Tag: nevin manimala

BMC Plant Biol. 2022 Dec 2;22(1):557. doi: 10.1186/s12870-022-03955-5.

ABSTRACT

Containing the largest number of species, the orchid family provides not only materials for studying plant evolution and environmental adaptation, but economically and culturally important ornamental plants for human society. Previously, we collected genome and transcriptome information of Dendrobium catenatum, Phalaenopsis equestris, and Apostasia shenzhenica which belong to two different subfamilies of Orchidaceae, and developed user-friendly tools to explore the orchid genetic sequences in the OrchidBase 4.0. The OrchidBase 4.0 offers the opportunity for plant science community to compare orchid genomes and transcriptomes and retrieve orchid sequences for further study.In the year 2022, two whole-genome sequences of Orchidoideae species, Platanthera zijinensis and Platanthera guangdongensis, were de novo sequenced, assembled and analyzed. In addition, systemic transcriptomes from these two species were also established. Therefore, we included these datasets to develop the new version of OrchidBase 5.0. In addition, three new functions including synteny, gene order, and miRNA information were also developed for orchid genome comparisons and miRNA characterization.OrchidBase 5.0 extended the genetic information to three orchid subfamilies (including five orchid species) and provided new tools for orchid researchers to analyze orchid genomes and transcriptomes. The online resources can be accessed at https://cosbi.ee.ncku.edu.tw/orchidbase5/.

PMID:36456919 | DOI:10.1186/s12870-022-03955-5

BMC Med Res Methodol. 2022 Dec 1;22(1):308. doi: 10.1186/s12874-022-01783-7.

ABSTRACT

BACKGROUND: Altering cover letter information to reduce non-response bias in trauma research could inadvertently leave survey participants unprepared for potentially upsetting questions. In an unsolicited, mailed survey, we assessed participants’ change in affect post-survey after altering key cover letter information and promising different incentives. We tested direct and indirect effects of participants carefully reading the cover letter on changes in their affect post-survey.

METHODS: In a 3X2X2 randomized, factorial trial, 480 male and 480 female, nationally representative Veterans who were applying for posttraumatic stress disorder disability benefits were randomized to receive one of 12 different cover letters. The cover letters provided general versus more explicit information about the survey’s trauma content and how their names were selected for study; we also promised different incentives for returning the survey. The main outcome was change in affect post-survey. We examined five potential moderators: combat or military sexual trauma exposure, posttraumatic stress disorder or serious mental illness diagnosis, and recency of military service. Mediators between reading the cover letter carefully and post-survey affect included how participants rated the cover letters’ information and whether they thought the cover letters prepared them for the survey’s content. A Bonferroni corrected alpha of 0.003 was the threshold for statistical significance.

RESULTS: One hundred ninety men and 193 women reported their pre-and post-survey affect. Across all study conditions, out of 16 possible points, the net change in affect post-survey was less than a quarter-point for men and women. Mean changes in post-survey affect did not differ statistically significantly across any of the study factors (ps > 0.06); nor were there statistically significant interactions between any of the study factors and the 5 moderators after accounting for multiple comparisons (ps > 0.02). After controlling for pre-survey affect, reading the cover letter carefully had small effects on changes in post-survey affect, with larger associations seen in the women compared to men. Mediators’ effects were often in opposite directions for men and women.

CONCLUSION: General descriptions of a survey’s trauma content appear ethically defensible. Research on cover letters’ impacts on survey participants’ emotional reactions and how those impacts differ by gender is needed.

PMID:36456912 | DOI:10.1186/s12874-022-01783-7

BMC Neurol. 2022 Dec 1;22(1):446. doi: 10.1186/s12883-022-02982-x.

ABSTRACT

BACKGROUND: Stroke is one of the most common causes of disability among adults. Post-stroke depression (PSD) is a frequent neuropsychiatric complication in stroke patients. Despite the increasing prevalence of stroke, there is a paucity of data on PSD and its determinants among stroke survivors in developing countries like Ethiopia. We aim to assess the factors associated with PSD in survivors of stroke.

METHOD: A hospital-based unmatched case-control study was conducted during the period of February to July 2020 at University of Gondar Hospital among stroke survivors. Study subjects were recruited consecutively. Socio-demographic and clinical data were obtained from patients’ interviews and medical record reviews. A diagnosis of PSD was made using the Patient Health Questionnaire (PHQ-9). EpiData version 3.1 was used to enter data, and SPSS version 26 was used to analyze it. Bivariate and multivariate logistic regressions were fitted to identify associated variables. The adjusted odds ratio (AOR) with 95% confidence interval (CI) and p-value 0.05 were used to determine the significance of the association.

RESULT: A total of 240 stroke survivors were included in the study (80 cases and 160 controls). The mean age was 60.8 years (SD ± 14.3) with an equal sex distribution. Variables statistically associated with PSD were male gender (AOR = 3.5, 95% CI: 1.64-7.46 C, P-value = 0.001), subcortical location of the largest lesion (AOR = 2.42, 95% CI: 1.06-5.56, p-value = 0.036), severity of the stroke (AOR = 52.34, 95% CI:10.64-256.87, p-value = 0.000), physical disability (AOR = 5.85. 95% CI:1.94-17.65, p-value = 0.002), previous history of stroke or transient ischemic attack (AOR = 5.90, 95% CI:2.04-17.10, p-value = 0.001) and ischemic heart disease (AOR = 9.97, 95% CI:3.4-29.22, p-value = 0.000).

CONCLUSION: Important factors in the occurrence of PSD in this study include prior history of stroke, physical disability, severity of the stroke, subcortical location of the lesion, male gender, and ischemic heart disease. Stroke patients with such factors need routine screening for PSD, particularly in LMICs where there is uncoordinated post-stroke care, a shortage of neurologists and mental health practitioners.

PMID:36456908 | DOI:10.1186/s12883-022-02982-x

BMC Geriatr. 2022 Dec 1;22(1):927. doi: 10.1186/s12877-022-03544-z.

ABSTRACT

BACKGROUND: Older people were subjected to significant restrictions on physical contacts with others during the COVID-19 pandemic. Social distancing impacts older people’s experiences of anxiety and loneliness. Despite a large body of research on the pandemic, there is little research on its effects on older people in residential care facilities (RCF) and in home care services (HCS), who are the frailest of the older population. We aimed to investigate the effect of the first wave of the COVID-19 pandemic in March-May 2020 on experiences of anxiety and loneliness among older people living in RCF or receiving HCS and the impact of the progression of the pandemic on these experiences.

METHODS: A retrospective cross-sectional design using data from the national user satisfaction survey (March – May 2020) by the Swedish National Board of Health and Welfare. Survey responses were retrieved from 27,872 older people in RCF (mean age 87 years) and 82,834 older people receiving HCS (mean age 84 years). Proportional-odds (cumulative logit) model was used to estimate the degree of association between dependent and independent variables.

RESULTS: Loneliness and anxiety were more prevalent among the older persons living in RCF (loneliness: 69%, anxiety: 63%) than those receiving HCS (53% and 47%, respectively). Proportional odds models revealed that among the RCF and HCS respondents, the cumulative odds ratio of experiencing higher degree of anxiety increased by 1.06% and 1.04%, respectively, and loneliness by 1.13% and 1.16%, respectively, for 1% increase in the COVID-19 infection rate. Poor self-rated health was the most influential factor for anxiety in both RCF and HCS. Living alone (with HCS) was the most influential factor affecting loneliness. Experiences of disrespect from staff were more strongly associated with anxiety and loneliness in RCF than in HCS.

CONCLUSION: Older people in RCF or receiving HCS experienced increasing levels of anxiety and loneliness as the first wave of the pandemic progressed. Older people’ mental and social wellbeing should be recognized to a greater extent, such as by providing opportunities for social activities. Better preparedness for future similar events is needed, where restrictions on social interaction are balanced against the public health directives.

PMID:36456904 | DOI:10.1186/s12877-022-03544-z

BMC Genomics. 2022 Dec 1;23(1):789. doi: 10.1186/s12864-022-09044-z.

ABSTRACT

BACKGROUND: The exact mechanism of atrial fibrillation (AF)-induced heart failure (HF) remains unclear. Proteomics and metabolomics were integrated to in this study, as to describe AF patients’ dysregulated proteins and metabolites, comparing patients without HF to patients with HF.

METHODS: Plasma samples of 20 AF patients without HF and another 20 with HF were analyzed by multi-omics platforms. Proteomics was performed with data independent acquisition-based liquid chromatography-tandem mass spectrometry (LC-MS/MS), as metabolomics was performed with LC-MS/MS platform. Proteomic and metabolomic results were analyzed separately and integrated using univariate statistical methods, multivariate statistical methods or machine learning model.

RESULTS: We found 35 up-regulated and 15 down-regulated differentially expressed proteins (DEPs) in AF patients with HF compared to AF patients without HF. Moreover, 121 up-regulated and 14 down-regulated differentially expressed metabolites (DEMs) were discovered in HF patients compared to AF patients without HF. An integrated analysis of proteomics and metabolomics revealed several significantly enriched pathways, including Glycolysis or Gluconeogenesis, Tyrosine metabolism and Pentose phosphate pathway. A total of 10 DEPs and DEMs selected as potential biomarkers provided excellent predictive performance, with an AUC of 0.94. In addition, subgroup analysis of HF classification was performed based on metabolomics, which yielded 9 DEMs that can distinguish between AF and HF for HF classification.

CONCLUSIONS: This study provides novel insights to understanding the mechanisms of AF-induced HF progression and identifying novel biomarkers for prognosis of AF with HF by using metabolomics and proteomics analyses.

PMID:36456901 | DOI:10.1186/s12864-022-09044-z

Neuroradiology. 2022 Dec 1. doi: 10.1007/s00234-022-03094-6. Online ahead of print.

ABSTRACT

PURPOSE: We aimed to evaluate whether the heterogeneity of tuber imaging features, evaluated on the structural imaging and apparent diffusion coefficient (ADC) map, can facilitate detecting epileptogenic tubers before surgery in tuberous sclerosis complex (TSC) patients.

METHODS: Twenty-three consecutive patients, who underwent tuber resection at our institute, were retrospectively selected. A total of 125 tubers (39 epileptogenic, 86 non-epileptogenic) were used for the analysis. Tuber heterogeneity was evaluated, using a 5-point visual scale and standard deviation of ADC values (ADC_sd). A 5-point visual scale reflected the degree of T1/T2 prolongation, presence of internal cystic degeneration, and their spatial distribution within the tuber. These results were statistically compared between epileptogenic and non-epileptogenic groups, and their performance in predicting the epileptogenicity was also evaluated by receiver operating characteristic (ROC) analysis.

RESULTS: A 5-point visual scale demonstrated that more heterogeneous tubers were significantly more epileptogenic (p < 0.001). Multiplicity of internal cystic degeneration moderately correlated with epileptogenicity (p < 0.03) based on the comparison between class 4 and class 5 tubers. ADC_sd was significantly higher in epileptogenic tubers (p < 0.001). ROC curves revealed that a 5-point visual scale demonstrated higher area under the curve (AUC) value than ADC_sd (0.75 and 0.72, respectively).

CONCLUSION: Tuber heterogeneity may help identify the epileptogenic tubers in presurgical TSC patients. Visual assessment and standard deviation of ADC value, which are easier to implement in clinical use, may be a useful tool predicting epileptogenic tubers, improving presurgical clinical management for TSC patients with intractable epilepsy.

PMID:36456893 | DOI:10.1007/s00234-022-03094-6

Endocrine. 2022 Dec 2. doi: 10.1007/s12020-022-03273-8. Online ahead of print.

ABSTRACT

PURPOSE: Thirty years into the genomic era, this study sought to explore events that helped transform the clinical landscape of hereditary medullary thyroid cancer (MTC).

METHOD: This retrospective analysis of prospectively collected data included all RET carriers referred to a tertiary center for neck surgery that was performed between 1986 and 2021, using descriptive statistics and Poisson regression analysis.

RESULTS: Altogether, 496 RET carriers were referred for thyroidectomy (388 carriers) or neck reoperation (108 carriers). Of these, 44 carriers had highest risk mutations (p.Met918Thr), 164 carriers high risk mutations (p.Cys634Arg/Gly/Phe/Ser/Trp/Tyr/insHisGluLeuCys), 116 carriers moderate-high risk mutations (p.Cys609/611/618/620/630Arg/Gly/Phe/Ser/Tyr) and 172 carriers low-moderate risk mutations (p.Glu768Asp, p.Leu790Phe, p.Val804Leu/Met, or p.Ser891Ala). Three event clusters drove referral numbers upward: a string of first reports of causative RET mutations between 1993 and 1998; the international consensus guidelines for diagnosis and therapy of MEN type 1 and type 2 in 2001; and the revised American Thyroid Association guidelines for the management of medullary thyroid carcinoma in 2015. Referrals for neck reoperation declined sluggishly over 30 years, ending in 2018. Index patients continued to be referred into 2021. Referrals for thyroidectomy, grouped in 5-year increments, peaked in 1996-2000 for carriers of highest and high risk mutations, and in 2006-2010 for carriers of moderate-high and low-moderate risk mutations, some 10 years later.

CONCLUSION: International management guidelines are critical in building and increasing the pressure towards screening of sporadic-appearing disease and offspring of known gene families by encompassing the complete disease spectrum early on.

PMID:36456885 | DOI:10.1007/s12020-022-03273-8

Graefes Arch Clin Exp Ophthalmol. 2022 Dec 2. doi: 10.1007/s00417-022-05923-z. Online ahead of print.

ABSTRACT

PURPOSE: To evaluate differences in acquisition time, peripheral extension, and chromaticity between 3 different commercialized ultra-wide-field (UWF) fundus cameras.

METHODS: Patients were prospectively enrolled from 07/2021 to 11/2021. Patients underwent fundus photography with the following scanning protocols: (1) single shot with Silverstone (Optos, California), two-shot montage with Clarus 500 (Carl Zeiss, Dublin, CA), and three-shot montage with iCare EIDON FA with UWF module (CenterVue Spa, a company of iCare Finland Oy; Vantaa, Finland). Acquisition time was calculated as the interval between the beginning and the end of the acquisition. Peripheral extension was quantified as the average ratio between the total retinal pixel area and the optic nerve head (ONH) pixel area. The average chromaticity of all pixels in the red-green-blue (RGB) space was calculated.

RESULTS: Twenty-three eyes of 13 prospectively enrolled healthy controls were included in the study. Optos Silverstone had a higher total retina area/ONH area ratio (509.1 [480.9;559.3]) compared to Zeiss Clarus (442.0 [431.9;510.5], p = 0.02) and iCare EIDON (369.7 [345.3;387.8], p < 0.0001). Silverstone demonstrated the shortest acquisition time (median [interquartile range]: 32 [20;58.5] s) compared to Zeiss Clarus (42 [28.5;53.5] s, p = 0.6733) and iCare EIDON (72 [68.5;78] s, p = 0.0003). iCare EIDON demonstrated the lowest variability of acquisition time (9.5 s), compared to Zeiss Clarus (25 s) and Optos Silverstone (38.5 s). A statistically significant difference was found in the RGB distribution between each of the 3 devices (p < 0.001). iCare EIDON demonstrated an average barycenter position (RGB = [0.412, 0.314, 0.275]) that represented the best color balance of the image. Zeiss Clarus had a noticeable red shift at the expense of the blue and green channels (RGB = [0.515, 0.294, 0.191]). Optos Silverstone showed an absence of the blue channel (RGB = [0.621, 0.372, 0.007]) which results in a distortion of the color of the image.

CONCLUSION: Optos Silverstone and Zeiss Clarus required less time than iCare EIDON to acquire a comparable size image and captured larger areas of the retina than iCare EIDON. iCare EIDON provided more color-balanced retinal images with greater richness of color content than the other two devices.

PMID:36456861 | DOI:10.1007/s00417-022-05923-z

J Immigr Minor Health. 2022 Dec 1. doi: 10.1007/s10903-022-01434-5. Online ahead of print.

ABSTRACT

This study explored factors that mediate the relationship between subjective wellbeing and depression in a sample of West Indian American immigrants. An intersectional theoretical framework was used to identify the relative contribution of psychological stressors-perceived discrimination, financial strain and acculturative stress-that mediate the relationship between subjective wellbeing and depression. A geographically diverse sample was recruited by an online survey (N = 255), consisting of 138 men, 115 women, 173 Indo-West Indians and 82 Afro-West Indians. Path analysis was used to identify the relative contribution of psychological stressors. Acculturative stress and financial strain were both statistically significant predictors of depression. Financial strain was identified as the major mediator between subjective wellbeing and depression in West Indian Americans. West Indian Americans are vulnerable to financial strain and acculturative stress. These sources of psychological stress are important contributors to depression in the community. More research is needed to clarify these relationships.

PMID:36456840 | DOI:10.1007/s10903-022-01434-5

J Digit Imaging. 2022 Dec 1. doi: 10.1007/s10278-022-00738-0. Online ahead of print.

ABSTRACT

Retinal fundus images are non-invasively acquired and faced with low contrast, noise, and uneven illumination. The low-contrast problem makes objects in the retinal fundus image indistinguishable and the segmentation of blood vessels very challenging. Retinal blood vessels are significant because of their diagnostic importance in ophthalmologic diseases. This paper proposes improved retinal fundus images for optimal segmentation of blood vessels using convolutional neural networks (CNNs). This study explores some robust contrast enhancement tools on the RGB and the green channel of the retinal fundus images. The improved images undergo quality evaluation using mean square error (MSE), peak signal to noise ratio (PSNR), Similar Structure Index Matrix (SSIM), histogram, correlation, and intersection distance measures for histogram comparison before segmentation in the CNN-based model. The simulation results analysis reveals that the improved RGB quality outperforms the improved green channel. This revelation implies that the choice of RGB to the green channel for contrast enhancement is adequate and effectively improves the quality of the fundus images. This improved contrast will, in turn, boost the predictive accuracy of the CNN-based model during the segmentation process. The evaluation of the proposed method on the DRIVE dataset achieves an accuracy of 94.47, sensitivity of 70.92, specificity of 98.20, and AUC (ROC) of 97.56.

PMID:36456839 | DOI:10.1007/s10278-022-00738-0