Category: Nevin Manimala

Phenomics. 2022 Apr 4;2(3):156-183. doi: 10.1007/s43657-022-00048-z. eCollection 2022 Jun.

ABSTRACT

During the last decade, there has been rapid adoption of ground and aerial platforms with multiple sensors for phenotyping various biotic and abiotic stresses throughout the developmental stages of the crop plant. High throughput phenotyping (HTP) involves the application of these tools to phenotype the plants and can vary from ground-based imaging to aerial phenotyping to remote sensing. Adoption of these HTP tools has tried to reduce the phenotyping bottleneck in breeding programs and help to increase the pace of genetic gain. More specifically, several root phenotyping tools are discussed to study the plant’s hidden half and an area long neglected. However, the use of these HTP technologies produces big data sets that impede the inference from those datasets. Machine learning and deep learning provide an alternative opportunity for the extraction of useful information for making conclusions. These are interdisciplinary approaches for data analysis using probability, statistics, classification, regression, decision theory, data visualization, and neural networks to relate information extracted with the phenotypes obtained. These techniques use feature extraction, identification, classification, and prediction criteria to identify pertinent data for use in plant breeding and pathology activities. This review focuses on the recent findings where machine learning and deep learning approaches have been used for plant stress phenotyping with data being collected using various HTP platforms. We have provided a comprehensive overview of different machine learning and deep learning tools available with their potential advantages and pitfalls. Overall, this review provides an avenue for studying various HTP platforms with particular emphasis on using the machine learning and deep learning tools for drawing legitimate conclusions. Finally, we propose the conceptual challenges being faced and provide insights on future perspectives for managing those issues.

PMID:36939773 | PMC:PMC9590503 | DOI:10.1007/s43657-022-00048-z

Phenomics. 2022 Feb 26;2(2):130-135. doi: 10.1007/s43657-022-00046-1. eCollection 2022 Apr.

ABSTRACT

The head of sperm was imaged with domestic digital holographic microscopy (DHM), and then the quantitative three-dimensional size information of normal sperm and teratozoospermic sperm was compared and analyzed. DHM sperm imaging and repeated quantitative evaluation were used to determine the morphology of the sperm head in two patients with teratozoospermia and four volunteers with normal semen parameters. Sixty and 139 sperm of teratozoospermia patients and normal people were photographed by digital hologram, respectively. The differences in head height and width were compared and statistically analyzed. The sperm head height of the teratozoospermia group was 3.06 ± 1.66 μm, which was significantly lower than that of the normal sperm group (4.54 ± 1.60 μm, p < 0.01), but there was no significant difference in the head width between the two groups. Compared with the traditional two-dimensional optical microscope observation method, the DHM system can provide three-dimensional quantitative information for the sperm head and thus may help in the comprehensive clinical evaluation of the sperm head structure.

PMID:36939764 | PMC:PMC9590537 | DOI:10.1007/s43657-022-00046-1

JAMA. 2023 Mar 20. doi: 10.1001/jama.2023.3212. Online ahead of print.

NO ABSTRACT

PMID:36939740 | DOI:10.1001/jama.2023.3212

JAMA Pediatr. 2023 Mar 20. doi: 10.1001/jamapediatrics.2023.0115. Online ahead of print.

ABSTRACT

IMPORTANCE: Children with medical complexity (CMC) have chronic conditions and high health needs and may experience fragmented care.

OBJECTIVE: To compare the effectiveness of a structured complex care program, Complex Care for Kids Ontario (CCKO), with usual care.

DESIGN, SETTING, AND PARTICIPANTS: This randomized clinical trial used a waitlist variation for randomizing patients from 12 complex care clinics in Ontario, Canada, over 2 years. The study was conducted from December 2016 to June 2021. Participants were identified based on complex care clinic referral and randomly allocated into an intervention group, seen at the next available clinic appointment, or a control group that was placed on a waitlist to receive the intervention after 12 months.

INTERVENTION: Assignment of a nurse practitioner-pediatrician dyad partnering with families in a structured complex care clinic to provide intensive care coordination and comprehensive plans of care.

MAIN OUTCOMES AND MEASURES: Co-primary outcomes, assessed at baseline and at 6, 12, and 24 months postrandomization, were service delivery indicators from the Family Experiences With Coordination of Care that scored (1) coordination of care among health care professionals, (2) coordination of care between health care professionals and families, and (3) utility of care planning tools. Secondary outcomes included child and parent health outcomes and child health care system utilization and cost.

RESULTS: Of 144 participants randomized, 141 had complete health administrative data, and 139 had complete baseline surveys. The median (IQR) age of the participants was 29 months (9-102); 83 (60%) were male. At 12 months, scores for utility of care planning tools improved in the intervention group compared with the waitlist group (adjusted odds ratio, 9.3; 95% CI, 3.9-21.9; P < .001), with no difference between groups for the other 2 co-primary outcomes. There were no group differences for secondary outcomes of child outcomes, parent outcomes, and health care system utilization and cost. At 24 months, when both groups were receiving the intervention, no primary outcome differences were observed. Total health care costs in the second year were lower for the intervention group (median, CAD$17 891; IQR, 6098-61 346; vs CAD$37 524; IQR, 9338-119 547 [US $13 415; IQR, 4572-45 998; vs US $28 136; IQR, 7002-89 637]; P = .01).

CONCLUSIONS AND RELEVANCE: The CCKO program improved the perceived utility of care planning tools but not other outcomes at 1 year. Extended evaluation periods may be helpful in assessing pediatric complex care interventions.

TRIAL REGISTRATION: ClinicalTrials.gov Identifier: NCT02928757.

PMID:36939728 | DOI:10.1001/jamapediatrics.2023.0115

JAMA Intern Med. 2023 Mar 20. doi: 10.1001/jamainternmed.2023.0144. Online ahead of print.

ABSTRACT

IMPORTANCE: The study results suggest that delirium is the most common postoperative complication in older adults and is associated with poor outcomes, including long-term cognitive decline and incident dementia.

OBJECTIVE: To examine the patterns and pace of cognitive decline up to 72 months (6 years) in a cohort of older adults following delirium.

DESIGN, SETTING, AND PARTICIPANTS: This was a prospective, observational cohort study with long-term follow-up including 560 community-dwelling older adults (older than 70 years) in the ongoing Successful Aging after Elective Surgery study that began in 2010. The data were analyzed from 2021 to 2022.

EXPOSURE: Development of incident delirium following major elective surgery.

MAIN OUTCOMES AND MEASURES: Delirium was assessed daily during hospitalization using the Confusion Assessment Method, which was supplemented with medical record review. Cognitive performance using a comprehensive battery of neuropsychological tests was assessed preoperatively and across multiple points postoperatively to 72 months of follow-up. We evaluated longitudinal cognitive change using a composite measure of neuropsychological performance called the general cognitive performance (GCP), which is scaled so that 10 points on the GCP is equivalent to 1 population SD. Retest effects were adjusted using cognitive test results in a nonsurgical comparison group.

RESULTS: The 560 participants (326 women [58%]; mean [SD] age, 76.7 [5.2] years) provided a total of 2637 person-years of follow-up. One hundred thirty-four participants (24%) developed postoperative delirium. Cognitive change following surgery was complex: we found evidence for differences in acute, post-short-term, intermediate, and longer-term change from the time of surgery that were associated with the development of postoperative delirium. Long-term cognitive change, which was adjusted for practice and recovery effects, occurred at a pace of about -1.0 GCP units (95% CI, -1.1 to -0.9) per year (about 0.10 population SD units per year). Participants with delirium showed significantly faster long-term cognitive change with an additional -0.4 GCP units (95% CI, -0.1 to -0.7) or -1.4 units per year (about 0.14 population SD units per year).

CONCLUSIONS AND RELEVANCE: This cohort study found that delirium was associated with a 40% acceleration in the slope of cognitive decline out to 72 months following elective surgery. Because this is an observational study, we cannot be sure whether delirium directly causes subsequent cognitive decline, or whether patients with preclinical brain disease are more likely to develop delirium. Future research is needed to understand the causal pathway between delirium and cognitive decline.

PMID:36939716 | DOI:10.1001/jamainternmed.2023.0144

Epileptic Disord. 2023 Mar 20. doi: 10.1002/epd2.20021. Online ahead of print.

ABSTRACT

OBJECTIVE: Risk factors for epilepsy in meningioma patients are not yet clearly defined, however, seizure freedom is a significant factor for quality of life after surgery.

METHODS: We performed a retrospective study of the 333 adult patients who received surgery for supratentorial meningioma at our centre. Various clinical, radiological, and surgical variables were included in the multivariate regression, and the outcomes measured were the occurrence of seizure(s) pre-operatively, during the hospitalization, and during the follow-up period.

RESULTS: A total of 89 (26,7%) patients experienced pre-operative seizures, of whom 62.9% were seizure-free after the surgery. Of 244 patients without epilepsy before surgery, 11.9% had at least one seizure post-operatively. In total, 63 of our patients (18.9%) experienced seizures after the surgery, of whom 20 had refractory epilepsy. Multivariate analysis identified the following predictors of pre-operative seizures: absence of headache (OR: 0.23, CI: 2.55-8.50), the presence of significant peritumoural oedema (OR: 4.35, CI: 2.57-7.35), and younger age (OR: 0.97 per year increase, CI: 0.95-0.99). Factors associated with early post-operative seizures were: younger age (OR: 0.96 per year increase, CI: 0.93-0.99) and presence of pre-operative seizures (OR: 2.73, CI: 1.13-6.57), while the presence of pre-operative seizures (OR: 4.73, CI: 2,05-10.92), tumour progression (OR: 5.38, CI: 2.25-12.89) and neurological worsening (OR: 5.21 CI: 1.72-15.81) were significant for late post-operative seizures.

SIGNIFICANCE: Our results from a single-centre meningioma cohort confirm, in general, data from some previous studies regarding patients’ characteristics for both pre-operative and overall post-operative epilepsy. Besides previously described risk factors, younger age was important for pre-operative and early post-operative seizures. Epilepsy is common in patients with recurrence of meningioma, but the variables of significance for refractory seizures in these patients require further examination.

PMID:36939715 | DOI:10.1002/epd2.20021

Transl Vis Sci Technol. 2023 Mar 1;12(3):19. doi: 10.1167/tvst.12.3.19.

ABSTRACT

PURPOSE: Performance comparison of optical coherence tomography (OCT) and visual field (VF) summary metrics for detecting glaucomatous progression.

METHODS: Thirty healthy control eyes (mean deviation [MD], -1.25 ± 2.03; pattern standard deviation [PSD] , 1.78 ± 0.77) and 91 patient eyes comprised of 54 glaucoma patients and 37 glaucoma suspects (MD, -1.58 ± 1.96; PSD, 2.82 ± 1.92) with a follow-up of at least 1 year formed a group to evaluate progression with event analyses (P-Event). A subset of eyes with an additional criterion of a minimum of four tests was used for trend analyses (P-Trend) (30 healthy controls and 73 patients). For P-Event analysis, test-retest variability thresholds (lower 5th percentile) were estimated with repeat tests within a 4-month period. A P-Event eye was considered a “progressor” if the difference between follow-up and baseline tests exceeded the variability thresholds. For the P-Trend analysis, rates of change were calculated based on least-squares regression. Negative rates with significant (P < 0.05) values were considered progressing. For a reference standard, 17 patient eyes were classified as definitely progressing based on clear evidence of structural and corresponding functional progression.

RESULTS: Isolated OCT and VF summary metrics were either inadequately sensitive or not too specific. Combinations of OCT-OCT and OCT-VF metrics markedly improved specificity to nearly 100%. A novel combination of OCT metrics (circumpapillary retinal nerve fiber layer and ganglion cell layer) showed high precision, with 13 of the 15 statistical progressors confirmed as true positives.

CONCLUSIONS: Although relying solely on metrics is not recommended for clinical purposes, in situations requiring very high specificity and precision, combinations of OCT-OCT metrics can be used.

TRANSLATIONAL RELEVANCE: All available OCT and VF metrics can miss eyes with progressive glaucomatous damage and/or can falsely identify progression in stable eyes.

PMID:36939711 | DOI:10.1167/tvst.12.3.19

JAMA Netw Open. 2023 Mar 1;6(3):e233572. doi: 10.1001/jamanetworkopen.2023.3572.

ABSTRACT

IMPORTANCE: The 21st Century Cures Act Final Rule mandates the immediate electronic availability of test results to patients, likely empowering them to better manage their health. Concerns remain about unintended effects of releasing abnormal test results to patients.

OBJECTIVE: To assess patient and caregiver attitudes and preferences related to receiving immediately released test results through an online patient portal.

DESIGN, SETTING, AND PARTICIPANTS: This large, multisite survey study was conducted at 4 geographically distributed academic medical centers in the US using an instrument adapted from validated surveys. The survey was delivered in May 2022 to adult patients and care partners who had accessed test results via an online patient portal account between April 5, 2021, and April 4, 2022.

EXPOSURES: Access to test results via a patient portal between April 5, 2021, and April 4, 2022.

MAIN OUTCOMES AND MEASURES: Responses to questions related to demographics, test type and result, reaction to result, notification experience and future preferences, and effect on health and well-being were aggregated. To evaluate characteristics associated with patient worry, logistic regression and pooled random-effects models were used to assess level of worry as a function of whether test results were perceived by patients as normal or not normal and whether patients were precounseled.

RESULTS: Of 43 380 surveys delivered, there were 8139 respondents (18.8%). Most respondents were female (5129 [63.0%]) and spoke English as their primary language (7690 [94.5%]). The median age was 64 years (IQR, 50-72 years). Most respondents (7520 of 7859 [95.7%]), including 2337 of 2453 individuals (95.3%) who received nonnormal results, preferred to immediately receive test results through the portal. Few respondents (411 of 5473 [7.5%]) reported that reviewing results before they were contacted by a health care practitioner increased worry, though increased worry was more common among respondents who received abnormal results (403 of 2442 [16.5%]) than those whose results were normal (294 of 5918 [5.0%]). The result of the pooled model for worry as a function of test result normality was statistically significant (odds ratio [OR], 2.71; 99% CI, 1.96-3.74), suggesting an association between worry and nonnormal results. The result of the pooled model evaluating the association between worry and precounseling was not significant (OR, 0.70; 99% CI, 0.31-1.59).

CONCLUSIONS AND RELEVANCE: In this multisite survey study of patient attitudes and preferences toward receiving immediately released test results via a patient portal, most respondents preferred to receive test results via the patient portal despite viewing results prior to discussion with a health care professional. This preference persisted among patients with nonnormal results.

PMID:36939703 | DOI:10.1001/jamanetworkopen.2023.3572

JAMA Netw Open. 2023 Mar 1;6(3):e233630. doi: 10.1001/jamanetworkopen.2023.3630.

ABSTRACT

IMPORTANCE: Surgical diseases account for approximately 30% of the global burden of disease. Gender diversity in biomedical research is critical to generate innovative patient-centered research in surgery.

OBJECTIVE: To examine the distribution of biomedical research funding by the National Institutes of Health (NIH) among women and men surgeon-scientists during a 25-year period.

DESIGN, SETTING, AND PARTICIPANTS: This cross-sectional study used publicly available data from the NIH RePORTER (Research Portfolio Online Reporting Tools: Expenditures and Results) database for research project grants awarded to women and men surgeon-scientists who were principal investigators between 1995 and 2020. Data were retrieved between January 20 and March 20, 2022. The representation of women surgeon-scientists among academic surgeons was compared with the representation of men surgeon-scientists over time.

MAIN OUTCOMES AND MEASURES: Distribution of NIH funding to women and men surgeon-scientists was examined via 2 metrics: holding a large-dollar (ie, R01-equivalent) grant and being a super principal investigator (SPI) with $750 000 or more in total annual research funding. Statistical analysis was performed between April 1 and August 31, 2022.

RESULTS: Between 1995 and 2020, 2078 principal investigator surgeons received funding from the NIH. The proportion of women academic surgeons who were surgeon-scientists remained unchanged during this same period (1995, 14 of 792 [1.8%] vs 2020, 92 of 3834 [2.4%]; P = .10). Compared with their men counterparts, women surgeon-scientists obtained their first NIH grant earlier in their career (mean [SD] years after first faculty appointment, 8.8 [6.2] vs 10.8 [7.9] years; P < .001) and were as likely to obtain large-dollar grants (aRR, 0.99 [95% CI, 0.95-1.03]) during the period 2016 to 2020. Despite this success, women surgeon-scientists remained significantly underrepresented among SPIs and were 25% less likely to be an SPI (aRR, 0.75 [95% CI, 0.60-0.95] during the period 2016 to 2020).

CONCLUSIONS AND RELEVANCE: The findings of this cross-sectional study of NIH-funded surgeons suggest that women surgeons remained underrepresented among surgeon-scientists over a 25-year period despite early career success in receiving NIH funding. This is concerning and warrants further investigation to increase the distribution of NIH funding among women surgeon-scientists.

PMID:36939702 | DOI:10.1001/jamanetworkopen.2023.3630

JAMA Netw Open. 2023 Mar 1;6(3):e233646. doi: 10.1001/jamanetworkopen.2023.3646.

ABSTRACT

IMPORTANCE: Metformin may have a protective association against developing osteoarthritis (OA), but robust epidemiological data are lacking.

OBJECTIVE: To determine the risk of OA and joint replacement in individuals with type 2 diabetes treated with metformin compared with a sulfonylurea.

DESIGN, SETTING, AND PARTICIPANTS: This retrospective cohort study used claims data from the Optum deidentified Clinformatics Data Mart Database between December 2003 and December 2019. Participants included individuals aged 40 years or older with at least 1 year of continuous enrollment and type 2 diabetes. Individuals with type 1 diabetes or a prior diagnosis of OA, inflammatory arthritis, or joint replacement were excluded. Time-conditional propensity score matching was conducted using age, sex, race, Charlson comorbidity score, and treatment duration to create a prevalent new-user cohort. Data were analyzed from April to December 2021.

EXPOSURES: Treatment with metformin or a sulfonylurea.

MAIN OUTCOMES AND MEASURES: The outcomes of interest were incident OA and joint replacement. Cox proportional hazard models were used to calculate adjusted hazard ratios (aHRs) of incident OA and joint replacement. In a sensitivity analysis, individuals only ever treated with metformin were compared with individuals only ever treated with a sulfonylurea, allowing for longer-term follow up of the outcome (even after stopping the medication of interest).

RESULTS: After time-conditional propensity score matching, the metformin and control groups each included 20 937 individuals (mean [SD] age 62.0 [11.5] years; 24 379 [58.2%] males). In the adjusted analysis, the risk of developing OA was reduced by 24% for individuals treated with metformin compared with a sulfonylurea (aHR, 0.76; 95% CI, 0.68-0.85; P < .001), but there was no significant difference for risk of joint replacement (aHR, 0.80; 95% CI, 0.50-1.27; P = .34). In the sensitivity analysis, the risk of developing OA remained lower in individuals treated with metformin compared with a sulfonylurea (aHR, 0.77; 95% CI, 0.65-0.90; P < .001) and the risk of joint replacement remained not statistically significant (aHR, 1.04; 95% CI, 0.60-1.82; P = .89).

CONCLUSIONS AND RELEVANCE: In this cohort study of individuals with diabetes, metformin treatment was associated with a significant reduction in the risk of developing OA compared with sulfonylurea treatment. These results further support preclinical and observational data that suggest metformin may have a protective association against the development of OA; future interventional studies with metformin for the treatment or prevention of OA should be considered.

PMID:36939700 | DOI:10.1001/jamanetworkopen.2023.3646