Fast and Efficient Root Phenotyping via Pose Estimation

Image segmentation is commonly used to estimate the location and shape of plants and their external structures. Segmentation masks are then used to localize landmarks of interest and compute other geometric features that correspond to the plant's phenotype. Despite its prevalence, segmentation-based approaches are laborious (requiring extensive annotation to train) and error-prone (derived geometric features are sensitive to instance mask integrity). Here, we present a segmentation-free approach that leverages deep learning-based landmark detection and grouping, also known as pose estimation. We use a tool originally developed for animal motion capture called SLEAP (Social LEAP Estimates Animal Poses) to automate the detection of distinct morphological landmarks on plant roots. Using a gel cylinder imaging system across multiple species, we show that our approach can reliably and efficiently recover root system topology at high accuracy, few annotated samples, and faster speed than segmentation-based approaches. In order to make use of this landmark-based representation for root phenotyping, we developed a Python library (sleap-roots) for trait extraction directly comparable to existing segmentation-based analysis software. We show that pose-derived root traits are highly accurate and can be used for common downstream tasks including genotype classification and unsupervised trait mapping. Altogether, this work establishes the validity and advantages of pose estimation-based plant phenotyping. To facilitate adoption of this easy-to-use tool and to encourage further development, we make sleap-roots, all training data, models, and trait extraction code available at: https://github.com/talmolab/sleap-roots and https://osf.io/k7j9g/.

Fast and efficient root phenotyping via pose estimation

Image segmentation is commonly used to estimate the location and shape of plants and their external structures. Segmentation masks are then used to localize landmarks of interest and compute other geometric features that correspond to the plant's phenotype. Despite its prevalence, segmentation-based approaches are laborious (requiring extensive annotation to train), and error-prone (derived geometric features are sensitive to instance mask integrity). Here we present a segmentation-free approach which leverages deep learning-based landmark detection and grouping, also known as pose estimation. We use a tool originally developed for animal motion capture called SLEAP (Social LEAP Estimates Animal Poses) to automate the detection of distinct morphological landmarks on plant roots. Using a gel cylinder imaging system across multiple species, we show that our approach can reliably and efficiently recover root system topology at high accuracy, few annotated samples, and faster speed than segmentation-based approaches. In order to make use of this landmark-based representation for root phenotyping, we developed a Python library (sleap-roots) for trait extraction directly comparable to existing segmentation-based analysis software. We show that landmark-derived root traits are highly accurate and can be used for common downstream tasks including genotype classification and unsupervised trait mapping. Altogether, this work establishes the validity and advantages of pose estimation-based plant phenotyping. To facilitate adoption of this easy-to-use tool and to encourage further development, we make sleap-roots, all training data, models, and trait extraction code available at: https://github.com/talmolab/sleap-roots and https://osf.io/k7j9g/.

Access of target groups to 1915(c) Medicaid home and community based waiver services

OBJECTIVES

The study examined the access of specific target groups to the 1915(c) home and community based waiver program in terms of the number of participants, services, and expenditures for 1992 and 1997.

METHODS

The study collected HCFA 372 waiver program statistics from each of the states and compared statistics for the two time periods. A regression examined the increase in program expenditures.

RESULTS

An unequal distribution of HCBS expenditures across target groups was found where individuals with developmental disability were 39 percent of participants but used 77 percent of the total $7.9 billion waiver expenditures in 1997. The aged and disabled were 58 percent of waiver participants but received 21 percent of expenditures. The program growth was primarily due to increases in participants and reimbursement rates.

CONCLUSIONS

Individuals with MR/DD used more costly services such as habilitation and residential care than other target groups. Studies are needed to examine what accounts for the unequal access and whether program expenditures are sufficient to meet the long-term care needs of various target groups.

Does investor ownership of nursing homes compromise the quality of care?

OBJECTIVES

Two thirds of nursing homes are investor owned. This study examined whether investor ownership affects quality.

METHODS

We analyzed 1998 data from state inspections of 13,693 nursing facilities. We used a multivariate model and controlled for case mix, facility characteristics, and location.

RESULTS

Investor-owned facilities averaged 5.89 deficiencies per home, 46.5% higher than nonprofit facilities and 43.0% higher than public facilities. In multivariate analysis, investor ownership predicted 0.679 additional deficiencies per home; chain ownership predicted an additional 0.633 deficiencies. Nurse staffing was lower at investor-owned nursing homes.

CONCLUSIONS

Investor-owned nursing homes provide worse care and less nursing care than do not-for-profit or public homes.

On the firing maps of a general class of forced integrate and fire neurons

Integrate and fire processes are fundamental mechanisms causing excitable and oscillatory behavior. Van der Pol [Philos. Mag. (7) 2 (11) (1926) 978] studied oscillations caused by these processes, which he called 'relaxation oscillations' and pointed out their relevance, not only to engineering, but also to the understanding of biological phenomena [Acta Med. Scand. Suppl. CVIII (108) (1940) 76], like cardiac rhythms and arrhythmias. The complex behavior of externally stimulated integrate and fire oscillators has motivated the study of simplified models whose dynamics are determined by iterations of 'firing circle maps' that can be studied in terms of Poincaré's rotation theory [Chaos 1 (1991) 20; Chaos 1 (1991) 13; SIAM J. Appl. Math. 41 (3) (1981) 503]. In order to apply this theory to understand the responses and bifurcation patterns of forced systems, it is fundamental to determine the regions in parameter space where the different regularity properties (e.g., continuity and injectivity) of the firing maps are satisfied. Methods for carrying out this regularity analysis for linear systems, have been devised and the response of integrate and fire neurons (with linear accumulation) to a cyclic input has been analyzed [SIAM J. Appl. Math. 41 (3) (1981) 503]. In this paper we are concerned with the most general class of forced integrate and fire systems, modelled by one first-order differential equation. Using qualitative analysis we prove theorems on which we base a new method of regularity analysis of the firing map, that, contrasting with methods previously reported in the literature, does not requires analytic knowledge of the solutions of the differential equation and therefore it is also applicable to non-linear integrate and fire systems. To illustrate this new methodology, we apply it to determine the regularity regions of a non-linear example whose firing maps undergo bifurcations that were unknown for the previously studied linear systems.

Predicting state Medicaid home and community based waiver participants and expenditures, 1992-1997

PURPOSE

The study examined trends and predictors of state Medicaid home and community based waiver participants and expenditures from 1992 to 1997 to identify factors of interest to policy makers and clinicians.

DESIGN AND METHODS

HCFA Form 372 data were collected from state officials for each waiver for each year. Two separate regression analyses were conducted to examine the effects of sociodemographic, economic, political, policy, and health services on state waiver participants and expenditures.

RESULTS

State waiver participants were positively associated with those aged 85 and over, personal income, residential care beds, and inpatient users and negatively with home health regulation and nursing home beds. State waiver expenditures were positively associated with democratic governors, personal income, home health reimbursement methods, Medicaid eligibility, home health agencies, and Medicare home health users.

IMPLICATIONS

The factors policy makers might consider changing include increasing the number of residential care beds and home health agencies, removing certificate of need for home health care, using Medicare home health reimbursement methods for Medicaid, and raising the Medicaid eligibility criteria. In some states with low nursing home occupancy rates, reducing the supply of nursing home beds may also be considered. All of these approaches would be controversial and should be based on additional cost-effectiveness analysis.

The regulation and enforcement of federal nursing home standards, 1991-1997

This article reports historical trend data on resident characteristics and conditions, problems, and deficiency patterns for nursing facilities from 1991 through 1997 from Health Care Financing Administration (HCFA) administrative records from the On-Line Survey, Certification, and Reporting System (OSCAR). Over this period, residents show some increases in dependency and conditions, although there was a decline in the use of restraints. The deficiencies reveal continued quality problems in some nursing homes, although the average number of deficiencies given to facilities declined by 44 percent between 1991 and 1997. The discussion considers possible explanations for the decline in deficiencies, including whether the quality of care in nursing homes has improved or whether the enforcement process has gradually been weakened.

Stakeholders' opinions regarding important measures of nursing home quality for consumers

This article reports on a survey of opinions about specific categories and indicators of quality used by the Health Care Financing Administration in the survey and certification process for nursing homes in the US. The survey was conducted of a selected sample of administrators, directors of nursing, state survey agency training coordinators, state ombudsmen, and nursing home advocates in 1996. General patterns of agreement were found across all respondent groups that the 3 most important categories of quality were as follows: quality of care, quality of life, and residents' rights. The 3 most important quality-of-care survey items were as follows: general quality of care, maintenance of activities of daily living, and appropriate treatment for impairment in activities of daily living. The 3 most important quality-of-life items were as follows: dignity, self-determination and participation, and accommodation of resident needs. Important residents' rights items were as follows: to be able to exercise general rights, to be informed of one's condition, and to be free of reprisal when making complaints. Quality assurance should focus greater attention on the areas considered to be the most important by the various stakeholders in nursing home care.

Nursing facility staffing in the states: the 1991 to 1995 period

Trends in the average nurse staffing levels are reported for certified nursing facilities in the United States from 1991 through 1995. Data from the federal On-Line Survey Certification and Reporting system show a small overall increase in the staffing levels for registered nurses (RNs), licensed vocational and licensed practical nurses (LVNs/LPNs), and nursing assistants over the 5 years, but there are substantial variations across states and regions. A two-stage least squares panel analysis examined predictors of nurse staff levels in states. States with higher resident case mix levels had higher RN and LVN/LPN hours. States with higher percentages of large facilities had lower RN and LVN/LPN levels and states with higher percentages of for-profit facilities had lower RN staff levels. States with a higher percentage of Medicaid residents had higher LVN/LPN staff levels. These findings indicate the need for more studies of staff variations and public policies that affect staffing.

Outcome of pediatric intensive care at six centers in Mexico and Ecuador

OBJECTIVE

To improve understanding of the causes of morbidity and mortality among critically ill children in the countries studied.

DESIGN

Survey of hospital records between 1992 and 1994.

SETTING

Six pediatric intensive care units (ICUs) (four ICUs in Mexico City and two ICUs in Ecuador).

PATIENTS

Consecutive patients (n = 1,061) admitted to the units studied.

INTERVENTIONS

None.

MEASUREMENTS AND MAIN RESULTS

The mortality rate for low-risk patients (pediatric Risk of Mortality [PRISM] score of < or = 10, n = 701) was more than four times the rate predicted by the PRISM score (8.1% vs. 1.8%, p < .001), with an additional 11.3% of this group incurring major morbidity. The mortality rate for moderate-risk patients (PRISM scores of 11 to 20, n = 232) was more than twice predicted (28% vs. 12%, p < .001). For low-risk patients, death was significantly associated with tracheal intubation, central venous cannulation, pneumonia, age of < 2 months, use of more than two antibiotics, and nonsurgical diagnosis (after controlling for PRISM score). Central venous cannulation and tracheal intubation in the lower-risk groups were performed more commonly in units in Mexico than in one comparison unit in the United States (p < .001).

CONCLUSIONS

For six pediatric ICUs in Mexico and Ecuador, mortality was significantly higher than predicted among lower-risk patients. Tracheal intubation, central catheters, pneumonia, sepsis, and nonsurgical status were associated with poor outcome for low-risk groups. We speculate that reducing the use of invasive central catheters and endotracheal intubation for lower-risk patients, coupled with improved infection control, could lower mortality rates in the population studied.

The effect of certificate of need and moratoria policy on change in nursing home beds in the United States

OBJECTIVES

This study examined the effects of state certificate of need and/or moratorium requirements on the change in nursing home bed growth in states over a 13-year period.

METHODS

Data were collected from five telephone surveys of state officials about state certificate of need and moratorium policies, state Medicaid nursing home reimbursement rates, and the licensed nursing home beds in each state for the 1979 through 1993 period. Two-stage least squares regression analysis treated certificate of need and/or moratorium and Medicaid reimbursement rates as endogenous variables in predicting the change in nursing home beds per aged population in states.

RESULTS

States that had a certificate of need and/or moratorium did have significant reductions in the growth in nursing home beds but Medicaid nursing home reimbursement rates were not related to change in bed stock. The percentage of the population living in a metropolitan area, the personal income per 1,000 population, the percent unemployed, a state's tax effort, and time were positively associated with change in nursing home beds. The ratio of nursing home beds per 1,000 aged population in the previous year was a negative predictor of change in bed stock in a given year.

CONCLUSIONS

State regulatory policies have an effect on bed growth in contrast to reimbursement policies.

AIDS and condom-related knowledge, beliefs, and behaviors in Mexican migrant laborers

AIDS and condom-related knowledge, beliefs, and behaviors were assessed in Mexican migrant laborers. The sample consisted of 55 men and 32 women who were administered a modified version of the Hispanic Condom Questionnaire. Results indicated that respondents were knowledgeable about actual modes of HIVtransmission butthata third to half of the sample believed they could contract AIDS from unlikely sources such as mosquito bites, public bathrooms, and kissing on the mouth. Knowledge of proper condom use was problematic, and frequency of condom use during the past year was no higher than half of the time. Concern about contracting AIDS was generally low but was highestfor migrants that were younger andfor those with multiple sex partners. Although respondents reportedfew negative beliefs about the consequences of condom use, most believed that women would be seen as promiscuous for carrying condoms.

Leiomyosarcoma of the pulmonary veins with extension to the left atrium

A leiomyosarcoma of the right pulmonary vein in a 43-year-old woman extended to the right atrial wall and compromised the posterior mitral leaflet. Successful surgical treatment was accomplished with a right pneumonectomy, partial resection of the left atrial wall, and mitral valve replacement under cardiopulmonary bypass. Six months later a mediastinal recurrence with extension to the left hemithorax was treated with resection and postoperative radiotherapy.

Analysis of an autonomous phase model for neuronal parabolic bursting

An understanding of the nonlinear dynamics of bursting is fundamental in unraveling structure-function relations in nerve and secretory tissue. Bursting is characterized by alternations between phases of rapid spiking and slowly varying potential. A simple phase model is developed to study endogenous parabolic bursting, a class of burst activity observed experimentally in excitable membrane. The phase model is motivated by Rinzel and Lee's dissection of a model for neuronal parabolic bursting (J. Math. Biol 25, 653-675 (1987)). Rapid spiking is represented canonically by a one-variable phase equation that is coupled bi-directionally to a two-variable slow system. The model is analyzed in the slow-variable phase plane, using quasi steady-state assumptions and formal averaging. We derive a reduced system to explore where the full model exhibits bursting, steady-states, continuous and modulated spiking. The relative speed of activation and inactivation of the slow variables strongly influences the burst pattern as well as other dynamics. We find conditions of the bistability of solutions between continuous spiking and bursting. Although the phase model is simple, we demonstrate that it captures many dynamical features of more complex biophysical models.

Variations and trends in state nursing facility capacity: 1978-93

The demand for nursing facility (NF) beds has been growing with the aging of the population and many other factors. As the need for nursing home care grows, the Nation's capacity to provide such care is the subject of increasing concern. This article examines licensed NFs and beds, presenting data on trends from 1978-93. Measures of the adequacy of NF beds in States are examined over time, including the ratio of beds per aged population, occupancy rates, and State official's opinions of the adequacy of supply. State and regional variations are shown over time, and we speculate on the factors which may be associated with the variation.

[Clinical usefulness of pulse oximetry in asthmatic children]

Abnormalities in exchange and tendency to acidosis and hypoxemia are present in acute asthma. Oxygen arterial saturation (pulse oximetry) is a simple and useful method to evaluate oxygenation conditions. Pulse oximetry and spirometry before and after albuterol nebulization (150 mcg/kg/dose) were performed in 35 subjects. 7 to 14 years, with acute asthma, 68% were mild and the rest moderate. Oxygen saturation before nebulization was less than 90% in 30 children and increased in 27 of them (90%). Spirometry before nebulization showed FEV1 20% predictive values in 18 children and increased in 10 of them. Seven were hospitalized because of worse symptoms. 4 of them showed metabolic acidosis by the presence of lactate. We conclude that pulse oximetry is a useful and simple method for an objective evaluation of acute asthma and its complications, but it is not predictive for a therapeutic decision.

Polytetrafluoroethylene microprosthesis in the arterial system of the rat

The experimental behavior of a 1-mm internal diameter (i.d.) polytetrafluoroethylene (PTFE) microprosthesis, as a substitute for an abdominal aortic segment in the rat, was reviewed. Fifty Wistar rats were divided into four groups: Group I--12 rats with autotransplant of an abdominal aortic segment (AAS); Group II--12 rats with allotransplant of an AAS obtained from Long-Evans rats; Group III--12 rats with xenotransplant of an AAS taken from rabbit femoral arteries; and Group IV--14 rats with substitution of an AAS by a 1-mm i.d. PTFE microprosthesis. The rats were sacrificed at different time intervals ranging from five to 360 days, with previous aortography. In Group I, there was a 100 percent patency at a mean of 152.41 days; in Group II, a 91.6 percent patency at a mean of 100.08 days; in Group III, an 83.3 percent patency with a 75 percent aneurysmal dilation at a mean of 107.58 days; in Group IV, a 71.42 percent patency with two anastomotic aneurysms at a mean of 105 days (P less than 0.05, chi square) between Groups I and IV, autotransplant vs. PTFE). The 1-mm PTFE microprosthesis placed in the arterial system of the rat proved to be a reliable alternative for microvascular substitution.

[Management of persistent ductus arteriosus in the newborn with respiratory insufficiency]

Sixteen newborn babies with severe respiratory distress and patent ductus arteriosus with congestive heart failure are presented. Fifteen of them were premature and one at full term. Management consisted of the accepted medical and ventilatory aids such as digitalis, diuretics, ventilators, etc. Thirteen cases were given indomethacin with clinical closure in five of them (38%). Ten cases underwent surgical closure with 30% mortality. It is recommended that these patients be given indomethacin inicially; if there is no response in 36 hours surgical closure of the duct should be performed prior to progressive deterioration and eventual death.