Assembly and annotation of the black spruce genome provide insights on spruce phylogeny and evolution of stress response.

Black spruce (Picea mariana [Mill.] B.S.P.) is a dominant conifer species in the North American boreal forest that plays important ecological and economic roles. Here, we present the first genome assembly of P. mariana with a reconstructed genome size of 18.3 Gbp and NG50 scaffold length of 36.0 kbp. A total of 66,332 protein-coding sequences were predicted in silico and annotated based on sequence homology. We analyzed the evolutionary relationships between P. mariana and 5 other spruces for which complete nuclear and organelle genome sequences were available. The phylogenetic tree estimated from mitochondrial genome sequences agrees with biogeography; specifically, P. mariana was strongly supported as a sister lineage to P. glauca and 3 other taxa found in western North America, followed by the European Picea abies. We obtained mixed topologies with weaker statistical support in phylogenetic trees estimated from nuclear and chloroplast genome sequences, indicative of ancient reticulate evolution affecting these 2 genomes. Clustering of protein-coding sequences from the 6 Picea taxa and 2 Pinus species resulted in 34,776 orthogroups, 560 of which appeared to be specific to P. mariana. Analysis of these specific orthogroups and dN/dS analysis of positive selection signatures for 497 single-copy orthogroups identified gene functions mostly related to plant development and stress response. The P. mariana genome assembly and annotation provides a valuable resource for forest genetics research and applications in this broadly distributed species, especially in relation to climate adaptation.

Sexually Transmitted Infections Risk and Interstate Sexual Networks Among Men Who Have Sex With Men in New England.

ABSTRACT: By investigating relationships between sexual mobility and sexual transmitted infection (STI) risk factors among men who have sex with men, we found that STI history, number of sexual partners, and substance use are associated with increased odds of interstate sexual encounters, suggesting that interjurisdictional approaches to STI prevention are needed.

CIViCdb 2022: evolution of an open-access cancer variant interpretation knowledgebase.

CIViC (Clinical Interpretation of Variants in Cancer; civicdb.org) is a crowd-sourced, public domain knowledgebase composed of literature-derived evidence characterizing the clinical utility of cancer variants. As clinical sequencing becomes more prevalent in cancer management, the need for cancer variant interpretation has grown beyond the capability of any single institution. CIViC contains peer-reviewed, published literature curated and expertly-moderated into structured data units (Evidence Items) that can be accessed globally and in real time, reducing barriers to clinical variant knowledge sharing. We have extended CIViC's functionality to support emergent variant interpretation guidelines, increase interoperability with other variant resources, and promote widespread dissemination of structured curated data. To support the full breadth of variant interpretation from basic to translational, including integration of somatic and germline variant knowledge and inference of drug response, we have enabled curation of three new Evidence Types (Predisposing, Oncogenic and Functional). The growing CIViC knowledgebase has over 300 contributors and distributes clinically-relevant cancer variant data currently representing >3200 variants in >470 genes from >3100 publications.

A comprehensive study of mobility functioning information in clinical notes: Entity hierarchy, corpus annotation, and sequence labeling.

BACKGROUND: Secondary use of Electronic Health Records (EHRs) has mostly focused on health conditions (diseases and drugs). Function is an important health indicator in addition to morbidity and mortality. Nevertheless, function has been overlooked in accessing patients' health status. The World Health Organization (WHO)'s International Classification of Functioning, Disability and Health (ICF) is considered the international standard for describing and coding function and health states. We pioneer the first comprehensive analysis and identification of functioning concepts in the Mobility domain of the ICF. RESULTS: Using physical therapy notes at the National Institutes of Health's Clinical Center, we induced a hierarchical order of mobility-related entities including 5 entities types, 3 relations, 8 attributes, and 33 attribute values. Two domain experts manually curated a gold standard corpus of 14,281 nested entity mentions from 400 clinical notes. Inter-annotator agreement (IAA) of exact matching averaged 92.3 % F1-score on mention text spans, and 96.6 % Cohen's kappa on attributes assignments. A high-performance Ensemble machine learning model for named entity recognition (NER) was trained and evaluated using the gold standard corpus. Average F1-score on exact entity matching of our Ensemble method (84.90 %) outperformed popular NER methods: Conditional Random Field (80.4 %), Recurrent Neural Network (81.82 %), and Bidirectional Encoder Representations from Transformers (82.33 %). CONCLUSIONS: The results of this study show that mobility functioning information can be reliably captured from clinical notes once adequate resources are provided for sequence labeling methods. We expect that functioning concepts in other domains of the ICF can be identified in similar fashion.

Estimating the Population Size of Female Sex Workers in Three South African Cities: Results and Recommendations From the 2013-2014 South Africa Health Monitoring Survey and Stakeholder Consensus.

BACKGROUND: Robust population size estimates of female sex workers and other key populations in South Africa face multiple methodological limitations, including inconsistencies in surveillance and programmatic indicators. This has, consequently, challenged the appropriate allocation of resources and benchmark-setting necessary to an effective HIV response. A 2013-2014 integrated biological and behavioral surveillance (IBBS) survey from South Africa showed alarmingly high HIV prevalence among female sex workers in South Africa's three largest cities of Johannesburg (71.8%), Cape Town (39.7%), and eThekwini (53.5%). The survey also included several multiplier-based population size estimation methods. OBJECTIVE: The objective of our study was to present the selected population size estimation methods used in an IBBS survey and the subsequent participatory process used to estimate the number of female sex workers in three South African cities. METHODS: In 2013-2014, we used respondent-driven sampling to recruit independent samples of female sex workers for IBBS surveys in Johannesburg, Cape Town, and eThekwini. We embedded multiple multiplier-based population size estimation methods into the survey, from which investigators calculated weighted estimates and ranges of population size estimates for each city's female sex worker population. Following data analysis, investigators consulted civil society stakeholders to present survey results and size estimates and facilitated stakeholder vetting of individual estimates to arrive at consensus point estimates with upper and lower plausibility bounds. RESULTS: In total, 764, 650, and 766 female sex workers participated in the survey in Johannesburg, Cape Town, and eThekwini, respectively. For size estimation, investigators calculated preliminary point estimates as the median of the multiple estimation methods embedded in the IBBS survey and presented these to a civil society-convened stakeholder group. Stakeholders vetted all estimates in light of other data points, including programmatic experience, ensuring inclusion only of plausible point estimates in median calculation. After vetting, stakeholders adopted three consensus point estimates with plausible ranges: Johannesburg 7697 (5000-10,895); Cape Town 6500 (4579-9000); eThekwini 9323 (4000-10,000). CONCLUSIONS: Using several population size estimates methods embedded in an IBBS survey and a participatory stakeholder consensus process, the South Africa Health Monitoring Survey produced female sex worker size estimates representing approximately 0.48%, 0.49%, and 0.77% of the adult female population in Johannesburg, Cape Town, and eThekwini, respectively. In data-sparse environments, stakeholder engagement and consensus is critical to vetting of multiple empirically based size estimates procedures to ensure adoption and utilization of data-informed size estimates for coordinated national and subnational benchmarking. It also has the potential to increase coherence in national and key population-specific HIV responses and to decrease the likelihood of duplicative and wasteful resource allocation. We recommend building cooperative and productive academic-civil society partnerships around estimates and other strategic information dissemination and sharing to facilitate the incorporation of additional data as it becomes available, as these additional data points may minimize the impact of the known and unknown biases inherent in any single, investigator-calculated method.

Pain evaluation in patients receiving intravenous patient-controlled analgesia after surgery.

STUDY OBJECTIVE: To evaluate the effectiveness of intravenous patient-controlled analgesia (PCA) in patients after surgery. DESIGN: Prospective, observational study. SETTING: University teaching hospital. PATIENTS: Sixty patients with American Society of Anesthesiologists physical status I-III receiving intravenous PCA for postoperative pain. The PCA was programmed to deliver morphine 1 mg or hydromorphone 0.1-0.2 mg, with a lockout interval of 10 and 6 minutes for 80% and 20% of the patients, respectively. MEASUREMENTS AND MAIN RESULTS: Patients were asked, up to 4 times during PCA use and once within 4 hours after PCA use, to describe and rate their intensity of pain at rest and after activity. During the first 12 hours of intravenous PCA use, 75% of the patients reported moderate-to-severe pain > or = 5 on a verbal numeric rating scale) at rest, 80% after activity. Corresponding values, respectively, were 33% and 72% for the 12-24-hour period, 43% and 76% for the 24-36-hour period, and 36% and 64% for the 36-48-hour period of intravenous PCA use. Within 4 hours of stopping PCA, 30% and 58% of the patients had moderate-to-severe pain at rest and after activity, respectively. In approximately 50% of patients, presence of pain was described with words signifying sensory and affective dimensions of pain. Pain control was rated as good or very good by 54% of patients during the first 12 hours of intravenous PCA. Ratings of pain control tended to improve with time. CONCLUSION: Successful postoperative pain management using PCA is difficult to achieve on a consistent basis unless treatment is individualized. Our data support the hypothesis that small fixed doses fail to achieve adequate relief in many patients.

Modafinil improves recovery after general anesthesia.

UNLABELLED: Recovery from general anesthesia often involves residual sedation, drowsiness, fatigue, and lack of energy that may last hours to days. Modafinil is a wakefulness-promoting drug approved for patients with excessive daytime sleepiness associated with narcolepsy. We evaluated the effect of single doses of modafinil (200 mg) and placebo in patients recovering from general anesthesia. Thirty-four subjects participated in this prospective, randomized, double-blind study approved by our IRB. Preoperatively, patients were asked to rate various symptoms they had experienced over the previous 24-h using a verbal analog scale (VAS) of 0 to 10 as well as discrete scale when indicated. Postoperatively, once the patient was able to tolerate oral intake and met our institutional discharge criteria, the study drug (modafinil 200 mg or placebo) was administered with a sip of water. Patients were contacted 24 (1) hours after dosing to evaluate postdischarge symptoms. Patients in the placebo group reported significantly more postoperative fatigue (4.8 [3.3] versus 1.4 [1.8]), exhaustion (4.3 [3.3] versus 2.4 [3.1]), or degree of feeling worn out (4.7 [3.6] versus 2.9 [2.4]). Significantly more patients reported moderate to severe fatigue in the placebo group (65% versus 12%). Two major themes of "alertness" and "energy" were expressed by 71% of the patients receiving modafinil versus 18% of those receiving placebo. Patients recovering from general anesthesia can significantly benefit from modafinil. IMPLICATIONS: Modafinil significantly reduces fatigue and improves feelings of alertness and energy in postoperative patients. Patients recovering from general anesthesia can significantly benefit from modafinil administration.