, ribosomes, frequently shift between fast and slow diffusive states. These states correspond to the independent movement of ribosomal subunits and the actively translating ribosome chains called polysomes, respectively. Our simulations demonstrate that the frequent transitions of the numerous ribosomes, which constitute a significant portion of the cell proteome, greatly enhance the mobility of other macromolecules within the bacterial cytoplasm. Considering that ribosomal protein synthesis is the largest consumer of ATP in growing bacterial cells, the translation process likely serves as the primary mechanism for fluidizing the cytoplasm in metabolically active cells.
DrivR-Base: A Feature Extraction Toolkit For Variant Effect Prediction Model Construction
Authors: Francis Amy , Campbell Colin , Gaunt Tom
Published: January 2024

Motivation

Recent advancements in sequencing technologies have led to the discovery of numerous variants in the human genome. However, understanding their precise roles in diseases remains challenging due to their complex functional mechanisms. Various methodologies have emerged to predict the pathogenic significance of these genetic variants. Typically, these methods employ an integrative approach, leveraging diverse data sources that provide critical insights into genomic function. Despite the abundance of publicly available data sources and databases, the process of navigating, extracting, and pre-processing features for machine learning models can be daunting. Furthermore, researchers often invest substantial effort in feature extraction, only to later discover that these features lack informativeness.

Results

In this paper, we presentDrivR-Base, an innovative resource that efficiently extracts and integrates molecular information (features) for single nucleotide variants from a wide range of databases and tools, including AlphaFold, ENCODE, andVariant Effect Predictor. The resulting features can be used as input for machine learning models designed to predict the pathogenic impact of human genome variants in disease. Moreover, these feature sets have applications beyond this, including haploinsufficiency prediction and the development of drug repurposing tools. We describe the resource’s development, practical applications, and potential for future expansion and enhancement.

Availability and Implementation

DrivR-Basesource code is available athttps://github.com/amyfrancis97/DrivR-Base.
An AI Method for Assessing Coding Consistency in a Large Dataset
Authors: Nelson Stuart J. , Yin Ying , Shao Yijun , Ma Phillip , Tuttle Mark S. , Zeng-Treitler Qing
Published: January 2024

Objective

We developed a method to assess the consistency of the assignment of ICD codes, using coding performed at a United States health system at the time of the transition from ICD-9CM to ICD-10CM.

Methods

Using clusters of equivalent codes derived from the US Centers for Disease Control General Equivalence Mapping (GEM) tables, ICD assignments occurring during the ICD-9CM to ICD-10CM transition were evaluated in EHR data from the US Veterans Administration Central Data Warehouse, using a deep learning model based on 860 covariates. The model was then used to detect abrupt changes across the transition; additionally changes at each VA station were examined.

Results

Many of the 687 most-used code clusters had ICD-10CM assignments differing greatly from that predicted by the GEM from the codes used in ICD-9CM. Notably, the observed transition patterns varied widely across care locations.

Conclusion

Machine learning can model variability across time and across location, enabling an assessment of coding consistency. Expert review is not scalable, deep learning model applied to a large dataset of EHR records provides an approximation of ground truth.
Experiences and observations from a care point for displaced Ukrainians: a community case study in Antwerp, Belgium
Authors: Morreel Stefan , Verhoeven Veronique , Bastians Hilde , Monten Katrien , van Olmen Josefien
Published: January 2024

Background

7307 Ukrainians refugees moved to Antwerp, Belgium during the study period (01/04/2023-31/12/2023). The city’s administration set up three care centers where these people were introduced in the Belgian primary care system, a medical file was created, and acute/preventive/chronic care was delivered. This community case study analyses the organization and contents of care and reflects upon its meaning for the mainstream health care system.

Methods

This is an observational study using routine electronic medical record data to measure uptake of care. For a sample of 200 subjects, a retrospective chart review was conducted in order to extract data from patient records.

Participants

all refugees with a medical file at one of the three participating care centers.

Main Outcomes

For the observational study, 2261 patients were reached (30% of the potential users) and 6450 contacts were studied. The nurses (including midwives) did 4929/6450 (76%) of all consultations, the GPs 1521/6450 (24%). Out of the 4929 nurse consultations, 955 (19%) were followed by another nurse consultation and 866 (18%) by a GP consultation. In the structured case reviews most contacts concerned acute problems (609/1074, 57%). The most prevalent reasons for encounter and diagnoses concerned typical primary care issues. The nurses were able to manage half of the cases independently (327, 55%), referred to the GP in 37% (N=217), and consulted a GP (live, by telephone or a dedicated app) for 8% (48). GPs mostly prescribed drugs, referred to a medical specialist and advised over-the-counter drugs while nurses more often advised over-the-counter drugs (mostly paracetamol, nose sprays and anti-inflammatory drugs), gave non-medical advice or ordered lab tests.

Discussion

The medical care points delivered mostly typical acute primary care in this first phase, with a key role for nurses. These results will inform policy makers on the use of primary care centers for newly arriving patients in times of crisis. A nurse first model seems feasible and efficient, but evaluation of safety and quality of care are needed. Once the acute phase of this crises fades away, questions about the comprehensiveness, continuity, and integration of care for migrants remain relevant.
Finite naturalness and quark-lepton unification
Authors: Fileviez Pérez Pavel , Murgui Clara , Patrone Samuel , Testa Adriano , Wise Mark B.
Published: January 2024

We study the implications of finite naturalness in Pati-Salam models where SU(3)C is embedded in SU(4). For the minimal realization at low scale of quark-lepton unification, which employs the inverse seesaw for neutrino masses, we find that radiative corrections to the Higgs boson mass are at least δmh2/mh2∼O(104). The one-loop contributions to the Higgs mass are suppressed by four powers of the hypercharge gauge coupling. We find that for the vector leptoquarks the naively leading part of the two-loop corrections cancel. We assume the Dirac Yukawa couplings for neutrinos are equal to the up-type quark Yukawa couplings as predicted in the minimal theory for quark-lepton unification. Despite these findings, the two-loop corrections still dominate the finite naturalness bound. We mention a way to relax the lower bound on the vector leptoquark mass and have δmh2/mh2∼O(102).

Published by the American Physical Society
2024
Self-healing unitarity is an optical illusion
Authors: Vidyarthi Archit
Published: January 2024

Among the vast variety of proposals put forward by the community to resolve tree-level unitarity violations in Higgs inflation models, there exists the concept of self-healing. It heals the theory from supposed tree-level violations for elastic scattering processes by summing over successive vacuum polarization loop corrections. In this work, we examine this technique to check whether unitarity is indeed restored and find that there exist underlying constraints in self-healing unitarity that pose the same perturbative unitarity bounds that it was expected to heal.

Published by the American Physical Society
2024
Exact Operator Map from Strong Coupling to Free Fields: Beyond Seiberg-Witten Theory
Authors: Bhargava Chinmaya , Buican Matthew , Jiang Hongliang
Published: January 2024

In quantum field theory above two spacetime dimensions, one is usually only able to construct exact operator maps from UV to IR of strongly coupled renormalization group flows for the most symmetry-protected observables. Famous examples include maps of chiral rings in 4D N=2 supersymmetry. In this Letter, we construct the first nonperturbative UV-IR map for less protected operators: starting from a particularly “simple” UV strongly coupled non-Lagrangian 4D N=2 quantum field theory, we show that a universal nonchiral quarter–Bogomol’nyi-Prasad-Sommerfield ring can be mapped exactly and bijectively to the IR. In particular, strongly coupled UV dynamics governing infinitely many null states manifest in the IR via Fermi statistics of free gauginos. Using the concept of arc space, this bijection allows us to compute the exact UV Macdonald index in the IR.

Published by the American Physical Society
2024
Nonmonotonic dynamics of nuclear-to-cellular volume ratio under osmotic shocks
Authors: Sui Jize
Published: January 2024

How the nuclear size dynamically scales with the cellular size during osmotic shock treatments remains controversial. We develop a dynamic model by incorporating the typical interactions between polydisperse biomolecules and the mechanical elasticity of the cytoplasm and nucleoplasm to investigate this long-standing critical issue. We find the nontrivial phenomenon that the nuclear-to-cellular volume ratio can vary nonmonotonically with time, instead of maintaining a constant as usually known, under the osmotic shocks. Combining simulations and analytical argument, we validly account for this nonmonotonic dynamic behavior, and identify its essential regulatory mechanism to be the collaboration of the excluded volume interactions between the polydisperse biomolecules and the spatial constraint from the nuclear envelope on the macromolecule diffusions. Our results agree well with the published experiments for cellular and nuclear size controls of the protoplasts. Our model offers energetic insight in characterizing biology-associated dynamic processes such as macromolecular crowding, and biophase separation occurring in cytoplasm and nucleoplasm.

Published by the American Physical Society
2024
Goal setting in mental health: a scoping review to inform occupational therapy practice
Authors: Okita Yuho , Kaneko Takao , Imai Hiroaki , Nair Monique , Tomori Kounosuke
Published: January 2024

Purpose

Goal setting is a crucial aspect of client-centered practice in occupational therapy (OT) for mental health conditions. However, it remains to be seen how goal-setting has been delivered in mental health, particularly the OT process. The purpose of this scoping review was to explore the nature and extent of goal setting delivered in mental health and informed OT practice.

Design/methodology/approach

The authors followed the guidelines of Arksey and O’Malley (2005) and searched three databases using key search terms: “mental disorder,” “goal setting,” and “occupational therapy” and their synonyms.

Findings

After excluding duplicate records, the authors initially screened 883 records and resulted in 20 records in total after the screening process. Most of the identified articles used goal-setting delivered by both a health professional and a client (n = 14), and focused on people with schizophrenia or schizoaffective disorder (n = 13), but three interventions were delivered by occupational therapists. Further research needs on goal-setting in mental health OT, exploring the reliability and validity of different goal-setting strategies and investigating the effectiveness of goal-setting for promoting behavior change and client engagement across various mental health conditions and settings.

Research limitations/implications

The scoping review has some limitations, such as not investigating the validity and reliability of goal-setting strategies identified, and excluding conference papers and non-English articles.

Originality/value

This scoping review presents a mapping of how goal-setting has been delivered in mental health and informed OT practice. The findings suggest limited research in OT and highlight the need for more studies to address the evidence gap in individualized client-centered OT.
Does internal cash flow-external financing sensitivity react to economic policy uncertainty and geopolitical risk? Evidence from Saudi Arabia
Authors: Guizani Moncef
Published: January 2024

Purpose

This study aims to investigate the influence of economic policy uncertainty (EPU) and geopolitical risk (GPR) on the relationship between internal cash flow and external financing in an emerging market, Saudi Arabia. It also examines the role of asset tangibility and financial crisis in establishing this relationship.

Design/methodology/approach

The sample was taken from non-financial sector companies listed on the Saudi Stock Exchange between 2002 and 2019. The data were analyzed using panel data regression analysis, including ordinary least squares and fixed effects model. The author addresses potential endogeneity through the generalized method of moments.

Findings

This study found that both EPU and GPR reduce the sensitivity of external financing to internal cash flow. This implies that firms depend more on internally generated funds during periods of increased EPU and GPR. Besides, this study found that the influence of EPU and GPR on the sensitivity of external financing to internal cash flow is more (less) negative for more tangible firms (during the financial crisis period). This result implies that Saudi firms boasting a higher level of tangibility are more flexible when it comes to seeking external financing. However, the presence of uncertainty during the crisis period makes the external financing costly, and therefore, firms will be less likely to raise funds from external sources.

Practical implications

This study has important implications for managers, policymakers and regulators. First, the paper findings provide insights for corporate decision-makers in helping them to focus on internal funds to finance their investment during uncertain times. Second, the findings help managers to understand the role of asset tangibility in raising external funding when firms face financial constraints due to uncertainty. Third, this study also helps corporates to focus on internal funds to finance their investment during the crisis period because EPU and GPR increase the cost of external finance. Finally, the results provide guidelines for policymakers and regulators to make appropriate policy measures to increase the easy availability of external finance during periods of increased EPU and GPR.

Originality/value

This paper is the first to shed light on the impact of internal funds on external financing while paying close attention to the role of EPU and GPR.
Polarization and reliability of news sources in Wikipedia
Authors: Yang Puyu , Colavizza Giovanni
Published: January 2024

Purpose

Wikipedia's inclusive editorial policy permits unrestricted participation, enabling individuals to contribute and disseminate their expertise while drawing upon a multitude of external sources. News media outlets constitute nearly one-third of all citations within Wikipedia. However, embracing such a radically open approach also poses the challenge of the potential introduction of biased content or viewpoints into Wikipedia. The authors conduct an investigation into the integrity of knowledge within Wikipedia, focusing on the dimensions of source political polarization and trustworthiness. Specifically, the authors delve into the conceivable presence of political polarization within the news media citations on Wikipedia, identify the factors that may influence such polarization within the Wikipedia ecosystem and scrutinize the correlation between political polarization in news media sources and the factual reliability of Wikipedia's content.

Design/methodology/approach

The authors conduct a descriptive and regression analysis, relying on Wikipedia Citations, a large-scale open dataset of nearly 30 million citations from English Wikipedia. Additionally, this dataset has been augmented with information obtained from the Media Bias Monitor (MBM) and the Media Bias Fact Check (MBFC).

Findings

The authors find a moderate yet significant liberal bias in the choice of news media sources across Wikipedia. Furthermore, the authors show that this effect persists when accounting for the factual reliability of the news media.

Originality/value

The results contribute to Wikipedia’s knowledge integrity agenda in suggesting that a systematic effort would help to better map potential biases in Wikipedia and find means to strengthen its neutral point of view policy.
Does individuals' age matter? A comparative study of generation X and generation Y on green housing purchase intention
Authors: Kumar Jitender , Rani Vinki , Rani Garima , Rani Manju
Published: January 2024

Purpose

This comparative research examines the factors influencing individuals' purchase intention toward green housing. By examining these factors, this study provides fruitful insights into the purchase intentions and behaviors for greenhouses among individuals of different age groups in India.

Design/methodology/approach

Data were gathered from Generation (Gen) X (313) and Generation (Gen) Y (297) using self-administered questionnaires. The “partial least squares structural equation modeling” was used to test the hypotheses.

Findings

The outcome shows that attitude and green trust substantially impact the green purchase intention of Gen X and Y. More specifically, environmental knowledge insignificantly influences the green purchase intention of Gen X while significantly influencing Gen Y. However, perceived risk insignificantly affects the purchase intention of both Gen X and Y. Consequently, green purchase intention substantially impacts the green purchase behavior in both studies.

Research limitations/implications

This research focuses primarily on India; future research may be conducted in different geographical contexts. This study could also be extended to all age groups individuals.

Practical implications

The findings of this article facilitate policymakers, real estate developers and professional bodies in formulating strategies for sustainable nations in the future.

Originality/value

The current article is the initial empirical attempt to examine the home-buying decisions of individuals in India. Moreover, the role of Generation X and Generation Y in green housing purchase decisions will provide fruitful insights into how different age groups impact the decision-making process of green housing.
Virtual influencer marketing: a study of millennials and gen Z consumer behaviour
Authors: Angmo Padma , Mahajan Rachna
Published: January 2024

Purpose

Virtual influencers (VIs), who are fictional characters, have gained popularity in recent years, particularly among Generation Z and millennials. With the hype surrounding VIs, more research is required. Thus, this study aims to examine how Gen Z members and millennials react to VIs used for marketing purposes.

Design/methodology/approach

This study follows an exploratory approach. The data were collected from 29 participants (14 male and 15 female) through two focus groups and semi-structured interviews.

Findings

The authors found that opinions about VIs were mixed, and two main themes emerged from the study: (1) challenges and potential and (2) decision-making and psychological aspects.

Originality/value

This study broadens the paradigm for analysing the efficacy of VIs. This emerging topic is of relevance for the marketing sector as well as for transdisciplinary research and practice.
Modelling animal social networks: New solutions and future directions
Authors: Farine Damien R.
Published: January 2024

Research Highlight: Ross, C. T., McElreath, R., & Redhead, D. (2023). Modelling animal network data in R using STRAND. Journal of Animal Ecology. https://doi.org/10.1111/1365‐2656.14021. One of the most important insights in ecology over the past decade has been that the social connections among animals affect a wide range of ecological and evolutionary processes. However, despite over 20 years of study effort on this topic, generating knowledge from data on social associations and interactions remains fraught with problems. Redhead et al. present an R package—STRAND—that extends the current animal social network analysis toolbox in two ways. First, they provide a simple R interfaces to implement generative network models, which are an alternative to regression approaches that draw inference by simulating the data‐generating process. Second, they implement these models in a Bayesian framework, allowing uncertainty in the observation process to be carried through to hypothesis testing. STRAND therefore fills an important gap for hypothesis testing using network data. However, major challenges remain, and while STRAND represents an important advance, generating robust results continues to require careful study design, considerations in terms of statistical methods and a plurality of approaches.
Life history scaling in a tropical forest
Authors: Grady John M. , Read Quentin D. , Record Sydne , Rüger Nadja , Zarnetske Phoebe L. , Dell Anthony I. , Hubbell Stephen P. , Michaletz Sean T. , Enquist Brian J.
Published: January 2024

Both tree size and life history variation drive forest structure and dynamics, but little is known about how life history frequency changes with size. We used a scaling framework to quantify ontogenetic size variation and assessed patterns of abundance, richness, productivity and light interception across life history strategies from >114,000 trees in a primary, neotropical forest. We classified trees along two life history axes: a fast–slow axis characterized by a growth–survival trade‐off, and a stature–recruitment axis with tall, long‐lived pioneers at one end and short, short‐lived recruiters at the other.

Relative abundance, richness, productivity and light interception follow an approximate power law, systematically shifting over an order of magnitude with tree size. Slow saplings dominate the understorey, but slow trees decline to parity with rapidly growing fast and long‐lived pioneer species in the canopy.

Like the community as a whole, slow species are the closest to obeying the energy equivalence rule (EER)—with equal productivity per size class—but other life histories strongly increase productivity with tree size. Productivity is fuelled by resources, and the scaling of light interception corresponds to the scaling of productivity across life history strategies, with slow and all species near solar energy equivalence. This points towards a resource‐use corollary to the EER: the resource equivalence rule.

Fitness trade‐offs associated with tree size and life history may promote coexistence in tropical forests by limiting niche overlap and reducing fitness differences.

Synthesis. Tree life history strategies describe the different ways trees grow, survive and recruit in the understorey. We show that the proportion of trees with a pioneer life history strategy increases steadily with tree size, as pioneers become relatively more abundant, productive, diverse and capture more resources towards the canopy. Fitness trade‐offs associated with size and life history strategy offer a mechanism for coexistence in tropical forests.
Maternal chronic hypertension in women veterans
Authors: Harding Ceshae C. , Goldstein Karen M. , Goldstein Sarah A. , Wheeler Sarahn M. , Mitchell Nia S. , Copeland Laurel A.
Published: January 2024

Objective

To describe the prevalence of maternal chronic hypertension (MCH), assess how frequently blood pressure is controlled before pregnancy among those with MCH, and explore management practices for antihypertensive medications (AHM) during the pre‐pregnancy and pregnancy periods.

Data Sources, Study Setting, and Study Design

We conducted a descriptive observational study using data abstracted from the Veterans Health Administration (VA) inclusive of approximately 11 million Veterans utilizing the VA in fiscal years 2010–2019.

Data Collection/Extraction Methods

Veterans aged 18–50 were included if they had a diagnosis of chronic hypertension before a documented pregnancy in the VA EMR. We identified chronic hypertension and pregnancy with diagnosis codes and defined uncontrolled blood pressure as ≥140/90 mm Hg on at least one measurement in the year before pregnancy. Sensitivity models were conducted for individuals with at least two blood pressure measurements in the year prior to pregnancy. Multivariable logistic regression explored the association of covariates with recommended and non‐recommended AHMs received 0–6 months before pregnancy and during pregnancy.

Principal Findings

In total, 8% (3767/46,178) of Veterans with a documented pregnancy in VA data had MCH. Among 2750 with MCH meeting inclusion criteria, 60% (n = 1626) had uncontrolled blood pressure on at least one BP reading and 31% (n = 846) had uncontrolled blood pressure on at least two BP readings in the year before pregnancy. For medications, 16% (n = 437) received a non‐recommended AHM during pregnancy. Chronic kidney disease (OR = 3.2; 1.6–6.4) and diabetes (OR = 2.3; 1.7–3.0) were most strongly associated with use of a non‐recommended AHM during pregnancy.

Conclusions

Interventions are needed to decrease the prevalence of MCH, improve preconception blood pressure control, and ensure optimal pharmacologic antihypertensive management among Veterans of childbearing potential.
Optical nanosensors based on noble metal nanoclusters for detecting food contaminants: A review
Authors: Pang Lidong , Pi Xiaowen , Zhao Qianyu , Man Chaoxin , Yang Xinyan , Jiang Yujun
Published: January 2024

Food contaminants present a significant threat to public health. In response to escalating global concerns regarding food safety, there is a growing demand for straightforward, rapid, and sensitive detection technologies. Noble metal nanoclusters (NMNCs) have garnered considerable attention due to their superior attributes compared to other optical materials. These attributes include high catalytic activity, excellent biocompatibility, and outstanding photoluminescence properties. These features render NMNCs promising candidates for crafting nanosensors for food contaminant detection, offering the potential for the development of uncomplicated, swift, sensitive, user‐friendly, and cost‐effective detection approaches. This review investigates optical nanosensors based on NMNCs, including the synthesis methodologies of NMNCs, sensing strategies, and their applications in detecting food contaminants. Furthermore, it involves a comparative assessment of the applications of NMNCs in optical sensing and their performance. Ultimately, this paper imparts fresh perspectives on the forthcoming challenges. Hitherto, optical (particularly fluorescent) nanosensors founded on NMNCs have demonstrated exceptional sensing capabilities in the realm of food contaminant detection. To enhance sensing performance, future research should prioritize atomically precise NMNCs synthesis, augmentation of catalytic activity and optical properties, development of high‐throughput and multimode sensing, integration of NMNCs with microfluidic devices, and the optimization of NMNCs storage, shelf life, and transportation conditions.
A cost‐effective blood DNA methylation‐based age estimation method in domestic cats, Tsushima leopard cats (Prionailurus bengalensis euptilurus) and Panthera species, using targeted bisulphite sequencing and machine learning models
Authors: Qi Huiyuan , Lim Qi Luan , Kinoshita Kodzue , Nakajima Nobuyoshi , Inoue‐Murayama Miho
Published: January 2024

Individual age can be used to design more efficient and suitable management plans in both in situ and ex situ conservation programmes for targeted wildlife species. DNA methylation is a promising marker of epigenetic ageing that can accurately estimate age from small amounts of biological material, which can be collected in a minimally invasive manner. In this study, we sequenced five targeted genetic regions and used 8–23 selected CpG sites to build age estimation models using machine learning methods at only about $3–7 per sample. Blood samples of seven Felidae species were used, ranging from small to big, and domestic to endangered species: domestic cats (Felis catus, 139 samples), Tsushima leopard cats (Prionailurus bengalensis euptilurus, 84 samples) and five Panthera species (96 samples). The models achieved satisfactory accuracy, with the mean absolute error of the most accurate models recorded at 1.966, 1.348 and 1.552 years in domestic cats, Tsushima leopard cats and Panthera spp. respectively. We developed the models in domestic cats and Tsushima leopard cats, which were applicable to individuals regardless of health conditions; therefore, these models are applicable to samples collected from individuals with diverse characteristics, which is often the case in conservation. We also showed the possibility of developing universal age estimation models for the five Panthera spp. using only two of the five genetic regions. We do not recommend building a common age estimation model for all the target species using our markers, because of the degraded performance of models that included all species.