GenBank 2024 Update.

GenBank® (https://www.ncbi.nlm.nih.gov/genbank/) is a comprehensive, public database that contains 25 trillion base pairs from over 3.7 billion nucleotide sequences for 557 000 formally described species. Daily data exchange with the European Nucleotide Archive (ENA) and the DNA Data Bank of Japan (DDBJ) ensures worldwide coverage. Recent updates include policies for including spatio-temporal metadata, clarified documentation for GenBank data processing, enhanced foreign contamination screening tools, new processes in the Submission Portal, migration of Entrez Genome and Assembly displays into NCBI Datasets, and the impending retirement of tbl2asn, replaced by table2asn.

GenBank 2023 update.

GenBank® (https://www.ncbi.nlm.nih.gov/genbank/) is a comprehensive, public database that contains 19.6 trillion base pairs from over 2.9 billion nucleotide sequences for 504 000 formally described species. Daily data exchange with the European Nucleotide Archive (ENA) and the DNA Data Bank of Japan (DDBJ) ensures worldwide coverage. Recent updates include resources for data from the SARS-CoV-2 virus, NCBI Datasets, BLAST ClusteredNR, the Submission Portal, table2asn, a Foreign Contamination Screening tool and BioSample.

GenBank.

GenBank® (https://www.ncbi.nlm.nih.gov/genbank/) is a comprehensive, public database that contains 15.3 trillion base pairs from over 2.5 billion nucleotide sequences for 504 000 formally described species. Recent updates include resources for data from the SARS-CoV-2 virus, including a SARS-CoV-2 landing page, NCBI Datasets, NCBI Virus and the Submission Portal. We also discuss upcoming changes to GI identifiers, a new data management interface for BioProject, and advice for providing contextual metadata in submissions.

Anxiety, Depression, and Coping Strategies during Chemotherapy Treatment: A Comparison of Older and Younger Adults with Advanced Cancer in Brazil.

We sought to examine differences in anxiety, depression and coping strategies among younger (<64-year old) and older (≥65-year old) patients. Patients were assessed at baseline (T1), mid-point (T2) and on the last day of treatment (T3) using the Hospital Anxiety and Depression Scale and the Ways of Coping. A linear mixed modeling approach was used. The study included 200 patients (gender: 70% women; diagnosis: 30% breast, 22% hematological, 18% gastrointestinal; disease stage: 60% advanced). Older patients who used an emotion-focused coping strategy had a greater decrease in anxiety at T3 compared to those that used problem-focused coping (p = .002).

Differences of biopsychosocial distress and requests for psychological assistance between Asian American and non-Hispanic White oncology patients.

OBJECTIVE: The purpose of this study was to compare Asian American (AA) to non-Hispanic White (NHW) cancer patients regarding biopsychosocial distress and requests for psychological assistance. METHODS: This retrospective study included 5627 eligible patients, newly diagnosed with cancer, who completed the 30-item SupportScreen® survey of biopsychosocial distress. The top 10 sources of high distress were assessed. Distress domains (Emotional, Physical/Functional, and Practical) were examined by race/ethnicity. Requests for psychological assistance were also explored by ethnic groups. RESULTS: Overall, the top 10 sources of high distress were similar between groups and approximately half consisted of concerns regarding physical symptoms. All patients preferred "talking" as their method of receiving assistance for these items. Ratings of emotional, practical, and physical/functional distress were similar between AA and NHW patients. However, AAs (vs. NHWs) requested more assistance regarding physical/functional and practical distress. No difference was observed between these two groups regarding requests for emotional support. CONCLUSIONS: Overall, our study suggests that healthcare providers should be aware of the physical and practical needs of AA cancer patients and provide culturally sensitive care that addresses these needs.

Collection and curation of prokaryotic genome assemblies from type strains at NCBI.

The public sequence databases are entrusted with the dual responsibility of providing an accessible archive to all submitters and supporting data reliability and its re-use to all users. Genomes from type materials can act as an unambiguous reference for a taxonomic name and play an important role in comparative genomics, especially for taxon verification or reclassification. The National Center for Biotechnology Information (NCBI) collects and curates information on prokaryotic type strains and genomes from type strains. The average nucleotide identity (ANI)-based quality control processes introduced at NCBI to verify the genomes from type strains and improve related sequence records are detailed here. Using the curated genomes from type strains as reference, the taxonomy of over 1.1 million GenBank genomes were verified and the taxonomy of over 7000 new submissions before acceptance to GenBank and over 1800 existing genomes in GenBank were reclassified.

GenBank.

GenBank® (https://www.ncbi.nlm.nih.gov/genbank/) is a comprehensive, public database that contains 9.9 trillion base pairs from over 2.1 billion nucleotide sequences for 478 000 formally described species. Daily data exchange with the European Nucleotide Archive and the DNA Data Bank of Japan ensures worldwide coverage. Recent updates include new resources for data from the SARS-CoV-2 virus, updates to the NCBI Submission Portal and associated submission wizards for dengue and SARS-CoV-2 viruses, new taxonomy queries for viruses and prokaryotes, and simplified submission processes for EST and GSS sequences.

Impact of the metabolic syndrome on prevalence and survival in motor neuron disease: a retrospective case series.

Metabolic dysfunction is an important factor in the pathogenesis of motor neuron disease, but its prevalence and association with survival in this disorder is unknown. We hypothesized that patients with motor neuron disease would show a higher prevalence of metabolic syndrome compared to the general New Zealand population, and that metabolic syndrome would be associated with worsened survival. We undertook a retrospective analysis in 109 motor neuron disease patients diagnosed and treated at Waikato Hospital from 2013 to 2020. Demographic, clinical, and laboratory data were collected. Survival was defined as the date of initial symptom onset to the date of death. Of 104 eligible patients, 34 patients (33%) had metabolic syndrome (33% of Europeans, 46% of Maori). Mean survival in motor neuron disease patients with metabolic syndrome was significantly reduced compared to patients without metabolic syndrome (38 vs. 61 months, P = 0.044), with a 5-year survival rate of 21% for the former and 38% for the latter (P = 0.012). Compared with the general New Zealand population, metabolic syndrome is highly prevalent amongst motor neuron disease patients in the Waikato region and it is associated with worsened survival. Metabolic dysfunction may be a key factor underlying the pathogenesis of motor neuron disease.

Primary hypothyroidism in childhood cancer survivors: Prevalence, risk factors, and long-term consequences.

BACKGROUND: Data on primary hypothyroidism and its long-term impact on the health, cognition, and quality of life (QOL) of childhood cancer survivors are limited. This study examined the prevalence of and risk factors for primary hypothyroidism and its associations with physical, neurocognitive, and psychosocial outcomes. METHODS: This was a retrospective study with a cross-sectional health outcome analysis of an established cohort comprising 2965 survivors of childhood cancer (52.8% male; median current age, 30.9 years, median time since cancer diagnosis, 22.3 years). Multivariable logistic regression estimated odds ratios (ORs) and 95% confidence intervals (CIs) for associations between primary hypothyroidism and cancer-related risk factors, cardiovascular disease risk factors, frailty, neurocognitive and QOL outcomes, social attainment, and subsequent thyroid carcinoma. Associations between serum free thyroxine and thyrotropin levels at assessment and health outcomes were explored. RESULTS: The prevalence of primary hypothyroidism was 14.7% (95% CI, 13.5%-16.0%). It was more likely in females (OR, 1.06; 95% CI, 1.03-1.08), was less likely in non-Whites (OR, 0.96; 95% CI, 0.93-0.99), was associated with thyroid radiotherapy (higher risk at higher doses), and was more common if cancer was diagnosed at an age ≥ 15.0 years versus an age < 5 years (OR, 1.05; 95% CI, 1.01-1.09). Primary hypothyroidism was associated with frailty (OR, 1.54; 95% CI, 1.05-2.26), dyslipidemia (OR, 1.52; 95% CI, 1.14-2.04), impaired physical QOL (OR, 1.66; 95% CI, 1.12-2.48), and having health care insurance (OR, 1.51; 95% CI, 1.07-2.12). CONCLUSIONS: Primary hypothyroidism is common in survivors and is associated with unfavorable physical health and QOL outcomes. The impact of thyroid hormone replacement practices on these outcomes should be investigated further.

Emotional Distress and Financial Toxicity in Younger Adult Patients Undergoing Oncologic Surgery.

BACKGROUND: There has been an alarming increase in the number of young adults (YA) diagnosed with cancer. The emotional, psychosocial, and financial distress experienced by newly diagnosed YA undergoing cancer surgery remains largely unknown. METHODS: A validated biopsychosocial distress screening tool (SupportScreen) was administered to patients diagnosed with cancer before surgery between 2009 and 2017 in a National Cancer Institute Comprehensive Cancer Center. Patients were stratified into YA less than or equal to 45 years and older adults (OA) above 45 years. Descriptive statistics and logistic regression were used to analyze distress outcomes. RESULTS: In total, 4297 patients were identified, with YA comprising 13.3% (n=573) of the cohort. YA reported higher emotional distress, including increased anxiety (33.8% vs 27.4%, P =0.002), greater fear of procedures (26.7% vs 22%, P =0.018), and difficulty managing emotions (26% vs 20.7%, P =0.006). YA struggled more frequently to manage work/school (29.5% vs 19.3%, P <0.001), finding resources (17.8% vs 11.8%, P <0.001), changes in physical appearance (22.2% vs 13.4%, P <0.001), fatigue (36% vs 27.3%, P <0.001), and ability to have children (18.4% vs 3%, P <0.001). Financial toxicity was significantly higher in the YA group (40.5% vs 28%, P <0.001). While income level was strongly protective against emotional distress and financial toxicity in OAs, it was less protective against the risk of financial toxicity in YA. Younger age was an independent predictor of financial toxicity in a model adjusted to income (odds ratio=1.52, P =0.020). CONCLUSIONS: YA in the prime of their personal and professional years of productivity require special attention when undergoing surgical evaluation for cancer. Resource allocation and counseling interventions should be integrated as part of their routine care to expedite their return to optimal physical and holistic health and mitigate psychosocial distress and financial toxicity.

A Cross-Sectional Study of Distress Levels in Patients with Newly Diagnosed Breast Cancer: The Impact of Race, Ethnicity, and Language Preference.

PURPOSE: Our objective was to assess distress levels in female breast cancer patients as a function of race, ethnicity, and preferred language. We hypothesized minority patients and non-English screen-takers would report higher distress levels compared to English screen-takers and non-Hispanic whites. METHODS: We conducted a retrospective observational study of female breast cancer patients at an NCI designated cancer center from 2009 to 2016 who were administered a validated biopsychosocial distress screening questionnaire. Self-reported data on race and ethnicity was collected. RESULTS: A total of 3,156 patients were included in the analysis; mean age of 56.3 (SD 12.25) years. The racial/ethnic cohort distribution included 54% non-Hispanic white (NHW), 19% Hispanic, 16% Asian, 7% Black/African American, and 4% other. On multivariable analysis only Hispanic patients were significantly more likely to report overall distress compared to NHW (OR [1.39; CI [1.03-1.87; p=0.03). Asians were significantly less likely to report distress in the functional domain (OR 0.71, CI [0.58-0.88]; p=0.002), while Black patients were significantly more likely to report highest distress levels in the physical (OR 1.53, CI [1.11-2.12]; p=0.01) domain. Hispanic Spanish screen-takers reported significantly more distress compared to Hispanic English screen-takers across all four domains of distress (p<0.05 for all). CONCLUSIONS: Top sources of distress in female breast cancer patients vary as a function of race, ethnicity, and preferred language. Future studies should focus on identifying effective, culturally appropriate targeted interventions to mitigate emotional distress levels in ethnic and racial minorities as well as non-English speaking patients with breast cancer.

Association between requests for supportive care assistance and patients' characteristics, prior to treatment in a comprehensive cancer center.

PURPOSE: Patients with cancer experience a wide array of distress symptoms (emotional, practical, physical, and functional), which often hinders their quality of life and survival. Unfortunately, only a small proportion of these patients request assistance for these problems. This study explored the relationship between requests for supportive care assistance and distress of patients newly diagnosed with cancer. METHODS: This study was conducted at city of hope, an NCI-designated comprehensive cancer center, and included 2658 patients treated between 2009 and 2017. Patients were asked to complete a 30-item biopsychosocial problem-related distress survey via SupportScreen® , prior to any treatment. Correlations between requests for assistance and distress domains were evaluated. Primary types of requests were examined for all patients, and general linear modeling was used to determine the significant predictors of requests for assistance. p-values <0.05 were considered significant. RESULTS: Strong correlations were observed between distress subscales and requests for assistance (r ranging from 0.67 to 0.69). The primary types of requests varied by domain: items such as feeling anxious or fearful, finances, and sleep ranked first within the emotional, practical, and physical-functional domains respectively (∼20% requests for each item). Verbal assistance was generally preferred to the written form of assistance, with the exception of a few items, including finances. Overall, household income of <$100,000 and completing the survey in Spanish were significant predictors of requests for assistance. Regarding the practical and physical-functional domains, having an advanced stage of disease was significantly related to an increase in demands for assistance. Being older was associated to a decrease in requests for assistance vis-à-vis both the emotional and physical functional subscales. CONCLUSION: We demonstrated that distress levels were strongly correlated with requests for assistance. Patients' clinical and demographic characteristics such as age, household income, disease stage and survey language were associated with inquiries for psychosocial support, highlighting the importance of targeting interventions towards those most likely to need them, to better aim patients' needs. Therefore, tailoring supportive care assistance to patients' characteristics could help boost the frequency of requests, reduce distress burden, and improve health outcomes.

GenBank.

GenBank® (www.ncbi.nlm.nih.gov/genbank/) is a comprehensive, public database that contains over 6.25 trillion base pairs from over 1.6 billion nucleotide sequences for 450 000 formally described species. Daily data exchange with the European Nucleotide Archive (ENA) and the DNA Data Bank of Japan (DDBJ) ensures worldwide coverage. Recent updates include a new version of Genome Workbench that supports GenBank submissions, new submission wizards for viral genomes, enhancements to BankIt and improved handling of taxonomy for sequences from pathogens.

The impact of COVID-19 on access to canine integrative medical care in Michigan, USA, and Ontario and British Columbia, Canada.

OBJECTIVE: To determine the effects of the COVID-19 associated restrictions on the ability of owners in Michigan (MI), USA versus Ontario (ON) and British Columbia (BC), Canada, to obtain care for their chronically painful dogs. STUDY DESIGN: Cross-sectional survey. POPULATION: A total of 90 owners met the inclusion criteria for the study. METHODS: An anonymous electronic survey was distributed to owners at four veterinary integrative medicine (IM) clinics during July and August 2020. Two clinics in MI and one each in ON and BC were recruited. Owners were asked about availability of IM care preceding and during COVID-19 restrictions and their opinions of the impact of COVID-19 on their dog's health. The survey asked where owners sought care for their dogs, types of chronic conditions treated, therapeutic modalities used, and if owners had a medical background. Comparisons were made within and between groups. Thematic analysis, Fisher's exact test, chi-square analyses, McNemar's and Wilcoxon signed-rank tests for paired comparisons were performed (p < 0.05). RESULTS: During COVID-19 restrictions, access to IM care was better for dogs in ON and BC than in MI (p < 0.001). The negative effect of the pandemic restrictions to IM care on quality of life was perceived greater by owners in MI than those in ON and BC (p < 0.001). The owners' medical backgrounds had no effect on attempts to access care during this time (p = 0.76). CONCLUSIONS AND CLINICAL RELEVANCE: The results suggest that a widespread disease in humans had an adverse impact on animal welfare. Providers of veterinary care should use this experience to establish protocols to ensure continuity of care for chronically painful animals in the event of a similar situation in the future.

Recruiting custodial grandmothers using Facebook.

OBJECTIVES: Recruitment through Facebook is gaining favor as an approach for research, including clinical trials, because of the platform's ability to reach broad and diverse populations. As older adults increase their social media use, recruitment through Facebook has become a viable option. The purposes of this paper are to report the methodological process and lessons learned from recruiting custodial grandmothers (CGMs) for a cross-sectional study examining parenting self-efficacy and psychological well-being. PARTICIPANTS: A total of 113 people consented and accessed the survey online, with 40 (35.4%) completing surveys. The final sample comprised 68 grandmothers, with 59% recruited via Facebook. METHODS: Facebook recruitment for the online survey included creating a dedicated Facebook study page, accessing existing Facebook pages for custodial grandparents, and using paid advertising. Face-to-face recruitment strategies also were used with paper surveys. RESULTS: We compared the characteristics of those completing online surveys versus paper surveys. CGMs completing the survey online were significantly younger and more likely to be Caucasian than those completing the paper survey. CONCLUSIONS: Findings indicated online recruitment via Facebook is an advantageous method to reach CGMs. However, additional research is needed to determine if other online and social media platforms would be useful in recruiting this population.

Needs of Grandparents Raising Grandchildren: A Qualitative Study.

This study identified custodial grandparents' perception of sources of stress that may affect their health and better understand their needs. Findings from this qualitative study are based on thematic analysis of interviews with 10 custodial grandparents. The following themes emerged: 1) grandparents' stress from perceived lack of readiness to care for grandchildren; 2) need for effective communication between and among family members; 3) sufficiency of financial and legal resources; 4) access to community resources, and 5) raising grandchildren reenergizes and revitalizes grandparents' physical and mental health. These findings provide insight into the stressful aspects of the role of raising grandchildren. Understanding stressors affecting custodial grandparents and their grandchildren will help school nurses, social workers, teachers, school administrators and other professionals collaborate to address their challenges.

Emotional problem-related distress screening and its prevalence by cancer type: Assessment by patients' characteristics and level of assistance requested.

OBJECTIVE: Emotional problem-related distress is a common issue faced by patients with cancer. However, patients suffering with this emotional burden do not typically seek assistance. This study sought to determine the prevalence of emotional problem-related distress by cancer type, and identify factors correlated with the level of assistance requested. METHODS: Using the SupportScreen®, patients were screened for emotional problem-related distress at their first or second visit to an NCI designated Comprehensive Cancer Center. General Linear Model was used to test the association between emotional problem-related distress and type of cancer, and the relationship between level of assistance requested and patients' characteristics. RESULTS: A total of 2,421 patients were included in this analysis. Patients were mostly female (62%), diagnosed with breast (24%), gynecological (16%) or gastrointestinal (15%) cancers. Highest levels of emotional problem-related distress were reported by patients diagnosed with lung, gynecological, breast and gastrointestinal cancers. Level of assistance requested were significantly associated with problem-related distress scores (p < 0.001), which were higher among patients with lower household incomes (p < 0.001) and Spanish as primary language (p = 0.001). CONCLUSION: Our study found an association between Level of assistance requested and emotional problem-related distress, which were heightened by lower income and Spanish-speaking. Intervention strategies should be considered to increase access to psychosocial support services.

Association between hospital anxiety and depression scale and problem-related distress in patients with cancer in a Brazilian private institution.

OBJECTIVE: Emotional symptoms are frequently reported among patients with cancer. We evaluated the association between emotional symptoms and problem-related distress in a sample of patients with cancer about to initiate chemotherapy within a private hospital in Brazil. METHODS: Patients were assessed before initiating chemotherapy, treatment mid-point, and on the last day of treatment for anxiety and depression (Hospital Anxiety and Depression Scale [HADS]) and for problem-related distress (Distress Thermometer Problem List). Problem-related distress variable was computed as the sum of practical, physical, spiritual and familial problems. Mixed-model analysis was applied to determine the association between HADS and problem-related distress, adjusting for age and gender. RESULTS: A total of 655 consecutive patients were enrolled. There was a significant main effect of time (F = 8.99, p = 0.0001), showing that emotional symptoms improve over time. A significant main effect was observed for problem-related distress (F = 371.56, p < 0.0001) revealing that patients with elevated problem-related distress at baseline tend to have higher HADS across the three time points, compared to patients with lower problem-related distress. There was an interaction effect between problem-related distress and time (F = 85.22, p < 0.0001), suggesting that HADS scores decreased differently over time, depending on patients' initial level of problem-related distress. CONCLUSION: Overall, emotional symptoms, while decreasing over time, remained associated with problem-related distress after chemotherapy in Brazil. The potential benefit of implementing a psychosocial intervention remains high throughout cancer treatment.

GenBank.

GenBank® (www.ncbi.nlm.nih.gov/genbank/) is a comprehensive database that contains publicly available nucleotide sequences for 420 000 formally described species. Most GenBank submissions are made using BankIt, the NCBI Submission Portal, or the tool tbl2asn, and are obtained from individual laboratories and batch submissions from large-scale sequencing projects, including whole genome shotgun (WGS) and environmental sampling projects. Daily data exchange with the European Nucleotide Archive (ENA) and the DNA Data Bank of Japan (DDBJ) ensures worldwide coverage. GenBank is accessible through the NCBI Nucleotide database, which links to related information such as taxonomy, genomes, protein sequences and structures, and biomedical journal literature in PubMed. BLAST provides sequence similarity searches of GenBank and other sequence databases. Complete bimonthly releases and daily updates of the GenBank database are available by FTP. Recent updates include an expansion of sequence identifier formats to accommodate expected database growth, submission wizards for ribosomal RNA, and the transfer of Expressed Sequence Tag (EST) and Genome Survey Sequence (GSS) data into the Nucleotide database.

Database resources of the National Center for Biotechnology Information.

The National Center for Biotechnology Information (NCBI) provides a large suite of online resources for biological information and data, including the GenBank® nucleic acid sequence database and the PubMed database of citations and abstracts published in life science journals. The Entrez system provides search and retrieval operations for most of these data from 38 distinct databases. The E-utilities serve as the programming interface for the Entrez system. Augmenting many of the web applications are custom implementations of the BLAST program optimized to search specialized data sets. New resources released in the past year include PubMed Labs and a new sequence database search. Resources that were updated in the past year include PubMed, PMC, Bookshelf, genome data viewer, Assembly, prokaryotic genomes, Genome, BioProject, dbSNP, dbVar, BLAST databases, igBLAST, iCn3D and PubChem. All of these resources can be accessed through the NCBI home page at www.ncbi.nlm.nih.gov.