LexicHash: sequence similarity estimation via lexicographic comparison of hashes.

MOTIVATION: Pairwise sequence alignment is a heavy computational burden, particularly in the context of third-generation sequencing technologies. This issue is commonly addressed by approximately estimating sequence similarities using a hash-based method such as MinHash. In MinHash, all k-mers in a read are hashed and the minimum hash value, the min-hash, is stored. Pairwise similarities can then be estimated by counting the number of min-hash matches between a pair of reads, across many distinct hash functions. The choice of the parameter k controls an important tradeoff in the task of identifying alignments: larger k-values give greater confidence in the identification of alignments (high precision) but can lead to many missing alignments (low recall), particularly in the presence of significant noise. RESULTS: In this work, we introduce LexicHash, a new similarity estimation method that is effectively independent of the choice of k and attains the high precision of large-k and the high sensitivity of small-k MinHash. LexicHash is a variant of MinHash with a carefully designed hash function. When estimating the similarity between two reads, instead of simply checking whether min-hashes match (as in standard MinHash), one checks how "lexicographically similar" the LexicHash min-hashes are. In our experiments on 40 PacBio datasets, the area under the precision-recall curves obtained by LexicHash had an average improvement of 20.9% over MinHash. Additionally, the LexicHash framework lends itself naturally to an efficient search of the largest alignments, yielding an O(n) time algorithm, and circumventing the seemingly fundamental O(n2) scaling associated with pairwise similarity search. AVAILABILITY AND IMPLEMENTATION: LexicHash is available on GitHub at https://github.com/gcgreenberg/LexicHash.

Implementation of a Virtual Asynchronous Scribe Program to Reduce Physician Burnout.

GOAL: Administrative burden is one of many potential root causes of physician burnout. Scribe documentation assistance can reduce this burden. However, traditional in-person scribe services are challenged by consistent staffing because the model requires the physical presence of a scribe and limits the team to a single individual. In addition, in-person scribes cannot provide the flexible support required for virtual care encounters, which can now pivot geographically and temporally. To respond to these challenges, our health network implemented an asynchronous virtual scribe model and evaluated the program's impact on clinician perceptions of burnout across multiple outpatient specialties. METHODS: Using a mixed-methods, pre-/postdesign, this evaluation measured the impact of an asynchronous virtual scribe program on physician burnout. Physicians were given the Professional Fulfillment Index tool (to self-assess their mental state) and free-text comment surveys before virtual scribe initiation and again at 3-, 6-, and 12-month intervals after program implementation. Descriptive statistics of survey results and qualitative review of free-text entries were analyzed for themes of facilitation and barriers to virtual scribe use. PRINCIPAL FINDINGS: Of 50 physician participants in this study, 42 (84%) completed the preintervention survey and 15 (36%) completed all 4 surveys; 25 participants (50%) discontinued scribe use after 12 months. Burnout levels-as defined by dread, exhaustion, lack of enthusiasm, decrease in empathy, and decrease in colleague connection-all trended toward improvement during this study. Importantly, quality, time savings, burnout, and productivity moved in positive directions as well. PRACTICAL APPLICATION: The cost burden to physicians and the COVID-19 pandemic inhibited the continued use of asynchronous virtual medical scribes. Nevertheless, those who continued in the program have reported positive outcomes, which indicates that the service can be a viable and effective tool to reduce physician burnout.

Adult Vaccination.

Adult vaccination rates are low in the United States, despite clear benefits for reducing morbidity and mortality. Vaccine science is evolving rapidly, and family physicians must maintain familiarity with the most recent guidelines. The recommended adult immunization schedule is updated annually by the Advisory Committee on Immunization Practices of the Centers for Disease Control and Prevention. All eligible patients should receive SARS-CoV-2 vaccines according to the current guidelines. Adults without contraindications should also receive an annual influenza vaccine. Hepatitis A vaccine is recommended for adults with specific risk factors. All pregnant patients, adults younger than 60 years, and those 60 years and older who have risk factors should receive a hepatitis B vaccine. A 15- or 20-valent pneumococcal conjugate vaccine is recommended for all patients who are 65 years and older. Patients who receive 15-valent pneumococcal conjugate vaccine should receive a dose of 23-valent pneumococcal polysaccharide vaccine one year later. Adults 19 to 64 years of age should receive a pneumococcal vaccination if they have medical risk factors. A single dose of measles, mumps, and rubella vaccine is recommended for adults without presumptive immunity, and additional doses are recommended for patients with HIV and postdelivery for pregnant patients who are not immune to rubella. A tetanus and diphtheria toxoids booster is recommended every 10 years. For pregnant patients and those in close contact with young infants, a tetanus toxoid, reduced diphtheria toxoid, and acellular pertussis vaccine should be administered. The human papillomavirus vaccine is recommended for all people through 26 years of age. Herpes zoster vaccine is indicated for all adults 50 years and older. .

Asynchronous Telehealth.

Asynchronous telehealth provides a viable option for improving access in a convenient and timely manner to patients seeking care as well as for physicians seeking subspecialty consultation. Access to technology, clear guidelines, standards, and expectations is required for this innovation to function well. Limitations in access due to patient and technology factors is an area that requires attention. Positive impact on access and quality has been demonstrated. Rapid development continues and was enhanced with the Sars-CoV-2 pandemic.

Improving bacterial genome assembly using a test of strand orientation.

SUMMARY: The complexity of genome assembly is due in large part to the presence of repeats. In particular, large reverse-complemented repeats can lead to incorrect inversions of large segments of the genome. To detect and correct such inversions in finished bacterial genomes, we propose a statistical test based on tetranucleotide frequency (TNF), which determines whether two segments from the same genome are of the same or opposite orientation. In most cases, the test neatly partitions the genome into two segments of roughly equal length with seemingly opposite orientations. This corresponds to the segments between the DNA replication origin and terminus, which were previously known to have distinct nucleotide compositions. We show that, in several cases where this balanced partition is not observed, the test identifies a potential inverted misassembly, which is validated by the presence of a reverse-complemented repeat at the boundaries of the inversion. After inverting the sequence between the repeat, the balance of the misassembled genome is restored. Our method identifies 31 potential misassemblies in the NCBI database, several of which are further supported by a reassembly of the read data. AVAILABILITY AND IMPLEMENTATION: A github repository is available at https://github.com/gcgreenberg/Oriented-TNF.git. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

The Impact of Telehealth on Primary Care Physician Panel Sizes: A Modeling Study.

INTRODUCTION: Most research on the use of telehealth in lieu of in-office visits has focused on its growth, its impact on access, and the experience of physicians and patients. One important issue that has not gotten much attention is the potential for telehealth to significantly increase physician capacity by reducing nonvalue adding activities and patient no-shows. We explore this in this article. METHODS: We use data from the electronic health records of 2 health care systems and information gathered from family medicine physician focus groups to develop estimates of visit durations and no-show rates for tele-visits. We use these in a simulation model to determine how patient panel sizes could be increased while maintaining high levels of access by substituting tele-visits for in-person visits. RESULTS: We found that tele-visits reduce the nonvalue-added time physicians spend with patients as well as patient no-shows. At current levels of tele-visit utilization, the use of tele-visits may translate into more than a 10% increase in patient panel sizes assuming a modest reduction in visit durations and no-shows, and as much as a 30% increase assuming that half of all visits could be effectively conducted virtually and result in a greater reduction in visit durations and no-shows. DISCUSSION: Our study provides evidence that a major benefit of using telehealth for many routine encounters is a reduction in wasted physician time and a substantial increase in the number of patients that a primary care physician can care for without jeopardizing access to care.

Key Factors Promoting Rapid Implementation of Virtual Screening Modalities for the COVID-19 Pandemic Response.

BACKGROUND: The COVID-19 (C-19) pandemic required swift response from health care organizations to mitigate spread and impact. A large integrated health network rapidly deployed and operationalized multiple access channels to the community, allowing assessment and triage to occur virtually. These channels were characterized by swift implementation of virtual models, including asynchronous e-visits and video visits for C-19 screening. PURPOSE: (1) Evaluate implementation characteristics of C-19 screening e-visits and video visits. (2) Identify volume of C-19 screening and other care provided via e-visits and video visits. (3) Discuss future implications of expanded virtual access models. METHODS: Retrospective analysis of implementation data for C-19 screening e-visits and video visits, including operational characteristics and visit/screening volumes conducted. RESULTS: Virtual channels were implemented and rapidly expanded during the first week C-19 testing was made available. During the study period, primary care clinicians conducted 10,673 e-visits and 31,226 video visits with 9,126 and 26,009 patients, respectively. Within these 2 virtual modalities, 4,267 C-19 tests were ordered (10% of visits). Four hundred forty-eight clinicians supported 24/7 access to these virtual modalities. DISCUSSION: Given ongoing patient interest and opportunity, virtual health care services will continue to be available for an expanded number of symptoms and diagnoses.

Hypertriglyceridemia: A strategic approach.

This review, and the at-a-glance tables that follow, detail indications and strategies for the treatment of adults with hypertriglyceridemia.

Continuous quality improvement methodology: a case study on multidisciplinary collaboration to improve chlamydia screening.

This article illustrates quality improvement (QI) methodology using an example intended to improve chlamydia screening in women. QI projects in healthcare provide great opportunities to improve patient quality and safety in a real-world healthcare setting, yet many academic centres lack training programmes on how to conduct QI projects. The choice of chlamydia screening was based on the significant health burden chlamydia poses despite simple ways to screen and treat. At the University of Michigan, we implemented a multidepartment process to improve the chlamydia screening rates using the plan-do-check-act model. Steps to guide QI projects include the following: (1) assemble a motivated team of stakeholders and leaders; (2) identify the problem that is considered a high priority; (3) prepare for the project including support and resources; (4) set a goal and ways to evaluate outcomes; (5) identify the root cause(s) of the problem and prioritise based on impact and effort to address; (6) develop a countermeasure that addresses the selected root cause effectively; (7) pilot a small-scale project to assess for possible modifications; (8) large-scale roll-out including education on how to implement the project; and (9) assess and modify the process with a feedback mechanism. Using this nine-step process, chlamydia screening rates increased from 29% to 60%. QI projects differ from most clinical research projects by allowing clinicians to directly improve patients' health while contributing to the medical science body. This may interest clinicians wishing to conduct relevant research that can be disseminated through academic channels.

Two-year longitudinal assessment of physicians' perceptions after replacement of a longstanding homegrown electronic health record: does a J-curve of satisfaction really exist?

This report describes a 2-year prospective, longitudinal survey of attending physicians in 3 clinical areas (family medicine, general pediatrics, internal medicine) who experienced a transition from a homegrown electronic health record (EHR) to a vendor EHR. Participants were already highly familiar with using EHRs. Data were collected 1 month before and 3, 6, 13, and 25 months post implementation. Our primary goal was to determine if perceptions followed a J-curve pattern in which they initially dropped but eventually surpassed baseline measures. A J-curve was not found for any measures, including workflow, safety, communication, and satisfaction. Only the reminders and alerts measure dropped and then returned to baseline (U-curve); a few remained flatlined. Most dropped and remained below baseline (L-curve). The only measure that remained above baseline was documenting in the exam room with the patient. This study adds to the literature about current controversies surrounding EHR adoption and physician satisfaction.

A Two-Year Longitudinal Assessment of Ophthalmologists' Perceptions after Implementing an Electronic Health Record System.

OBJECTIVES: To understand the attitudes and perceptions of ophthalmologists toward an electronic health record (EHR) system, before and after its clinical implementation. METHODS: Ophthalmologists at a single large academic ophthalmology department were surveyed longitudinally before and after implementation of a new EHR system. The survey measured ophthalmologists' attitudes toward implementation of a new EHR. Questions focused on satisfaction, efficiency, and documentation. All attending physicians (between 56 and 61 at various time points) in the University of Michigan Department of Ophthalmology and Visual Sciences were surveyed. We plotted positive responses to survey questions and assessed whether perceptions followed a J-curve with an initial decrease followed by an increase surpassing pre-implementation levels. RESULTS: Survey responses were received from 32 (52%) ophthalmologists pre-implementation, and 28 (46%) at 3 months, 35 (57%) at 7 months, 40 (71%) at 13 months and 39 (67%) at 24 months post-implementation. After EHR implementation respondents were more likely to express concerns about their ability to create high-quality documentation (p<0.01) and the impact of an electronic health record on meaningful patient interaction (p<0.01). Physicians did not report a significant change in the amount of time spent documenting outside of regular clinical work hours (p=0.54) or on their clinic efficiency and workflow (p=0.97). There was no significant change in overall job satisfaction during the study period (p=0.69). We did not observe a J-curve for any of the survey responses analyzed. CONCLUSIONS: As ophthalmology practices continue to transition to EHRs, adapting them to their specific culture and needs is important to maintain efficiency and user satisfaction. This study identifies areas of concern to ophthalmologists that may be addressed through education of physicians and customization of software as other practices move forward with EHR implementation.

A Systems Approach to Improving Tdap Immunization Within 5 Community-Based Family Practice Settings: Working Differently (and Better) by Transforming the Structure and Process of Care.

OBJECTIVES: We examined how family medicine clinic physicians and staff worked in collaborative teams to implement an automated clinical reminder to improve tetanus, diphtheria, and acellular pertussis (Tdap) booster vaccine administration and documentation. METHODS: A clinical reminder was developed at 5 University of Michigan family medicine clinics to identify patients 11 to 64 years old who were in need of the Tdap booster vaccine. Quality improvement cycles were used to improve clinic care processes. Immunization rates from 2008 to 2011 were compared with rates at 4 primary care control clinics. RESULTS: Vaccination rates among eligible patients increased from 15.5% to 47.3% within the family medicine clinics and from 14.1% to 30.2% within the control clinics. After adjustment for covariates, family medicine patients had a higher probability of vaccination than control patients during each measurement period (0.17 vs 0.15 at baseline, 0.53 vs 0.22 during year 1, and 0.50 vs 0.30 during year 2). CONCLUSIONS: Automated clinical reminders, when designed and implemented via a consensus-based framework that addresses the process of care, can dramatically improve provision of preventive health care.

Prevention of group B streptococcal disease in the newborn.

Group B streptococcus (GBS) is a leading cause of morbidity and mortality among newborns. Universal screening for GBS among women at 35 to 37 weeks of gestation is more effective than administration of intrapartum antibiotics based on risk factors. Lower vaginal and rectal cultures for GBS are collected at 35 to 37 weeks of gestation, and routine dindamycin and erythromycin susceptibility testing is performed in women allergic to penicillin. Women with GBS bacteriuria in the current pregnancy and those who previously delivered a GBS-septic newborn are not screened but automatically receive intrapartum antibiotics. Intrapartum chemoprophylaxis is selected based on maternal allergy history and susceptibility of GBS isolates. Intravenous penicillin G is the preferred antibiotic, with ampicillin as an alternative. Penicillin G should be administered at least four hours before delivery for maximum effectiveness. Cefazolin is recommended in women allergic to penicillin who are at low risk of anaphylaxis. Clindamycin and erythromycin are options for women at high risk for anaphylaxis, and vancomycin should be used in women allergic to penicillin and whose cultures indicate resistance to clindamycin and erytbromycin or when susceptibility is unknown. Asymptomatic neonates born to GBS-colonized mothers should be observed for at least 24 hours for signs of sepsis. Newborns who appear septic should have diagnostic work-up including blood culture followed by initiation of ampicillin and gentamicin. Studies indicate that intrapartum prophylaxis of GBS carriers and selective administration of antibiotics to newborns reduce neonatal GBS sepsis by as much as 80 to 95 percent.