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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 -
Australian Occupational Therapy Journal Jun 2024The purpose of this study was to examine the feasibility of adapting and translating an evidence-based occupational therapist-delivered program shown to be effective in...
INTRODUCTION
The purpose of this study was to examine the feasibility of adapting and translating an evidence-based occupational therapist-delivered program shown to be effective in the community to residential aged care (RAC). The program aims to improve quality of care and quality of life for people living with dementia and the wellbeing of the family care partner.
METHODS
This study took place in a not-for-profit RAC home in Adelaide, South Australia. Mixed methods, specifically questionnaires, activity logs, focus group, and one-on-one interviews were used to evaluate the feasibility of the program implementation. Staff working in the participating home, occupational therapists trained to deliver the program, and residents and their family carer partners were included. Quantitative data were analysed using proportions, means, and standard deviations. Qualitative data were analysed using a thematic approach.
CONSUMER AND COMMUNITY INVOLVEMENT
This study was conducted together with a consumer (person living with dementia) and a carer representative (family member of someone residing in RAC). These representatives provided input towards the study design, interpretation of study data, discussion of results, and recommendations for future consideration.
RESULTS
Small changes to the program improved feasibility and acceptability for delivery in RAC. While the care home staff required added support during implementation, the intervention therapists felt that the program could be delivered in this setting. Family care partners of residents with dementia felt that the program may be better suited if provided upon entry to RAC or in early stages of dementia.
CONCLUSION
Adapting a community-based dementia care program to RAC can be safe and feasible. Program adaptations are necessary for feasibility. Further adaptations and evaluations of associated outcomes (related to residents with dementia and their family care partners) are needed to assess the program effectiveness in larger scale.
PLAIN LANGUAGE SUMMARY
Spending quality time with family members in residential aged care is important. However, many struggle to know what to say or do when visiting a family member who lives with dementia. Programs that teach families about how to communicate with people living with dementia, how to support them to take part in important everyday living activities, or how to understand why changes in behaviours may occur have not been available in residential aged care. This paper describes how we adapted one such evidence-based program from community to residential aged care settings. We consulted with people living with dementia, carers, and families and found that the program could also be valuable in this care setting. Residential aged care staff described how the program is very different to what is usually available in residential aged care, but they were optimistic that with the right support, it could be a valuable way to support residents with dementia and their families. Family members of residents with dementia and therapists delivering the program felt that residents in early stages of living in residential aged care and/or early stages of dementia could benefit the most from these programs. We found that including family members in the intervention process can be useful and empowering for families and residents. Future work should also focus on involving other staff members caring for residents in the process. Communication between staff and families is the key for program delivery and success and treating each person as an individual.
PubMed: 38937870
DOI: 10.1111/1440-1630.12978 -
Trials Jun 2024Randomized controlled trials (RCTs) are rigorous scientific research designs for evaluating intervention effectiveness. However, implementing RCTs in a real-world...
Strengths, challenges, and strategies for implementing pragmatic multicenter randomized controlled trials (RCTs): example of the Personalized Citizen Assistance for Social Participation (APIC) trial.
BACKGROUND
Randomized controlled trials (RCTs) are rigorous scientific research designs for evaluating intervention effectiveness. However, implementing RCTs in a real-world context is challenging. To develop strategies to improve its application, it is essential to understand the strengths and challenges of this design. This study thus aimed to explore the strengths, challenges, and strategies for improving the implementation of a pragmatic multicenter, prospective, two-arm RCT evaluating the effects of the Personalized Citizen Assistance for Social Participation (Accompagnement-citoyen Personnalisé d'Intégration Communautaire: APIC; weekly 3-h personalized stimulation sessions given by a trained volunteer over a 12-month period) on older adults' health, social participation, and life satisfaction.
METHODS
A multiple case study was conducted with 14 participants, comprising one research assistant, seven coordinators, and six managers of six community organizations serving older adults, who implemented the APIC in the context of a RCT. Between 2017 and 2023, qualitative data were extracted from 24 group meetings, seven semi-directed interviews, emails exchanged with the research team, and one follow-up document.
RESULTS
Aged between 30 and 60 (median ± SIQR: 44.0 ± 6.3), most participants were women from organizations already offering social participation interventions for older adults and working with the public sector. Reported strengths of this RCT were its relevance in assessing an innovative intervention to support healthy aging, and the sharing of common goals, expertise, and strategies with community organizations. Challenges included difficulties recruiting older adults, resistance to potential control group assignments, design complexity, and efforts to mobilize and engage volunteers. The COVID-19 pandemic lockdown and health measures exacerbated challenges related to recruiting older adults and mobilizing volunteers and complicated delivery of the intervention. The strategies that mostly overcame difficulties in recruiting older adults were reducing sample size, simplifying recruitment procedures, emphasizing the health follow-up, extending partnerships, and recognizing and supporting volunteers better. Because of the lockdown and physical distancing measures, the intervention was also adapted for remote delivery, including via telephone or videoconferencing.
CONCLUSION
Knowledge of the strengths and challenges of pragmatic RCTs can contribute to the development of strategies to facilitate implementation studies and better evaluate health and social participation interventions delivered under real-life conditions.
TRIAL REGISTRATION
NCT03161860; Pre-results. Registered on May 22, 2017.
Topics: Humans; Social Participation; Female; Male; Middle Aged; Prospective Studies; Adult; Volunteers; Research Design; COVID-19; Randomized Controlled Trials as Topic; Pragmatic Clinical Trials as Topic; Aged; Personal Satisfaction; Multicenter Studies as Topic
PubMed: 38937798
DOI: 10.1186/s13063-024-08248-w