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Background: Recent endeavours in metagenomics, exemplified by projects such as the human microbiome project and TARA Oceans, have illuminated the complexities of microbial biomes. A robust bioinformatic pipeline and meticulous evaluation of their methodology have contributed to the success of these projects. The soil environment, however, with its unique challenges, requires a specialized methodological exploration to maximize microbial insights. A notable limitation in soil microbiome studies is the dearth of soil-specific reference databases available to classifiers that emulate the complexity of soil communities. There is also a lack of in-vitro mock communities derived from soil strains that can be assessed for taxonomic classification accuracy. Results: In this study, we generated a custom in-silico mock community containing microbial genomes commonly observed in the soil microbiome. Using this mock community, we simulated shotgun sequencing data to evaluate the performance of three leading metagenomic classifiers: Kraken2 (supplemented with Bracken, using a custom database derived from GTDB-TK genomes along with its own default database), Kaiju, and MetaPhlAn, utilizing their respective default databases for a robust analysis. Our results highlight the importance of optimizing taxonomic classification parameters, database selection, as well as analysing trimmed reads and contigs. Our study showed that classifiers tailored to the specific taxa present in our samples led to fewer errors compared to broader databases including microbial eukaryotes, protozoa, or human genomes, highlighting the effectiveness of targeted taxonomic classification. Notably, an optimal classifier performance was achieved when applying a relative abundance threshold of 0.001% or 0.005%. The Kraken2 supplemented with bracken, with a custom database demonstrated superior precision, sensitivity, F1 score, and overall sequence classification. Using a custom database, this classifier classified 99% of in-silico reads and 58% of real-world soil shotgun reads, with the latter identifying previously overlooked phyla using a custom database. Conclusion: This study underscores the potential advantages of in-silico methodological optimization in metagenomic analyses, especially when deciphering the complexities of soil microbiomes. We demonstrate that the choice of classifier and database significantly impacts microbial taxonomic profiling. Our findings suggest that employing Kraken2 with Bracken, coupled with a custom database of GTDB-TK genomes and fungal genomes at a relative abundance threshold of 0.001% provides optimal accuracy in soil shotgun metagenome analysis. [ABSTRACT FROM AUTHOR]

In order to survey noroviruses in our environment, it is essential that both wet-lab and computational methods are fit for purpose. Using a simulated sequencing data set, denoising-based (DADA2, Deblur and USEARCH-UNOISE3) and clustering-based pipelines (VSEARCH and FROGS) were compared with respect to their ability to represent composition and sequence information. Open source classifiers (Ribosomal Database Project [RDP], BLASTn, IDTAXA, QIIME2 naive Bayes, and SINTAX) were trained using three different databases: a custom database, the NoroNet database, and the Human calicivirus database. Each classifier and database combination was compared from the perspective of their classification accuracy. VSEARCH provides a robust option for analyzing viral amplicons based on composition analysis; however, all pipelines could return OTUs with high similarity to the expected sequences. Importantly, pipeline choice could lead to more false positives (DADA2) or underclassification (FROGS), a key aspect when considering pipeline application for source attribution. Classification was more strongly impacted by the classifier than the database, although disagreement increased with norovirus GII.4 capsid variant designation. We recommend the use of the RDP classifier in conjunction with VSEARCH; however, maintenance of the underlying database is essential for optimal use. [ABSTRACT FROM AUTHOR]

Background: Legislation requiring mammography facilities to notify women if they have dense breast tissue found on mammography has been enacted in 34 US states. The impact of dense breast notifications (DBNs) on women with limited English proficiency (LEP) is unknown.Objective: This study sought to understand Spanish-speaking women's experience receiving DBNs in a Massachusetts safety-net hospital.Design: Eligible women completed one audio-recorded, semi-structured interview via telephone with a native Spanish-speaking research assistant trained in qualitative methods. Interviews were professionally transcribed verbatim and translated. The translation was verified by a third reviewer to ensure fidelity with audio recordings.Participants: Nineteen Spanish-speaking women ages 40-74 who received mammography with a normal result and recalled receiving a DBN.Approach: Using the verified English transcripts, we conducted a content analysis to identify women's perceptions and actions related to receiving the notification. A structured codebook was developed. Transcripts were independently coded and assessed for agreement with a modification of Cohen's kappa. Content codes were grouped to build themes related to women's perceptions and actions after receiving a DBN.Key Results: Nineteen Spanish-speaking women completed interviews. Nine reported not receiving the notification in their native language. Four key themes emerged: (1) The novelty of breast density contributed to notification-induced confusion; (2) women misinterpreted key messages in the notification; (3) varied actions were taken to seek further information; and (4) women held unrealized expectations and preferences for follow-up.Conclusions: Not having previous knowledge of breast density and receiving notifications in English contributed to confusion about its meaning and inaccurate interpretations of key messages by Spanish speakers. Tools that promote understanding should be leveraged in seeking equity in risk-based breast cancer screening for women with dense breasts. [ABSTRACT FROM AUTHOR]

The article reports on the functions of melatonin in the fields of health and disease. Melatonin is a hormone made in the brain by the pineal gland. It is involved in some physiologic actions including the coordination of the circadian rhythm, sleep regulation and tumor-growth inhibition. Although most research on melatonin focus on its ability to synchronize the biorhythms of the body and promote sleep, recent studies explore its potential benefit for antioxidant activities and immune system.

A significant decrease in norovirus prevalence and concentration was observed in oyster production areas in Ireland during winter 2020 to 2021. Oyster production areas impacted by human wastewater discharges that had been undergoing norovirus surveillance since 2018 were investigated. Samples collected in the winter seasons of 2018 to 2019 and 2019 to 2020, prior to when the COVID-19 pandemic interventions were applied, showed a prevalence of 94.3 and 96.6%, respectively, and geometric mean concentrations of 533 and 323 genome copies per g, respectively. These values decreased significantly during the winter of 2020 to 2021 (prevalence of 63.2% and geometric concentration of below the limit of quantification), coinciding with the control measures to mitigate the transmission of severe acute respiratory syndrome coronavirus 2 of the genus Betacoronavirus. Divergence between norovirus GI and GII prevalence and concentrations was observed over the 3-year monitoring period. Norovirus GII was the dominant genogroup detected in winter 2020 to 2021, with over half of samples positive, although concentrations detected were significantly lower than prepandemic winters, with a geometric mean concentration of below the limit of quantification. Oyster surveillance revealed the norovirus rate during the COVID-19 pandemic. SARS-CoV-2 mitigation measures had an indirect impact on norovirus transmission. A decrease in norovirus levels was seen in 2020 to 2021 compared with prepandemic winters. Norovirus concentrations were significantly lower than in previous winter periods. [ABSTRACT FROM AUTHOR]

The article presents a study which evaluates the efficacy of objective structured clinical evaluation (OSCE) in assessing the negotiation of professional boundary challenges in the U.S. The study was administered by letting 15 post graduate resident doctors undergo an expanded version of various role-play regarding the proper management of narcotic administration. It reveals that enhanced communication and consultation skills are needed to achieve an effective resolution of the issues.

Methadone and buprenorphine are effective treatment for opioid use disorder (OUD), yet they are vastly under-utilized across US hospitals. To inform a national trial assessing the effectiveness of implementation strategies to increase adoption of an inpatient hospital-based opioid treatment (HBOT) model (NCT04921787), we explored barriers and facilitators to expanding medication for opioid use disorder (MOUD) within community hospitals across the United States. From November 2021 to March 2022, we used purposeful and snowball sampling to identify and interview participants involved in inpatient care of patients with OUD from twelve community hospitals. We conducted semi-structured interviews on providers' experiences and perspectives on current treatment approaches as well as potential influences on MOUD expansion in their hospitals. We used thematic analysis to identify key barriers and facilitators that could impact implementation of an HBOT model, and organized these findings based on the Consolidated Framework for Implementation Research (CFIR). From qualitative interviews with 57 participants (30 physicians, 7 pharmacists, 6 nurses, and 14 professionals involved in the care of patients with OUD), we identified key barriers and facilitators mapped to CFIR's internal and outer settings. The most salient inner setting domains included tension for change and relative priority, compatibility, available resources, organizational culture, access to knowledge and information, relational connections and communications, and information technology infrastructure. Outer setting domains included policies and laws, financing, and partnerships and connections. Identifying potential barriers and facilitators can inform hospital-specific strategies to support implementation of HBOT. Implementation strategies that address barriers such as staff availability, knowledge, and attitudes may support increased HBOT adoption. On a broader scale, national policy changes such as increased financing and public reporting of quality metrics would address other barriers we identified and may also encourage hospitals to adopt HBOT models. • Across regions, providers were motivated to improve hospital-based OUD treatment. • Initiating MOUD fits well in existing inpatient workflows. • With understaffing, providers did not have time to learn medication guidelines. • External barriers, including financing, also challenge efforts to increase OUD treatment. • Practice facilitation may support hospitals expanding OUD treatment. [ABSTRACT FROM AUTHOR]

Background: Individuals with opioid use disorder have high rates of hospital admissions, which represent a critical opportunity to engage patients and initiate medications for opioid use disorder (MOUD). However, few patients receive MOUD and, even if MOUD is initiated in the hospital, patients may encounter barriers to continuing MOUD in the community.Describe hospital providers’ experiences and perspectives to inform initiatives and policies that support hospital-based MOUD initiation and continuation in community treatment programs.As part of a broader implementation study focused on inpatient MOUD (NCT#04921787), we conducted semi-structured interviews with hospital providers.Fifty-seven hospital providers from 12 community hospitals.Thematic analysis examined an emergent topic on challenges transitioning patients to outpatient MOUD treatment and related impacts on MOUD initiation by inpatient providers.Participants described structural barriers to transitioning hospitalized patients to continuing outpatient MOUD including (a) limited outpatient buprenorphine prescriber availability, (b) the siloed nature of addiction treatment, and (c) long wait times. As a result of observing these structural barriers, participants experienced a sense of futility that deterred them from initiating MOUD. Participants proposed strategies that could better support these patient transitions, including developing partnerships between hospitals and outpatient addiction treatment and supporting in-reach services from community providers.We identified concerns about inadequate and inaccessible community-based care and transition pathways that discouraged hospital providers from prescribing MOUD. As hospital-based opioid treatment models continue to expand, programmatic and policy strategies to support inpatient transitions to outpatient addiction treatment are needed.04921787.Objective: Individuals with opioid use disorder have high rates of hospital admissions, which represent a critical opportunity to engage patients and initiate medications for opioid use disorder (MOUD). However, few patients receive MOUD and, even if MOUD is initiated in the hospital, patients may encounter barriers to continuing MOUD in the community.Describe hospital providers’ experiences and perspectives to inform initiatives and policies that support hospital-based MOUD initiation and continuation in community treatment programs.As part of a broader implementation study focused on inpatient MOUD (NCT#04921787), we conducted semi-structured interviews with hospital providers.Fifty-seven hospital providers from 12 community hospitals.Thematic analysis examined an emergent topic on challenges transitioning patients to outpatient MOUD treatment and related impacts on MOUD initiation by inpatient providers.Participants described structural barriers to transitioning hospitalized patients to continuing outpatient MOUD including (a) limited outpatient buprenorphine prescriber availability, (b) the siloed nature of addiction treatment, and (c) long wait times. As a result of observing these structural barriers, participants experienced a sense of futility that deterred them from initiating MOUD. Participants proposed strategies that could better support these patient transitions, including developing partnerships between hospitals and outpatient addiction treatment and supporting in-reach services from community providers.We identified concerns about inadequate and inaccessible community-based care and transition pathways that discouraged hospital providers from prescribing MOUD. As hospital-based opioid treatment models continue to expand, programmatic and policy strategies to support inpatient transitions to outpatient addiction treatment are needed.04921787.Design: Individuals with opioid use disorder have high rates of hospital admissions, which represent a critical opportunity to engage patients and initiate medications for opioid use disorder (MOUD). However, few patients receive MOUD and, even if MOUD is initiated in the hospital, patients may encounter barriers to continuing MOUD in the community.Describe hospital providers’ experiences and perspectives to inform initiatives and policies that support hospital-based MOUD initiation and continuation in community treatment programs.As part of a broader implementation study focused on inpatient MOUD (NCT#04921787), we conducted semi-structured interviews with hospital providers.Fifty-seven hospital providers from 12 community hospitals.Thematic analysis examined an emergent topic on challenges transitioning patients to outpatient MOUD treatment and related impacts on MOUD initiation by inpatient providers.Participants described structural barriers to transitioning hospitalized patients to continuing outpatient MOUD including (a) limited outpatient buprenorphine prescriber availability, (b) the siloed nature of addiction treatment, and (c) long wait times. As a result of observing these structural barriers, participants experienced a sense of futility that deterred them from initiating MOUD. Participants proposed strategies that could better support these patient transitions, including developing partnerships between hospitals and outpatient addiction treatment and supporting in-reach services from community providers.We identified concerns about inadequate and inaccessible community-based care and transition pathways that discouraged hospital providers from prescribing MOUD. As hospital-based opioid treatment models continue to expand, programmatic and policy strategies to support inpatient transitions to outpatient addiction treatment are needed.04921787.Participants: Individuals with opioid use disorder have high rates of hospital admissions, which represent a critical opportunity to engage patients and initiate medications for opioid use disorder (MOUD). However, few patients receive MOUD and, even if MOUD is initiated in the hospital, patients may encounter barriers to continuing MOUD in the community.Describe hospital providers’ experiences and perspectives to inform initiatives and policies that support hospital-based MOUD initiation and continuation in community treatment programs.As part of a broader implementation study focused on inpatient MOUD (NCT#04921787), we conducted semi-structured interviews with hospital providers.Fifty-seven hospital providers from 12 community hospitals.Thematic analysis examined an emergent topic on challenges transitioning patients to outpatient MOUD treatment and related impacts on MOUD initiation by inpatient providers.Participants described structural barriers to transitioning hospitalized patients to continuing outpatient MOUD including (a) limited outpatient buprenorphine prescriber availability, (b) the siloed nature of addiction treatment, and (c) long wait times. As a result of observing these structural barriers, participants experienced a sense of futility that deterred them from initiating MOUD. Participants proposed strategies that could better support these patient transitions, including developing partnerships between hospitals and outpatient addiction treatment and supporting in-reach services from community providers.We identified concerns about inadequate and inaccessible community-based care and transition pathways that discouraged hospital providers from prescribing MOUD. As hospital-based opioid treatment models continue to expand, programmatic and policy strategies to support inpatient transitions to outpatient addiction treatment are needed.04921787.Approach: Individuals with opioid use disorder have high rates of hospital admissions, which represent a critical opportunity to engage patients and initiate medications for opioid use disorder (MOUD). However, few patients receive MOUD and, even if MOUD is initiated in the hospital, patients may encounter barriers to continuing MOUD in the community.Describe hospital providers’ experiences and perspectives to inform initiatives and policies that support hospital-based MOUD initiation and continuation in community treatment programs.As part of a broader implementation study focused on inpatient MOUD (NCT#04921787), we conducted semi-structured interviews with hospital providers.Fifty-seven hospital providers from 12 community hospitals.Thematic analysis examined an emergent topic on challenges transitioning patients to outpatient MOUD treatment and related impacts on MOUD initiation by inpatient providers.Participants described structural barriers to transitioning hospitalized patients to continuing outpatient MOUD including (a) limited outpatient buprenorphine prescriber availability, (b) the siloed nature of addiction treatment, and (c) long wait times. As a result of observing these structural barriers, participants experienced a sense of futility that deterred them from initiating MOUD. Participants proposed strategies that could better support these patient transitions, including developing partnerships between hospitals and outpatient addiction treatment and supporting in-reach services from community providers.We identified concerns about inadequate and inaccessible community-based care and transition pathways that discouraged hospital providers from prescribing MOUD. As hospital-based opioid treatment models continue to expand, programmatic and policy strategies to support inpatient transitions to outpatient addiction treatment are needed.04921787.Key Results: Individuals with opioid use disorder have high rates of hospital admissions, which represent a critical opportunity to engage patients and initiate medications for opioid use disorder (MOUD). However, few patients receive MOUD and, even if MOUD is initiated in the hospital, patients may encounter barriers to continuing MOUD in the community.Describe hospital providers’ experiences and perspectives to inform initiatives and policies that support hospital-based MOUD initiation and continuation in community treatment programs.As part of a broader implementation study focused on inpatient MOUD (NCT#04921787), we conducted semi-structured interviews with hospital providers.Fifty-seven hospital providers from 12 community hospitals.Thematic analysis examined an emergent topic on challenges transitioning patients to outpatient MOUD treatment and related impacts on MOUD initiation by inpatient providers.Participants described structural barriers to transitioning hospitalized patients to continuing outpatient MOUD including (a) limited outpatient buprenorphine prescriber availability, (b) the siloed nature of addiction treatment, and (c) long wait times. As a result of observing these structural barriers, participants experienced a sense of futility that deterred them from initiating MOUD. Participants proposed strategies that could better support these patient transitions, including developing partnerships between hospitals and outpatient addiction treatment and supporting in-reach services from community providers.We identified concerns about inadequate and inaccessible community-based care and transition pathways that discouraged hospital providers from prescribing MOUD. As hospital-based opioid treatment models continue to expand, programmatic and policy strategies to support inpatient transitions to outpatient addiction treatment are needed.04921787.Conclusions: Individuals with opioid use disorder have high rates of hospital admissions, which represent a critical opportunity to engage patients and initiate medications for opioid use disorder (MOUD). However, few patients receive MOUD and, even if MOUD is initiated in the hospital, patients may encounter barriers to continuing MOUD in the community.Describe hospital providers’ experiences and perspectives to inform initiatives and policies that support hospital-based MOUD initiation and continuation in community treatment programs.As part of a broader implementation study focused on inpatient MOUD (NCT#04921787), we conducted semi-structured interviews with hospital providers.Fifty-seven hospital providers from 12 community hospitals.Thematic analysis examined an emergent topic on challenges transitioning patients to outpatient MOUD treatment and related impacts on MOUD initiation by inpatient providers.Participants described structural barriers to transitioning hospitalized patients to continuing outpatient MOUD including (a) limited outpatient buprenorphine prescriber availability, (b) the siloed nature of addiction treatment, and (c) long wait times. As a result of observing these structural barriers, participants experienced a sense of futility that deterred them from initiating MOUD. Participants proposed strategies that could better support these patient transitions, including developing partnerships between hospitals and outpatient addiction treatment and supporting in-reach services from community providers.We identified concerns about inadequate and inaccessible community-based care and transition pathways that discouraged hospital providers from prescribing MOUD. As hospital-based opioid treatment models continue to expand, programmatic and policy strategies to support inpatient transitions to outpatient addiction treatment are needed.04921787.NCT Trial Number: Individuals with opioid use disorder have high rates of hospital admissions, which represent a critical opportunity to engage patients and initiate medications for opioid use disorder (MOUD). However, few patients receive MOUD and, even if MOUD is initiated in the hospital, patients may encounter barriers to continuing MOUD in the community.Describe hospital providers’ experiences and perspectives to inform initiatives and policies that support hospital-based MOUD initiation and continuation in community treatment programs.As part of a broader implementation study focused on inpatient MOUD (NCT#04921787), we conducted semi-structured interviews with hospital providers.Fifty-seven hospital providers from 12 community hospitals.Thematic analysis examined an emergent topic on challenges transitioning patients to outpatient MOUD treatment and related impacts on MOUD initiation by inpatient providers.Participants described structural barriers to transitioning hospitalized patients to continuing outpatient MOUD including (a) limited outpatient buprenorphine prescriber availability, (b) the siloed nature of addiction treatment, and (c) long wait times. As a result of observing these structural barriers, participants experienced a sense of futility that deterred them from initiating MOUD. Participants proposed strategies that could better support these patient transitions, including developing partnerships between hospitals and outpatient addiction treatment and supporting in-reach services from community providers.We identified concerns about inadequate and inaccessible community-based care and transition pathways that discouraged hospital providers from prescribing MOUD. As hospital-based opioid treatment models continue to expand, programmatic and policy strategies to support inpatient transitions to outpatient addiction treatment are needed.04921787. [ABSTRACT FROM AUTHOR]

Purpose: Dysphagia (swallowing difficulty) impacts physical health, quality of life, and mealtime enjoyment. Staff who provide mealtime assistance to people with dysphagia require adequate training to help ensure that the mealtimes are safe and enjoyable. This systematic review examined literature relating to training in dysphagia (e.g., recognizing signs and symptoms) and mealtime assistance, its components, and benefits for people with dysphagia. Method: In July 2020, five scientific databases were searched for papers meeting the inclusion criteria relating to mealtime assistance training. The quality of the studies was evaluated using the Quality Assessment Tool for Studies of Diverse Design, with scores ranging from 38.1% to 83.3%. We completed a qualitative synthesis using the data extracted from the included studies. Results: Twenty-four studies met the inclusion criteria. Participants in these studies benefited from both group training and one-on-one training. Training programs had many formats including computer-based, face-to-face, individual training, and group training. Each included study demonstrated some level of positive impact to the learners, such as improved knowledge and skills in mealtime management for people with dysphagia. No studies reported negative outcomes. Training duration ranged from 30 min to 5 days. Conclusions: The benefits of different components of mealtime training (e.g., group training, or face-to-face training) for mealtime assistance for people with dysphagia were reviewed. Further research is needed to compare the effectiveness of different training formats, involving not only the assistant but also people with dysphagia as both trainers and trainees, and determine the health outcomes of training programs for people with dysphagia. [ABSTRACT FROM AUTHOR]