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Performance of biological food processing interfaces: Perspectives on the science of mollusc radula.Biointerphases May 2024The Mollusca comprises a diverse range of organisms, with the class Gastropoda alone boasting approximately 80 000 extant species. Their adaptability across various... (Review)
Review
The Mollusca comprises a diverse range of organisms, with the class Gastropoda alone boasting approximately 80 000 extant species. Their adaptability across various habitats is facilitated by the evolution of the radula, a key structure for food acquisition. The radula's composition and mechanical properties, including its chitinous membrane, teeth, and supporting structures, enable efficient food gathering and processing. Through adaptive tooth morphology and composition, an interplay between radular components is facilitated, which results in collective effects to withstand forces encountered during feeding and reduce structural failure, with the broad range of variations reflecting ecological niches. Furthermore, teeth consist of composite materials with sometimes high contents of iron, calcium, or silicon to reduce wear. During interaction with the food, the radula performs complex three-dimensional motions, challenging to document. Here, we provide a review on the morphology, the mechanical properties, the composition, and various other parameters that contribute to radular performance. Due to, e.g., the smallness of these structures, there are, however, limitations to radular research. However, numerical simulations and physical models tested on substrates offer avenues for further understanding radular function and performance during feeding. These studies not only advance our knowledge of molluscan biology and ecology but also provide inspirations for biomimetic design and further advances in materials engineering.
Topics: Animals; Mollusca; Feeding Behavior; Biomechanical Phenomena
PubMed: 38940493
DOI: 10.1116/6.0003672 -
Health and Social Care Delivery Research Jun 2024People with learning disabilities are living longer. Despite government policy to encourage people to lead supported lives in their community, family carers often...
BACKGROUND
People with learning disabilities are living longer. Despite government policy to encourage people to lead supported lives in their community, family carers often maintain support due to dissatisfaction with services. This can lead to people moving from the family home in a crisis.
OBJECTIVES
(1) Find out what is known about health needs and resources for older people with learning disabilities (aged ≥ 40 years); (2) identify exemplars of good services for older people with learning disabilities; (3) explore service exemplars through ethnographic case studies; (4) evaluate support for older people with learning disabilities and their families through co-producing and testing future planning tools and (5) co-produce recommendations and resources.
DESIGN AND METHODS
Work package 1 rapid scoping reviews - three reviews focused on the health and social care needs of older people with learning disabilities and 'behaviours that challenge others', and family carers, and the co-ordination of support for this group. Work package 2 scoping and mapping exemplars of good practice - analysis of published service standards to assess excellence criteria, by mapping services, interviews ( = 30), survey ( = 9) and informal discussion with commissioners. Work package 3 ethnography of case studies of exemplar provision; independent supported living ( = 4); residential/nursing home ( = 2); day activities ( = 1), Shared Lives ( = 2). Fieldwork (20 days per model), interviews ( = 77) with older people with learning disabilities, family carers, support staff and commissioners. Work package 4 - co-producing and testing resources for older people with learning disabilities and their families involved interviews and focus groups with 36 people with learning disabilities, parents, and siblings, and experience-based co-design with 11 participants. Eight families evaluated the resources. Work package 5 - three stakeholder workshops co-produced service recommendations.
FINDINGS
The reviews confirmed an inadequate evidence base concerning the experiences and support of family carers and older people with learning disabilities and 'behaviours that challenge others'. Criteria of excellence were produced, and a shortlist of 15 services was identified for consideration in work package 3. The ethnographic work found that environmental, organisational and social factors were important, including supporting independence and choice about who people live with, matching staff to people, consistent relationships and adapting to ageing. Practices of institutionalisation were observed. In work package 4, we found that families were worried about the future and unsupported to explore options. 'Planning Ahead' cards and a booklet to record discussions were produced, and the evaluation was positively rated. Finally, formative discussion informed recommendations. Outputs include training packages, a carers' forum, a film, a podcast and academic papers.
CONCLUSIONS
There is little focus on older people with learning disabilities and family carers. Services vary in their approach to planning for older-age support. Families are unsupported to plan, leaving people without choice. 'Behaviours that challenge others' was found to be unhelpful terminology. Recommendations: A new strategy is recommended for older people with learning disabilities and family carers that encompasses commissioning practices, professional input and peer learning, proactive support in ageing well and excellent service design.
LIMITATIONS
The COVID-19 pandemic created recruitment challenges. Reliance on providers for recruitment resulted in a lack of diversity in work package 3. Families' plans, and therefore change, may be frustrated by insufficient service resources.
FUTURE WORK
Given the lack of focus in this area, there is a range of future work to consider: experiences of older people with learning disabilities from diverse ethnic backgrounds; supporting people to age and die 'in place'; best practice regarding designing/commissioning services, including housing; the role of social workers; access to nature; accessing mainstream support; and evaluation of the 'Planning Ahead' cards.
TRIAL REGISTRATION
This trial is registered as ISRCTN74264887.
FUNDING
This award was funded by the National Institute for Health and Care Research (NIHR) Health and Social Care Delivery Research programme (NIHR award ref: NIHR129491) and is published in full in ; Vol. 12, No. 16. See the NIHR Funding and Awards website for further award information.
Topics: Humans; Caregivers; Aged; Learning Disabilities; Female; Male; Middle Aged; Adult; Social Support; Qualitative Research; Aged, 80 and over; Anthropology, Cultural; Health Services Needs and Demand
PubMed: 38940476
DOI: 10.3310/MTHW2644 -
Bioinformatics (Oxford, England) Jun 2024The current paradigm of deep learning models for the joint representation of molecules and text primarily relies on 1D or 2D molecular formats, neglecting significant 3D...
MOTIVATION
The current paradigm of deep learning models for the joint representation of molecules and text primarily relies on 1D or 2D molecular formats, neglecting significant 3D structural information that offers valuable physical insight. This narrow focus inhibits the models' versatility and adaptability across a wide range of modalities. Conversely, the limited research focusing on explicit 3D representation tends to overlook textual data within the biomedical domain.
RESULTS
We present a unified pre-trained language model, MolLM, that concurrently captures 2D and 3D molecular information alongside biomedical text. MolLM consists of a text Transformer encoder and a molecular Transformer encoder, designed to encode both 2D and 3D molecular structures. To support MolLM's self-supervised pre-training, we constructed 160K molecule-text pairings. Employing contrastive learning as a supervisory signal for learning, MolLM demonstrates robust molecular representation capabilities across four downstream tasks, including cross-modal molecule and text matching, property prediction, captioning, and text-prompted molecular editing. Through ablation, we demonstrate that the inclusion of explicit 3D representations improves performance in these downstream tasks.
AVAILABILITY AND IMPLEMENTATION
Our code, data, pre-trained model weights, and examples of using our model are all available at https://github.com/gersteinlab/MolLM. In particular, we provide Jupyter Notebooks offering step-by-step guidance on how to use MolLM to extract embeddings for both molecules and text.
Topics: Natural Language Processing; Deep Learning; Computational Biology
PubMed: 38940177
DOI: 10.1093/bioinformatics/btae260 -
Bioinformatics (Oxford, England) Jun 2024High-throughput RNA sequencing has become indispensable for decoding gene activities, yet the challenge of reconstructing full-length transcripts persists. Traditional...
MOTIVATION
High-throughput RNA sequencing has become indispensable for decoding gene activities, yet the challenge of reconstructing full-length transcripts persists. Traditional single-sample assemblers frequently produce fragmented transcripts, especially in single-cell RNA-seq data. While algorithms designed for assembling multiple samples exist, they encounter various limitations.
RESULTS
We present Aletsch, a new assembler for multiple bulk or single-cell RNA-seq samples. Aletsch incorporates several algorithmic innovations, including a "bridging" system that can effectively integrate multiple samples to restore missed junctions in individual samples, and a new graph-decomposition algorithm that leverages "supporting" information across multiple samples to guide the decomposition of complex vertices. A standout feature of Aletsch is its application of a random forest model with 50 well-designed features for scoring transcripts. We demonstrate its robust adaptability across different chromosomes, datasets, and species. Our experiments, conducted on RNA-seq data from several protocols, firmly demonstrate Aletsch's significant outperformance over existing meta-assemblers. As an example, when measured with the partial area under the precision-recall curve (pAUC, constrained by precision), Aletsch surpasses the leading assemblers TransMeta by 22.9%-62.1% and PsiCLASS by 23.0%-175.5% on human datasets.
AVAILABILITY AND IMPLEMENTATION
Aletsch is freely available at https://github.com/Shao-Group/aletsch. Scripts that reproduce the experimental results of this manuscript is available at https://github.com/Shao-Group/aletsch-test.
Topics: Algorithms; RNA-Seq; Software; Humans; High-Throughput Nucleotide Sequencing; Sequence Analysis, RNA
PubMed: 38940157
DOI: 10.1093/bioinformatics/btae215 -
Bioinformatics (Oxford, England) Jun 2024Metastasis formation is a hallmark of cancer lethality. Yet, metastases are generally unobservable during their early stages of dissemination and spread to distant...
MOTIVATION
Metastasis formation is a hallmark of cancer lethality. Yet, metastases are generally unobservable during their early stages of dissemination and spread to distant organs. Genomic datasets of matched primary tumors and metastases may offer insights into the underpinnings and the dynamics of metastasis formation.
RESULTS
We present metMHN, a cancer progression model designed to deduce the joint progression of primary tumors and metastases using cross-sectional cancer genomics data. The model elucidates the statistical dependencies among genomic events, the formation of metastasis, and the clinical emergence of both primary tumors and their metastatic counterparts. metMHN enables the chronological reconstruction of mutational sequences and facilitates estimation of the timing of metastatic seeding. In a study of nearly 5000 lung adenocarcinomas, metMHN pinpointed TP53 and EGFR as mediators of metastasis formation. Furthermore, the study revealed that post-seeding adaptation is predominantly influenced by frequent copy number alterations.
AVAILABILITY AND IMPLEMENTATION
All datasets and code are available on GitHub at https://github.com/cbg-ethz/metMHN.
Topics: Humans; Genomics; Neoplasm Metastasis; Lung Neoplasms; Disease Progression; Neoplasms; Adenocarcinoma of Lung; Mutation; Tumor Suppressor Protein p53; Cross-Sectional Studies; ErbB Receptors
PubMed: 38940126
DOI: 10.1093/bioinformatics/btae250 -
Journal of Child & Adolescent Trauma Jun 2024The majority of children with traumatic experiences who seek treatment have had multiple traumatic experiences resulting in complex trauma. Complex trauma is associated...
The majority of children with traumatic experiences who seek treatment have had multiple traumatic experiences resulting in complex trauma. Complex trauma is associated with multiple adverse outcomes for children and caregivers. Treating complex trauma has the potential to significantly improve child mental and physical health, caregiver mental health, and reduce family conflict. One promising approach is the Attachment, Regulation, and Competency (ARC) Framework. Yet, there is limited research on the effectiveness of interventions using the ARC framework. The purpose of this rapid scoping review was to assess the state of the evidence of ARC and ARC adaptations. The databases APA PsycINFO, Social Work Abstracts, and Applied Social Sciences Index & Abstracts were searched. The search was limited to articles involving interventions using the ARC framework and written in English. To be as comprehensive as possible quantitative, qualitative and mixed methods designs were included and there was no date restriction. Ten articles were included in the review. Results show all studies were quasi experimental, half did not include a comparison group, and interventions using the ARC framework varied in duration (12-180 sessions), setting (outpatient therapy, residential treatment, community outreach and school-based intervention) and age (birth-22). Findings indicate the ARC framework shows promise in reducing children's trauma related symptoms including post-traumatic stress disorder (PTSD), externalizing, and internalizing problems, and improving trauma sensitive classroom environments. Additional outcomes included increased permanent placements, reduced caregiver stress and increased caregiver functioning. Future research is needed utilizing randomized controlled trials to establish efficacy of this promising intervention.
PubMed: 38938964
DOI: 10.1007/s40653-023-00575-5 -
Journal of Child & Adolescent Trauma Jun 2024This study explored the impact of a sensory processing assessment, recommendations and feedback process on the functioning at school and after-hours environments of...
UNLABELLED
This study explored the impact of a sensory processing assessment, recommendations and feedback process on the functioning at school and after-hours environments of children who had been traumatised by abuse. A mixed methods design (Schoonenboom & Johnson, 2017) was utilized incorporating pre (12 months prior) and post (four to eight months after the report) repeated child focused measure, alongside thematic analysis of participants qualitative survey feedback. The methodology included two stages: firstly, an occupational therapy assessment of young people referred by clinicians for a sensory processing assessment and secondly, an evaluation was conducted of the impact of occupational therapy on the young person's behaviour and their carers. The study found significant improvement in family life and relationships as well as a reduction in impairment as evidenced by decreases in HoNOSCA scores across problems with family life and relationships, non-accidental self-injury, problems with emotional and related symptoms, poor school attendance and on the social subscale. These findings were supported by clinician participant reports. A sensory processing assessment provided young people, their carers and teachers with information which contributed to environmental adaptations. These environmental adaptations were associated with improved functioning and behaviour of young people impacted by child abuse. It is recommended future research attempt to replicate and extend our understanding of how sensory processing assessments and interventions can increase children's wellbeing.
SUPPLEMENTARY INFORMATION
The online version contains supplementary material available at 10.1007/s40653-023-00607-0.
PubMed: 38938944
DOI: 10.1007/s40653-023-00607-0 -
IET Nanobiotechnology 2024The desire to reduce reliance on oil resources arises from the concerns about carbon footprint and nonrenewability. Conversely, the global presence of over 100 million...
The desire to reduce reliance on oil resources arises from the concerns about carbon footprint and nonrenewability. Conversely, the global presence of over 100 million palm trees poses a significant challenge due to the substantial amount of biowaste generated annually. Additionally, the use of nanocellulose (NC) as a cost-effective material is steadily gaining recognition for its growing adaptability over time. The main goal of this study is to biosynthesized NC from Iraqi date palm leaves waste with low-concentration acid-alkali treatment. The date palm leaves waste yields 20 g of NC from 100 g of leaves before acid hydrolysis treatment. The chemical components of biosynthesized NC were 47.90%, 26.78%, and 24.67% for -cellulose, hemicellulose, and lignin, respectively. In order to study their properties, NC from raw date palm leaves was studied by microscopic techniques such as scanning electron microscopy (SEM), energy dispersive X-ray (EDX) spectroscopy, and atomic force microscope (AFM). SEM results revealed rod-like structured NC as well as combined long-fine fibrous structures rather than compacted bundles with sizes ranging between 31 and 74 nm. With EDX, all spectra exhibit the peaks of carbon and oxygen as the main elements with 63.8% and 10.44%, respectively, in their compositions, which relate to the typical composition of cellulose. The 3D image of AFM NC with a tapping mode presented a highly uniform distribution of NC with a size of ∼15 nm. The statistical roughness analysis shows that the obtained roughness average is 7.20 nm with the root-mean-square roughness value of 21.56 nm, which corresponded relatively with the micrographs of SEM. The results of this study demonstrate the promise of using date palm waste as raw material to produce NC as green nanocomposite from biodegradable nanomaterials for water purification and sustained drug delivery for biomedical applications. In this regard and because of the insufficient reports about the extraction of NC from palm tree leaves waste, the objective of this study was designed to fabricate NC biologically from fibers sourced from the waste of Iraqi date palm leaves that left in agricultural lands or burned, which can be an ecological and health problem as a bionanocomposites in the medical and industrial field and as alternative resources of wood materials.
Topics: Cellulose; Phoeniceae; Plant Leaves; Nanostructures
PubMed: 38938743
DOI: 10.1049/2024/7867463 -
Kidney Medicine Jul 2024In the wake of the coronavirus disease 2019 (COVID-19) pandemic, the United States federal government expanded originating telemedicine sites to include outpatient...
RATIONALE & OBJECTIVE
In the wake of the coronavirus disease 2019 (COVID-19) pandemic, the United States federal government expanded originating telemedicine sites to include outpatient dialysis units. For the first time, nephrology practitioners across the United States could replace face-to-face visits with telemedicine for patients receiving in-center hemodialysis. This study describes patients' perspectives on the use of telemedicine during in-center hemodialysis.
STUDY DESIGN
A qualitative study.
SETTING & PARTICIPANTS
Thirty-two patients from underserved populations (older, less educated, unemployed, persons of color) receiving in-center hemodialysis who used telemedicine with their nephrologist during the COVID-19 pandemic.
ANALYTICAL APPROACH
Telephone semistructured interviews were conducted in English or Spanish. Transcripts were thematically analyzed.
RESULTS
We identified 6 themes with subthemes: adapting to telemedicine (gaining familiarity and confidence, overcoming and resolving technical difficulties, and relying on staff for communication); ensuring availability of the physician (enabling an immediate response to urgent medical needs, providing peace of mind, addressing patient needs adequately, and enhanced attention and contact from physicians); safeguarding against infection (limiting COVID-19 exposures and decreasing use); straining communication and physical interactions (loss of personalized touch, limited physical examination, and unable to reapproach physicians about forgotten issues); maintaining privacy (enhancing privacy and projecting voice enables others to hear); and supporting confidence in telemedicine (requiring established rapport with physicians, clinical stabilty of health, and ability to have in-person visits when necessary).
LIMITATIONS
Interviews were conducted later in the pandemic when some nephrology care providers were using telemedicine infrequently.
CONCLUSIONS
Patients receiving in-center hemodialysis adapted to telemedicine visits by their nephrologists in the context of the COVID-19 pandemic and observed its benefits. However, further considerations regarding communication, privacy, and physical assessments are necessary. Integrating telemedicine into future in-center hemodialysis care using a hybrid approach could potentially build trust, optimize communication, and augment care.
PubMed: 38938646
DOI: 10.1016/j.xkme.2024.100848 -
Journal of Experimental Botany Jun 2024The flowering time (FT), which determines when fruits or seeds can be harvested, is subject to phenotypic plasticity, i.e. the ability of a genotype to display different...
The flowering time (FT), which determines when fruits or seeds can be harvested, is subject to phenotypic plasticity, i.e. the ability of a genotype to display different phenotypes in response to environmental variations. Here, we investigated how the environment affects the genetic architecture of FT in cultivated strawberry (Fragaria ×ananassa) and modifies its QTL effects. To this end, we used a bi-parental segregating population grown for two years at widely divergent latitudes (5 European countries) and combined climatic variables with genomic data (Affymetrix® SNP array). Examination, using different phenological models, of the response of FT to photoperiod, temperature and global radiation, indicated that temperature is the main driver of FT in strawberry. We next characterized in the segregating population the phenotypic plasticity of FT by using three statistical approaches that generated plasticity parameters including reaction norm parameters. We detected 25 FT QTL summarized into 10 unique QTL. Mean values and plasticity parameters QTL were co-localized in three of them, including the major 6D_M QTL whose effect is strongly modulated by temperature. The design and validation of a genetic marker for the 6D_M QTL offers great potential for breeding programs, for example for selecting early-flowering strawberry varieties well adapted to different environmental conditions.
PubMed: 38938160
DOI: 10.1093/jxb/erae279