Nevin Manimala

Open Biol. 2023 Oct;13(10):230148. doi: 10.1098/rsob.230148. Epub 2023 Oct 4.

ABSTRACT

Diatoms are ancestrally photosynthetic microalgae. However, some underwent a major evolutionary transition, losing photosynthesis to become obligate heterotrophs. The molecular and physiological basis for this transition is unclear. Here, we isolate and characterize new strains of non-photosynthetic diatoms from the coastal waters of Singapore. These diatoms occupy diverse ecological niches and display glucose-mediated catabolite repression, a classical feature of bacterial and fungal heterotrophs. Live-cell imaging reveals deposition of secreted extracellular polymeric substance (EPS). Diatoms moving on pre-existing EPS trails (runners) move faster than those laying new trails (blazers). This leads to cell-to-cell coupling where runners can push blazers to make them move faster. Calibrated micropipettes measure substantial single-cell pushing forces, which are consistent with high-order myosin motor cooperativity. Collisions that impede forward motion induce reversal, revealing navigation-related force sensing. Together, these data identify aspects of metabolism and motility that are likely to promote and underpin diatom heterotrophy.

PMID:37788707 | DOI:10.1098/rsob.230148

Biomed Phys Eng Express. 2023 Oct 3. doi: 10.1088/2057-1976/acff76. Online ahead of print.

ABSTRACT

The aim of this study is to develop software to automatically assess the laser alignment on the ACR CT phantom and evaluate its accuracy on sixteen CT scanners. 
Methods: Software for an automated method of laser alignment assessment on the ACR CT phantom was developed. Laser alignment assessment was based on the positions of the ball-bearing markers at the edge of the phantom. The automatic assessment was performed using several steps, including segmentation to acquire the coordinates of ball-bearing markers and determination of the distances between lines connecting the ball-bearing markers with lines through the center of the image. A comparison of the results from automatic method with those from the manual method was performed. The manual measurements were carried out using MicroDicom Viewer. A Mann-Whitney U test was performed to determine the statistical difference between both methods. The evaluation was performed on images of ACR CT phantom scanned with 16 CT scanners from 5 different CT manufacturers. 
Results: The results revealed that developed software successfully segments the ball-bearing markers and determines the laser alignment assessment on the ACR CT phantom. Evaluation of the algorithm with images of 16 CT scanners revealed that the difference between the results from automatic and manual methods were about 0.2 mm with a p value of around 0.7 (no statistical difference). Misalignment in the y-axis was more perceived by majority of the scanners rather than the misalignment in x-axis. It is found that the phantom tended to be placed 2 mm higher than iso-center. 
Conclusions: Software to automatically asses CT laser alignment with the ACR CT phantom was successfully developed and evaluated. The automatic assessment was comparable to the manual assessment. In addition, the automatic method was user independent and fast.

PMID:37788647 | DOI:10.1088/2057-1976/acff76

J Pediatr Endocrinol Metab. 2023 Oct 5. doi: 10.1515/jpem-2023-0237. Online ahead of print.

ABSTRACT

OBJECTIVES: This prospective study compares testosterone injection type and effects on biochemical changes, clinical effects, and quality of life amongst transgender and gender diverse (TGD) adolescents assigned female at birth (AFAB) over the first 6 months of subcutaneous (SQ) vs. intramuscular (IM) testosterone injections as part of their gender affirming care.

METHODS: Subjects were testosterone-naïve transgender adolescents, AFAB, ages 14-18 years old. Subjects were either randomized to injection type or selected a preferred injection type. At enrollment, subjects completed baseline labs and PedsQL™ quality of life questionnaire. At 3 month and 6 month follow up, subjects completed peak and trough testosterone levels, PedsQL™, masculinizing effects, and medication experience questionnaires.

RESULTS: Twenty-six subjects participated with a median age 15.5 years. By 6-month follow up, trough testosterone levels were comparable between the two groups. Peak testosterone levels were higher in the IM group at 3-month follow up. Mild adverse effects were rare (12 %, all in SQ subjects) and limited to skin reaction only. Self-reported masculinization effects and quality of life were not statistically different between injection groups. A total of 92 % of participants was self-injecting by 3-month follow up.

CONCLUSIONS: In this prospective study, clinical and biochemical effects are similar between SQ and IM testosterone injections for transgender adolescents. Subjects expressed preference for both injection types. Both SQ and IM injection modalities are safe and effective for TGD youth initiating testosterone and both options should be offered to patients.

PMID:37788646 | DOI:10.1515/jpem-2023-0237

Eur Heart J Cardiovasc Imaging. 2023 Oct 4:jead247. doi: 10.1093/ehjci/jead247. Online ahead of print.

ABSTRACT

AIMS: Cardiovascular magnetic resonance parametric mapping enables non-invasive quantitative myocardial tissue characterisation. Human myocardium has normal ranges of T1- and T2-values, deviation from which may indicate disease or change in physiology. Normal myocardial T1- and T2-values are affected by biological sex. Consequently, normal ranges created with insufficient numbers of each sex may result in sampling biases, misclassification of healthy values versus disease, and even misdiagnoses. We investigated the impact of using male normal ranges for classifying female cases as normal or abnormal (and vice versa).

METHODS AND RESULTS: 142 healthy volunteers (male and female) were scanned on two Siemens 3 T MR systems, providing averaged global myocardial T1- and T2-values on a per-subject basis. The Monte Carlo method was used to generate simulated normal ranges from these values, to estimate the statistical accuracy of classifying healthy female or male cases correctly as ‘normal’ when using sex-specific versus mixed-sex normal ranges. Normal male and female T1- and T2-mapping values were significantly different by sex, after adjusting for age and heart rate.

CONCLUSION: Using 15 healthy volunteers which are not sex-specific to establish a normal range typically misclassified up to 36% of healthy females and 37% of healthy males as having abnormal T1-values, and up to 16% of healthy females and 12% of healthy males as having abnormal T2-values. This paper highlights the potential adverse impact on diagnostic accuracy that can occur when local normal ranges contain insufficient numbers of both sexes. Sex-specific reference ranges should thus be routinely adopted into clinical practice.

PMID:37788638 | DOI:10.1093/ehjci/jead247

J Addict Med. 2023 Sep-Oct 01;17(5):587-591. doi: 10.1097/ADM.0000000000001184. Epub 2023 Jun 1.

ABSTRACT

OBJECTIVE: Although medications for opioid use disorder improve both maternal and neonatal outcomes, little is known about opioid-exposed infants born during episodes of incarceration. The study sought to examine birth outcomes for infants born with opioid exposure during perinatal incarceration.

METHODS: Participants were identified from clinic rosters in a Southeastern women’s prison (2016-2019). Included infants born to pregnant people with opioid use disorder incarcerated in the study facility at the time of delivery. We abstracted hospital length of stay, neonatal opioid withdrawal syndrome (NOWS) severity, and discharge plan from hospital records and report descriptive statistics, analysis of variance F tests, and chi-square tests to compare outcomes by opioid exposure type.

RESULTS: There were 125 infants born after exposure to methadone (n = 34), buprenorphine (n = 15), oxycodone (n = 22), or no opioid medication (n = 54) during prenatal incarceration. Most infants exposed to methadone or buprenorphine had difficulty with eating, sleeping, or consoling (97% and 80%), and 59% and 47% were treated with medication for NOWS, respectively. The majority with prenatal opioid exposure required intervention for NOWS symptoms after their birthing parent was discharged to the prison. The average hospital length of stay was different for infants with no opioid, methadone, buprenorphine, and oxycodone exposure during incarceration (4, 15, 12, and 9 days, respectively, P < 0.001).

CONCLUSIONS: Neonatal hospitalization experiences of infants with perinatal opioid exposures during maternal incarceration mirror those of similarly exposed infants born outside the context of incarceration, except for hospital length of stay. Consideration of avoiding separation of the parent-infant dyad may be needed to improve outcomes for these infants.

PMID:37788614 | DOI:10.1097/ADM.0000000000001184

J Addict Med. 2023 Sep-Oct 01;17(5):557-562. doi: 10.1097/ADM.0000000000001177. Epub 2023 May 18.

ABSTRACT

OBJECTIVES: Impairments in neuropsychological functioning (mainly memory, learning, attention, and executive functioning) among persons with long-term opioid use disorder (OUD) have been widely reported, with few studies suggesting that these are not permanent and can improve with abstinence. Thus, present study aimed to evaluate the neuropsychological functioning in persons with OUD and examine the effects of abstinence on the same over a period 8 weeks.

METHODS: A total of 50 patients with diagnosis of OUD as per the Diagnostic and Statistical Manual of Mental Disorders , Fifth Edition ( DSM-5 ) criteria underwent serial longitudinal neuropsychological assessments for executive functioning, attention and concentration, and verbal and nonverbal memory at baseline, 2 weeks, and 8 weeks of abstinence.

RESULTS: The mean performance scores representative of attention, concentration, verbal memory, and nonverbal memory showed significant improvement in the initial 2 weeks, and executive functioning showed significant improvement by 8 weeks of abstinence (all P ‘s < 0.01). A significant negative correlation was found between the duration of opioid use and performance on verbal memory tests (0.014), the frequency of intake per day and performance on nonverbal memory and executive functioning tests, and the severity of opioid dependence and performance on nonverbal memory test (0.019).

CONCLUSIONS: Neuropsychological functioning in certain domains was associated with the duration of opioid use, the frequency of daily opioid intake, and the severity of opioid dependence among persons with OUD at baseline. It showed significant improvement in domains of attention, concentration, verbal and nonverbal memory, and executive functions over a period of 8 weeks of abstinence.

PMID:37788609 | DOI:10.1097/ADM.0000000000001177

Mol Biol Evol. 2023 Oct 4:msad208. doi: 10.1093/molbev/msad208. Online ahead of print.

ABSTRACT

The transition from oviparity to viviparity has occurred independently over 150 times across vertebrates, presenting one of the most compelling cases of phenotypic convergence. However, whether the repeated, independent evolution of viviparity is driven by redeployment of similar genetic mechanisms and whether these leave a common signature in genomic divergence remains largely unknown. Whilst recent investigations into the evolution of viviparity have demonstrated striking similarity among the genes and molecular pathways involved across disparate vertebrate groups, quantitative tests for genome-wide convergent have provided ambivalent answers. Here, we investigate the potential role of molecular convergence during independent transitions to viviparity across an order of ray-finned freshwater fish (Cyprinodontiformes). We assembled de novo genomes and utilized publicly-available genomes of viviparous and oviparous species to test for molecular convergence across both coding and non-coding regions. We found no evidence for an excess of molecular convergence in amino acid substitutions and in rates of sequence divergence, implying independent genetic changes are associated with these transitions. However, both statistical power and biological confounds could constrain our ability to detect significant correlated evolution. We therefore identified candidate genes with potential signatures of molecular convergence in viviparous Cyprinodontiformes lineages. Motif-enrichment and gene ontology analyses suggest transcriptional changes associated with early morphogenesis, brain development and immunity occurred alongside the evolution of viviparity. Overall, however, our findings indicate that independent transitions to viviparity in these fish is not strongly associated with an excess of molecular convergence, but a few genes show convincing evidence of convergent evolution.

PMID:37789509 | DOI:10.1093/molbev/msad208

J Biophotonics. 2023 Oct 3:e202300236. doi: 10.1002/jbio.202300236. Online ahead of print.

ABSTRACT

Many optical techniques have been used in various diagnostics and biomedical applications since a decade and polarization imaging is one of the non-invasive and label free optical technique to investigate biological samples making it an important tool in diagnostics, biomedical applications. We report a multispectral polarization-based imaging of oral tissue by utilizing a polarization microscope system with a broadband-light source. Experiments were performed on oral tissue samples and multispectral Stokes mapping was done by recording a set of intensity images. Polarization-based parameters like degree of polarization, angle of fast axis, retardation and linear birefringence have been retrieved. The statistical moments of these polarization components have also been reported at multiples wavelengths. The polarimetric properties of oral tissue at different stages of cancer have been analyzed and significant changes from normal to pre-cancerous lesions to the cancerous are observed in linear birefringence quantification as (1.7± 0.1) ×10^-3 , (2.5± 0.2) ×10^-3 and (3.3±0.2) ×10^-3 respectively. This article is protected by copyright. All rights reserved.

PMID:37789505 | DOI:10.1002/jbio.202300236

Fungal Biol Biotechnol. 2023 Oct 3;10(1):20. doi: 10.1186/s40694-023-00167-w.

ABSTRACT

BACKGROUND: Trichoderma atroviride is a competitive soil-borne mycoparasitic fungus with extensive applications as a biocontrol agent in plant protection. Despite its importance and application potential, reference genes for RT-qPCR analysis in T. atroviride have not been evaluated. Light exerts profound effects on physiology, such as growth, conidiation, secondary metabolism, and stress response in T. atroviride, as well as in other fungi. In this study, we aimed to address this gap by identifying stable reference genes for RT-qPCR experiments in T. atroviride under different light conditions, thereby enhancing accurate and reliable gene expression analysis in this model mycoparasite. We measured and compared candidate reference genes using commonly applied statistical algorithms.

RESULTS: Under cyclic light-dark cultivation conditions, tbp and rho were identified as the most stably expressed genes, while act1, fis1, btl, and sar1 were found to be the least stable. Similar stability rankings were obtained for cultures grown under complete darkness, with tef1 and vma1 emerging as the most stable genes and act1, rho, fis1, and btl as the least stable genes. Combining the data from both cultivation conditions, gapdh and vma1 were identified as the most stable reference genes, while sar1 and fis1 were the least stable. The selection of different reference genes had a significant impact on the calculation of relative gene expression, as demonstrated by the expression patterns of target genes pks4 and lox1.

CONCLUSION: The data emphasize the importance of validating reference genes for different cultivation conditions in fungi to ensure accurate interpretation of gene expression data.

PMID:37789459 | DOI:10.1186/s40694-023-00167-w

Artif Intell Med. 2023 Oct;144:102645. doi: 10.1016/j.artmed.2023.102645. Epub 2023 Aug 29.

ABSTRACT

The widespread use of information technology in healthcare leads to extensive data collection, which can be utilised to enhance patient care and manage chronic illnesses. Our objective is to summarise previous studies that have used data mining or process mining methods in the context of chronic diseases in order to identify research trends and future opportunities. The review covers articles that pertain to the application of data mining or process mining methods on chronic diseases that were published between 2000 and 2022. Articles were sourced from PubMed, Web of Science, EMBASE, and Google Scholar based on predetermined inclusion and exclusion criteria. A total of 71 articles met the inclusion criteria and were included in the review. Based on the literature review results, we detected a growing trend in the application of data mining methods in diabetes research. Additionally, a distinct increase in the use of process mining methods to model clinical pathways in cancer research was observed. Frequently, this takes the form of a collaborative integration of process mining, data mining, and traditional statistical methods. In light of this collaborative approach, the meticulous selection of statistical methods based on their underlying assumptions is essential when integrating these traditional methods with process mining and data mining methods. Another notable challenge is the lack of standardised guidelines for reporting process mining studies in the medical field. Furthermore, there is a pressing need to enhance the clinical interpretation of data mining and process mining results.

PMID:37783545 | DOI:10.1016/j.artmed.2023.102645