Bioculture Journal
Not a member yet
1309 research outputs found
Sort by
Translating mass spectra to peptides with deep learning
No full textThesis (Ph.D.)--University of Washington, 2025Tandem mass spectrometry is the leading technique to study proteins at scale, and a fundamental challenge in mass spectrometry-based proteomics is the identification of the peptide that generated each acquired tandem mass spectrum. Approaches that leverage known peptide sequence databases cannot detect unexpected peptides and can be impractical or impossible to apply in some settings. Thus, the ability to assign peptide sequences to tandem mass spectra without prior information—de novo peptide sequencing—is valuable for tasks including antibody sequencing, immunopeptidomics, and metaproteomics. Although many methods have been developed to address this problem, it remains an outstanding challenge in part due to the difficulty of modeling the irregular data structure of tandem mass spectra. In this work, we describe Casanovo, a machine learning model that uses a transformer neural network architecture to translate the sequence of peaks in a tandem mass spectrum into the sequence of amino acids that comprise the generating peptide. Casanovo is trained on a repository-scale dataset and it significantly advances the state-of-the-art in de novo peptide sequencing. We show that Casanovo's superior performance improves the analysis of immunopeptidomics and metaproteomics experiments and allows us to delve deeper into the dark proteome. Finally, we go beyond the de novo peptide sequencing problem and demonstrate Casanovo's capabilities as a foundation model in mass spectrometry proteomics
Potential of functional candies from ethanol extracts of Myristica fragrans and Phyllanthus acidus as antioxidant and anti-anxiety agents: A comprehensive review
Full text linkBackground: Anxiety disorders are a major global health burden, with recent WHO data indicating a 1.79% increase in case incidence rate (CIR) and a 6.25% rise in disability-adjusted life years (DALY) over the past five years. Conventional pharmacotherapies such as SSRIs and benzodiazepines are limited by adverse effects and dependency risks, highlighting the urgent need for safer, effective alternatives. Myristica fragrans (nutmeg) and Phyllanthus acidus (otaheite gooseberry) are rich in myristicin and flavonoids, respectively, both of which exhibit promising anxiolytic and neuroprotective properties. However, the synergistic efficacy and safety of their combined use remain underexplored. Methods: A comprehensive review was conducted following PRISMA guidelines. Out of 512 studies identified from Scopus, PubMed, ScienceDirect, and EBSCO, 36 met inclusion criteria after quality appraisal using CASP, with 2 clinical trials extracted for quantitative synthesis. Data extraction focused on changes in anxiety scores (e.g., HAM-A), stress biomarkers (cortisol, MDA), antioxidant enzyme activities (SOD, CAT), and neurochemical modulation (serotonin, GABA, dopamine). Findings: analysis revealed that combined administration of nutmeg and otaheite gooseberry extracts reduced anxiety scores by a weighted mean difference (WMD) of –7.3 (95% CI: –9.1 to –5.5, p<0.001) on the HAM-A scale compared to placebo. Cortisol levels decreased by 18.4% (p=0.002), while MDA levels dropped by 22.7% (p=0.001), and SOD activity increased by 31.6% (p<0.001) in preclinical models. Myristicin (500 mg/kg) produced significant anxiolytic effects via serotonergic and GABAergic modulation, while flavonoids (1.2–3.5% content) provided robust neuroprotection against oxidative stress. No antagonistic interactions or increased toxicity were observed; the combination outperformed single extracts and showed comparable efficacy to SSRIs and benzodiazepines with fewer adverse effects. Conclusions: The integration of Myristica fragrans and Phyllanthus acidus extracts offers a synergistic, natural therapeutic approach for anxiety disorders, combining potent anxiolytic and neuroprotective effects with an excellent safety profile. Novelty/Originality of this article: This review is the first to quantitatively demonstrate the synergistic anxiolytic and antioxidant efficacy of nutmeg and otaheite gooseberry extracts, supporting their development as innovative functional candies for mental health management
Turnover Within the Child Welfare System
No full textMaster of Social Work (MSW)This Capstone identifies a mandatory training that would be provided to child welfare workers within their first year of employment up to their 3rd year of employment
Community Care Circles: Supporting Community Mental Health Workers
No full textMaster of Social Work (MSW)The nonprofit Community Behavioral Health (CBH) sector is experiencing a critical workforce shortage that jeopardizes equitable mental health care for Medicaid populations. Low wages, chronic underfunding, and high levels of provider burnout fuel this crisis, disproportionately affecting marginalized communities. Existing approaches have often focused on individual-level solutions, such as recruitment drives and training, without addressing underlying systemic barriers. Recent interventions emphasize organizational and multicomponent strategies-such as the Availability, Responsiveness, and Continuity (ARC) intervention and participatory workplace programs-that target workload, team cohesion, and institutional culture to improve staff retention and well-being. This paper proposes Community Care Circles, a structured peer-support intervention informed by the Compassion Satisfaction-Compassion Fatigue Model, Organizational Support Theory, and Maslach's Theory of Burnout. The program comprises twelve monthly facilitated sessions where staff collaboratively address emotional exhaustion, secondary trauma, and systemic stressors. By prioritizing inclusivity and trauma-informed facilitation, Community Care Circles aim to build resilience, strengthen professional relationships, and enhance perceived organizational support. Evaluation involves pre- and post-intervention assessments using validated measures of burnout, compassion fatigue, and team cohesion. Anticipated outcomes include reduced emotional exhaustion, improved workplace satisfaction, and greater retention of mental health professionals serving Medicaid populations. By centering marginalized perspectives and fostering a supportive agency culture, this intervention addresses an urgent need for sustainable solutions in CBH, ultimately ensuring that vulnerable clients receive the consistent, high-quality mental health care they deserve
How does corporate social responsibility create value for consumers?
No full textPurpose - Research examining corporate social responsibility (CSR) demonstrates a relatively consistent level of positive support by consumers. However, CSR is poorly defined and little is known about the mechanisms by which this response occurs. This paper seeks to understand how consumers define CSR and how it can enhance the overall value proposition for consumers. Design/methodology/approach - The value typology developed by Sheth et al. is integrated with qualitative data to enhance understanding of these value paths. Interviews were conducted with consumers through the heart of the current recession, when consumers were particularly aware of value when making purchase decisions. Findings - The way in which CSR manifests itself determines consumer support. CSR can provide three forms of value to consumers: emotional, social, and functional. Each of these enhances or diminishes the overall value proposition for consumers. Further, value created by one form of CSR can either enhance or diminish other product attributes. Practical implications - The current research helps managers understand how CSR can create value for consumers. As a result, managers can better position products in order to enhance overall value. Further, practitioners can match the value with which consumers identify from CSR to the dominant value driver in their product category. Originality/value - This study highlights that CSR includes a range of activities with differential means of adding value to consumers
Social Psychological Challenges to Sharing Space and Sharing Goals With Diverse Groups
No full textThesis (Ph.D.)--University of Washington, 2025In a diverse and unequal society, what pitfalls should we avoid when striving to share space as neighbors and share goals as political allies? In the first paper, I start by considering the current state of the national housing crisis and propose a theoretical framework that identifies cultural barriers to enacting housing solutions. I argue that our existing housing policies and stereotypes are not natural nor benign. Instead, they reflect and perpetuate cherished American values which overlook the multiplicity of ways to live while also exacerbating the dire shortage of housing. This theoretical framework clarifies why policymakers need to consider not just the economic feasibility of housing solutions, but the cultural feasibility as well. Next, in the second paper I investigate the potential psychological harms of a widespread urban phenomenon thought to promote thriving, mixed-income neighborhoods: gentrification. Using a combination of field surveys and controlled online experiments, I demonstrate that gentrification creates psychological disparities by harming lower-income individuals’ sense of belonging to their neighborhoods while boosting higher-income individuals’ belonging. To address this belonging gap, I show that neighborhood investment that reflects a community-driven effort, rather than a profit-driven effort that is typical of gentrification, is significantly more well-received by lower-income individuals. Lastly, in the third paper I examine how prevailing narratives of race and racism may inform flawed strategies for building coalitions between different racial minority groups. I find that among Asian Americans racism is more commonly understood as the relative advantages that White people have over people of color rather than the relative disadvantages Black people have compared to non-Black people. However, a downside of this framework is that it dampens Asian Americans’ perceived responsibility for addressing racism. This suggests that prevailing strategies for building intraminority coalitions, which rely on white supremacy frameworks of racism, may inadvertently shield Asian Americans from recognizing their own complicity in systems of oppression. Collectively, this dissertation identifies how some of our commonly proposed solutions can be incomplete or misguided, and underscores the value of interdisciplinary, applied research into the causes and consequences of inequality
Inter-rater agreement among physical therapists in using Neurologic Movement System Diagnosis (N-MSD)
No full textThesis (Ph.D.)--University of Washington, 2025Movement optimization was adopted by the American Physical Therapy Association (APTA) as the core of physical therapy practice in 2013. While Physical Therapists (PTs) observe, assess, diagnose, and treat movement impairments in clinical practice, evidence-based clinical practice guidelines are centered around neurological medical diagnoses rather than movement deficits. Therefore, in physical therapy practice, pathophysiological impairments and health conditions often guide assessment, treatment, and prognosis instead of the movement deficits.To make movement the focus of the clinical decision-making process, several movement system diagnoses were developed. While some of the previously published frameworks were commonly used in clinical practice and educational settings, few studies have examined the reliability, validity, and clinical application of any of these systems. This dissertation study examined the agreement among PTs in utilizing the Neurologic Movement System Diagnosis (N-MSD) framework in individuals with various neurological health conditions.
The N-MSD includes frameworks for movement observation and analysis of key functional tasks as well as movement-based diagnoses. This body of work examined the agreement among PTs, between experienced and early-career PTs and against an expert considered as the gold standard.
The findings demonstrated that experienced PTs with prior knowledge about the Movement System were in higher agreement with an expert when making movement system diagnoses. Moreover, PTs demonstrated greater agreement, a narrower range of scores, with assessments of static tasks as compared to their assessments of dynamic tasks. Among dynamic tasks however, assessment of transitional movements such as Sit to Stand and Step Up showed more scattered results across PTs compared to gait. Subsequently, agreement among PTs in selecting movement system diagnoses with key features related to dynamic tasks was lower as compared to other diagnoses. The collective results of these studies suggest that with proper training on N-MSD, physical therapists could come to moderate to strong agreement when assessing certain functional tasks and consensus on a primary movement diagnosis. These research findings also lay the groundwork for future research efforts, including development of a more uniform process for analyzing tasks with emphasis on dynamic tasks, psychometric evaluation of the new evaluation framework, and insight into the underlying clinical reasoning during the examination process and for a movement system diagnosis
The role of humans in the sustainability of marine ecosystems: A case study on the conservation of parrotfish and its ecological impact
No full textBackground: Life is supported by the ecology and natural resources that exist on earth. Continents and oceans are the two main natural resources that host life and ecosystems around the world. 75% of the Earth's surface is covered by ocean waters that are rich in marine life. Although the oceans are vast, this does not mean that they are limitless. Population growth and development have led to an increase in the demand for marine resources. Increased demand and over-utilization of marine resources have led to strong pressures that have led to a decline in marine ecosystem services. Karimunjawa is famous for the natural beauty of its underwater coral reefs. Methods: This study employs a qualitative approach using literature and secondary data to examine the impact of parrotfish populations on coral reef sustainability. Findings: Based on current conditions, excessive catching of parrotfish has a negative impact on the sustainability of coral reefs in Karimunjawa National Park. It is necessary for local communities to understand the importance of the role of parrot fish for the sustainability of marine ecosystems. Parrotfish spend 90% of their time eating algae attached to coral reefs. Damage to the coral reef ecosystem causes coastal erosion in Karimunjawa National Park. Therefore, the role of the community in managing parrotfish resources is very necessary so as not to threaten the population for the sustainability of the marine ecosystem. Conclusion: The results of this research illustrate the role of humans, namely the community and tourists who come to Karimunjawa to carry out activities to preserve damaged coral reefs and create new coral reef areas. Novelty/Originality of this article: There are also government policies that must be considered and implemented properly for the sustainability of coral reef ecosystems and the conservation of parrotfish in Karimunjawa
Potential of Tamarind (Tamarindus indica L.) leaves as funtional food
Full text linkBackground: Public interest in functional foods, which provide health benefits beyond basic nutrition, is growing in Indonesia and worldwide. Despite their recognized medicinal properties, tamarind leaves remain underutilized in functional food applications. This review examines their potential as a valuable local resource for disease prevention. Methods: A literature search on "Tamarindus indica leaf" was conducted using databases such as Scopus and Web of Science. Data were collected from sources published between 2010 to 2024, adhering to specific inclusion criteria. Analytical methods included thematic categorization and comparison of findings, with an emphasis on the health benefits and functional food potential of tamarind leaves. Finding: Tamarind leaves have been proven to have extensive functional benefits including as a source of antioxidants, antibacterial, antifungal, blood cholesterol lowering agents, antidiarrhea, antiobesity, antidiabetic, anti-inflammatory. Tamarind leaves have the potential to be processed into functional drinks and as a mixture of food products such as snacks. Conclusion: Tamarind leaves are an underutilized functional food; further research and innovation are essential for their development. Novelty/Originality of this article: There has been no publication that specifically discusses the potential of tamarind leaves as a functional food. This publication is expected to fill this knowledge gap
Staying With the Patient: An Ethnography of Primary Care
No full textThesis (Ph.D.)--University of Washington, 2025This dissertation is an ethnography of Primary Care Medicine. It explores the characteristic tools and organizational form of Primary Care, and offers an account of the role of medical records in the production of clinical judgment and patient care in a California County Hospital. This dissertation argues that genres of medical writing play a special role in the provision of medical care by mediating interactions between clinicians, across the sites and specialties that make up a medical system. Since the first decades of the 20th century, Western medicine has conceived of itself as a collective practice requiring multiple specialties, presenting a problem for general medical practitioners. Primary Care Physicians formed professionally around that area of a medical expertise that deals with complex patients, multiple organ systems, and multiple specialties. I argue that Primary Care creates medical, financial, and patient value through the distribution of patient problems across long networks of care through clinical judgment (phronesis), a type of case-based decision-making related to ethical and legal thought that emphasizes health management over diagnosis. Through the description of Primary Care, and its comparison with other social-scientific analyses of clinical medicine, I offer a novel conceptual candidate for the replacement of the concept of biomedicine as the general type of medicine in the West