Nevin Manimala

BMC Bioinformatics. 2022 Sep 24;23(1):388. doi: 10.1186/s12859-022-04928-z.

ABSTRACT

BACKGROUND: In RNA-sequencing studies a large number of hypothesis tests are performed to compare the differential expression of genes between several conditions. Filtering has been proposed to remove candidate genes with a low expression level which may not be relevant and have little or no chance of showing a difference between conditions. This step may reduce the multiple testing burden and increase power.

RESULTS: We show in a simulation study that filtering can lead to some increase in power for RNA-sequencing data, too aggressive filtering, however, can lead to a decline. No uniformly optimal filter in terms of power exists. Depending on the scenario different filters may be optimal. We propose an adaptive filtering strategy which selects one of several filters to maximise the number of rejections. No additional adjustment for multiplicity has to be included, but a rule has to be considered if the number of rejections is too small.

CONCLUSIONS: For a large range of simulation scenarios, the adaptive filter maximises the power while the simulated False Discovery Rate is bounded by the pre-defined significance level. Using the adaptive filter, it is not necessary to pre-specify a single individual filtering method optimised for a specific scenario.

PMID:36153479 | DOI:10.1186/s12859-022-04928-z

BMC Bioinformatics. 2022 Sep 24;23(1):387. doi: 10.1186/s12859-022-04926-1.

ABSTRACT

The recent global focus on big data in medicine has been associated with the rise of artificial intelligence (AI) in diagnosis and decision-making following recent advances in computer technology. Up to now, AI has been applied to various aspects of medicine, including disease diagnosis, surveillance, treatment, predicting future risk, targeted interventions and understanding of the disease. There have been plenty of successful examples in medicine of using big data, such as radiology and pathology, ophthalmology cardiology and surgery. Combining medicine and AI has become a powerful tool to change health care, and even to change the nature of disease screening in clinical diagnosis. As all we know, clinical laboratories produce large amounts of testing data every day and the clinical laboratory data combined with AI may establish a new diagnosis and treatment has attracted wide attention. At present, a new concept of radiomics has been created for imaging data combined with AI, but a new definition of clinical laboratory data combined with AI has lacked so that many studies in this field cannot be accurately classified. Therefore, we propose a new concept of clinical laboratory omics (Clinlabomics) by combining clinical laboratory medicine and AI. Clinlabomics can use high-throughput methods to extract large amounts of feature data from blood, body fluids, secretions, excreta, and cast clinical laboratory test data. Then using the data statistics, machine learning, and other methods to read more undiscovered information. In this review, we have summarized the application of clinical laboratory data combined with AI in medical fields. Undeniable, the application of Clinlabomics is a method that can assist many fields of medicine but still requires further validation in a multi-center environment and laboratory.

PMID:36153474 | DOI:10.1186/s12859-022-04926-1

Egypt Heart J. 2022 Sep 24;74(1):68. doi: 10.1186/s43044-022-00305-6.

ABSTRACT

BACKGROUND: Increased nighttime BP variability (BPV) was associated with stroke. Left atrial (LA) enlargement is the default clinical hallmark of structural remodeling that often occurs in response to LA pressure and volume overload. Blood pressure has proven to be an essential determinant of LA enlargement. We aimed to evaluate the influence of BPV as a risk factor for cryptogenic stroke and highlight the importance of including the (APBM) in the workup for those patients and test the relation between BPV and LA remodeling in these patients, which could be used as a clue to add APM monitoring to their workup. Also, LA remodeling may be a substrate for occult atrial fibrillation (AF). We included Group I (108 consecutive patients with cryptogenic ischemic stroke) and Group II (100 consecutive adult participants without a history of stroke or any structural heart disease). We measured the maximal LA volume index (Max LAVI) and minimal LA volume index (Min LAVI). We calculated the left atrial ejection fraction (LAEF). All the participants were subjected to ABPM.

RESULTS: In our prospective, cross-sectional cohort study, the patients in Group I had statistically significantly higher Min LAVI and Max LAVI and Less LA EF than Group II, with a P value of (0.001, 0.001, and 0.008), respectively. The Group I patients had higher BPV as measured by SD parameters than patients in Group II, with a P value of 0.001 for all SD parameters. The BPV parameters, as measured by SD parameters, were positively related to the LA remodeling parameters in both groups. After adjusting all variables, we found that age, night systolic SD, and night diastolic SD parameters were independent predictors of LA remodeling.

CONCLUSIONS: The patients with cryptogenic stroke had higher short-term BPV, Min LAVI, and Max LAVI but lower LA EF. Careful monitoring of BPV may be of value for both primary and secondary preventions of ischemic stroke.

PMID:36153447 | DOI:10.1186/s43044-022-00305-6

EJNMMI Phys. 2022 Sep 24;9(1):66. doi: 10.1186/s40658-022-00494-8.

ABSTRACT

BACKGROUND: [¹⁸F] FDG PET-CT has an important role in the initial staging of lung cancer; however, accurate differentiation between activity in malignant and benign intrathoracic lymph nodes on PET-CT scans can be challenging. The purpose of the current study was to investigate the effect of incorporating primary tumour data and clinical features to differentiate between [¹⁸F] FDG-avid malignant and benign intrathoracic lymph nodes.

METHODS: We retrospectively selected lung cancer patients who underwent PET-CT for initial staging in two centres in the Netherlands. The primary tumour and suspected lymph node metastases were annotated and cross-referenced with pathology results. Lymph nodes were classified as malignant or benign. From the image data, we extracted radiomic features and trained the classifier model using the extreme gradient boost (XGB) algorithm. Various scenarios were defined by selecting different combinations of data input and clinical features. Data from centre 1 were used for training and validation of the models using the XGB algorithm. To determine the performance of the model in a different hospital, the XGB model was tested using data from centre 2.

RESULTS: Adding primary tumour data resulted in a significant gain in the performance of the trained classifier model. Adding the clinical information about distant metastases did not lead to significant improvement. The performance of the model in the test set (centre 2) was slightly but statistically significantly lower than in the validation set (centre 1).

CONCLUSIONS: Using the XGB algorithm potentially leads to an improved model for the classification of intrathoracic lymph nodes. The inclusion of primary tumour data improved the performance of the model, while additional knowledge of distant metastases did not. In patients in whom metastases are limited to lymph nodes in the thorax, this may reduce costly and invasive procedures such as endobronchial ultrasound or mediastinoscopy procedures.

PMID:36153446 | DOI:10.1186/s40658-022-00494-8

Spinal Cord. 2022 Sep 24. doi: 10.1038/s41393-022-00850-6. Online ahead of print.

ABSTRACT

STUDY DESIGN: Cross-sectional survey.

OBJECTIVES: To describe design and methods of Australian arm of International Spinal Cord Injury (Aus-InSCI) community survey, reporting on participation rates, potential non-response bias and cohort characteristics.

SETTING: Survey of community-dwelling people with SCI at least 12 months post-injury, recruited between March 2018 and January 2019, from state-wide SCI services, a government insurance agency and not-for-profit consumer organisations across four Australian states.

METHODS: The Aus-InSCI survey combined data for people with SCI from nine custodians, using secure data-linkage processes, to create a population-based, anonymised dataset. The Aus-InSCI questionnaire comprised 193 questions. Eligibility, response status and participation rates were calculated. Descriptive statistics depict participant characteristics. Logistic regression models were developed for probability of participation, and inverse probability weights generated to assess potential non-response bias.

RESULTS: 1579 adults with SCI were recruited, a cooperation rate of 29.4%. Participants were predominantly male (73%), with 50% married. Mean age was 57 years (range 19-94) and average time post-injury 17 years (range 1-73). Paraplegia (61%) and incomplete lesions (68%) were most common. Males were more likely than females to have traumatic injuries (p < 0.0001) and complete lesions (p = 0.0002), and younger age-groups were more likely to have traumatic injuries and tetraplegia (p < 0.0001). Potential non-response bias evaluated using selected outcomes was found to be negligible in the Aus-InSCI cohort.

CONCLUSIONS: The Aus-InSCI survey made efforts to maximise coverage, avoid recruitment bias and address non-response bias. The distributed, linked and coded (re-identifiable at each custodian level) ‘virtual quasi-registry’ data model supports systematic cross-sectional and longitudinal research.

PMID:36153439 | DOI:10.1038/s41393-022-00850-6

Ophthalmol Ther. 2022 Sep 24. doi: 10.1007/s40123-022-00567-y. Online ahead of print.

ABSTRACT

INTRODUCTION: This study investigated choroidal structural changes on optical coherence tomography (OCT) using choroidal vascularity index (CVI) and choroidal thickness (CT) in patients with Best vitelliform macular dystrophy (BVMD).

METHODS: This retrospective case control study included 78 patients with BVMD of different clinical stages and 242 age- and gender-matched healthy controls. Subfoveal OCT scans were analysed. Total choroidal area (TCA), luminal area (LA) and CT were measured after image segmentation and binarization. CVI, a novel marker for choroidal angioarchitecture, was defined as the ratio of LA to TCA. CVI and CT were compared between BVMD and control group, as well as among the BVMD subgroups.

RESULTS: Mean CVI was lower in eyes with BVMD (65.0 ± 3.5%) compared to that in control eyes (67.5 ± 3.9%) and this was statistically significant (p < 0.0001). There was no significant difference in subfoveal CT between BVMD (302.88 ± 81.68 μm) and control (309.31 ± 65.46 μm) eyes (p = 0.4799). In the subgroup analysis, all stages of BVMD showed lower CVI compared to control while SFCT remained similar. Within the BVMD subgroups, CVI and subfoveal CT did not differ significantly and both were not shown to be associated with visual acuity.

CONCLUSION: Decreased CVI was shown in eyes with BVMD compared to control eyes, while no significant difference in subfoveal CT was seen. CVI may be helpful in the understanding of choroidal pathology in BVMD.

PMID:36153433 | DOI:10.1007/s40123-022-00567-y

Int Ophthalmol. 2022 Sep 24. doi: 10.1007/s10792-022-02509-w. Online ahead of print.

ABSTRACT

PURPOSE: This retrospective study aimed to analyze the relationship between the volume of the fractured and the normal orbit in patients with unilateral orbital fractures with and without indirect traumatic optic neuropathy (TON).

SUBJECTS: Data of 25 patients with unilateral orbital fractures who underwent computer tomography between January 2016 and December 2020 were investigated. Emergency imaging was performed within 2 hours of arrival at the emergency room. The subjects were categorized into two groups: unilateral orbital fractures with and without TON.

METHODS AND MEASURES: The assessment of TON was performed during a comprehensive ophthalmologic examination by an ophthalmologist. The stereographic orbit was reconstructed, and the volume was calculated. Other variables examined included age, sex, and cause of orbital trauma. The variables were compared using paired t-tests. Statistical significance was set at p < 0.05.

RESULTS: The orbital volume of the non-fractured orbit was 27.50 ± 2.26 and 27.48 ± 2.64 cm³ in the groups with and without TON, respectively. The average volume of the fractured orbit in the TON group was 27.78 ± 2.56 cm³, and there was no significant volumetric difference between the fractured and non-fractured sides in this group. However, the average volume of the fractured orbit without TON was 28.76 ± 3.18 cm³, larger than that of the non-fractured orbit (p = 0.016).

CONCLUSIONS: Non-expansion of the fractured orbit was a risk factor for indirect TON in patients with unilateral orbital fractures. Volumetric analysis from primary imaging would expedite the diagnosis and treatment of TON, resulting in optimal outcomes.

PMID:36153431 | DOI:10.1007/s10792-022-02509-w

Sci Rep. 2022 Sep 24;12(1):15935. doi: 10.1038/s41598-022-19997-6.

ABSTRACT

In the early stages after larval settlement, coral spat can be rapidly overgrown and outcompeted by algae, reducing overall survival for coral reef replenishment and supply for restoration programs. Here we investigated three antifouling (AF) coatings for their ability to inhibit algal fouling on coral settlement plugs, a commonly-used restoration substrate. Plugs were either fully or partially coated with the AF coatings and incubated in mesocosm systems with partial recirculation for 37 days to track fouling succession. In addition, settlement of Acropora tenuis larvae was measured to determine whether AF coatings were a settlement deterrent. Uncoated control plugs became heavily fouled, yielding only 4-8% bare substrate on upper surfaces after 37 days. During this period, an encapsulated dichlorooctylisothiazolinone (DCOIT)-coating was most effective in reducing fouling, yielding 61-63% bare substrate. Antiadhesive and cerium dioxide (CeO_2-x) nanoparticle (NP) coatings were less effective, yielding 11-17% and 2% bare substrate, respectively. Average settlement of A. tenuis larvae on the three types of AF-coated plugs did not statistically differ from settlement on uncoated controls. However, settlement on the NP-coating was generally the highest and was significantly higher than settlement found on the antiadhesive- and DCOIT-coating. Furthermore, on plugs only partially-covered with AF coatings, larval settlement on coated NP- areas was significantly higher than settlement on coated antiadhesive- and DCOIT-areas. These results demonstrate that AF coatings can reduce fouling intensity on biologically-relevant timescales while preserving robust levels of coral settlement. This represents an important step towards reducing fine-scale competition with benthic fouling organisms in coral breeding and propagation.

PMID:36153418 | DOI:10.1038/s41598-022-19997-6

Vet Ophthalmol. 2022 Sep 24. doi: 10.1111/vop.13026. Online ahead of print.

ABSTRACT

OBJECTIVE: To describe the clinical outcomes and efficacy of diamond burr debridement (DBD) treatment for corneal ulceration in cats.

PROCEDURE(S): Medical records of cats that received DBD at two private practices between 2015 and 2021 were retrospectively reviewed. DBD was performed using a battery-powered, handheld motorized burr and a bandage contact lens was placed in 18/21 eyes. Corneal ulceration was considered resolved if the cornea was fluorescein negative with a stable epithelial surface. Recurrence was defined as return of corneal ulceration. Descriptive statistics and a Fisher’s exact test were conducted on the study population.

RESULTS: Twenty-one eyes from 20 cats with superficial corneal ulcers refractory to medical treatment underwent DBD. Domestic and Burmese were the most commonly encountered breeds and the median age of affected cats was 8.83 years (range 0.5-20 years). Corneal ulceration was present for a median of 14 days prior to DBD. Healing was achieved in 81% of eyes; with four eyes failing to heal and requiring further intervention. Corneal sequestrum was reported in one case that failed to heal. Of the healed cases, three cases recurred (17.6%) at a mean of 116.3 days (range 79-135 days). Burmese were overrepresented (p < .001) in cases that failed to heal or recurred (6/7 eyes; 85.7%). The median postoperative follow-up time was 93 days (range 6-1613 days).

CONCLUSIONS: Diamond burr debridement is a safe, non-invasive treatment for corneal ulceration in cats but, compared with published results, it had a lower success rate than superficial lamellar keratectomy.

PMID:36152338 | DOI:10.1111/vop.13026

J Neurosurg Spine. 2022 Sep 23:1-11. doi: 10.3171/2022.7.SPINE22536. Online ahead of print.

ABSTRACT

OBJECTIVE: The purpose of this study was to evaluate the safety and efficacy of a posterior facet replacement device, the Total Posterior Spine (TOPS) System, for the treatment of one-level symptomatic lumbar stenosis with grade I degenerative spondylolisthesis. Posterior lumbar arthroplasty with facet replacement is a motion-preserving alternative to lumbar decompression and fusion. The authors report the preliminary results from the TOPS FDA investigational device exemption (IDE) trial.

METHODS: The study was a prospective, randomized controlled FDA IDE trial comparing the investigational TOPS device with transforaminal lumbar interbody fusion (TLIF) and pedicle screw fixation. The minimum follow-up duration was 24 months. Validated patient-reported outcome measures included the Oswestry Disability Index (ODI) and visual analog scale (VAS) for back and leg pain. The primary outcome was a composite measure of clinical success: 1) no reoperations, 2) no device breakage, 3) ODI reduction of ≥ 15 points, and 4) no new or worsening neurological deficit. Patients were considered a clinical success only if they met all four measures. Radiographic assessments were made by an independent core laboratory.

RESULTS: A total of 249 patients were evaluated (n = 170 in the TOPS group and n = 79 in the TLIF group). There were no statistically significant differences between implanted levels (L4-5: TOPS, 95% and TLIF, 95%) or blood loss. The overall composite measure for clinical success was statistically significantly higher in the TOPS group (85%) compared with the TLIF group (64%) (p = 0.0138). The percentage of patients reporting a minimum 15-point improvement in ODI showed a statistically significant difference (p = 0.037) favoring TOPS (93%) over TLIF (81%). There was no statistically significant difference between groups in the percentage of patients reporting a minimum 20-point improvement on VAS back pain (TOPS, 87%; TLIF, 64%) and leg pain (TOPS, 90%; TLIF, 88%) scores. The rate of surgical reintervention for facet replacement in the TOPS group (5.9%) was lower than the TLIF group (8.8%). The TOPS cohort demonstrated maintenance of flexion/extension range of motion from preoperatively (3.85°) to 24 months (3.86°).

CONCLUSIONS: This study demonstrates that posterior lumbar decompression and dynamic stabilization with the TOPS device is safe and efficacious in the treatment of lumbar stenosis with degenerative spondylolisthesis. Additionally, decompression and dynamic stabilization with the TOPS device maintains segmental motion.

PMID:36152329 | DOI:10.3171/2022.7.SPINE22536