Category: Nevin Manimala

PLoS Comput Biol. 2022 Jan 5;18(1):e1009731. doi: 10.1371/journal.pcbi.1009731. Online ahead of print.

ABSTRACT

Operon prediction in prokaryotes is critical not only for understanding the regulation of endogenous gene expression, but also for exogenous targeting of genes using newly developed tools such as CRISPR-based gene modulation. A number of methods have used transcriptomics data to predict operons, based on the premise that contiguous genes in an operon will be expressed at similar levels. While promising results have been observed using these methods, most of them do not address uncertainty caused by technical variability between experiments, which is especially relevant when the amount of data available is small. In addition, many existing methods do not provide the flexibility to determine the stringency with which genes should be evaluated for being in an operon pair. We present OperonSEQer, a set of machine learning algorithms that uses the statistic and p-value from a non-parametric analysis of variance test (Kruskal-Wallis) to determine the likelihood that two adjacent genes are expressed from the same RNA molecule. We implement a voting system to allow users to choose the stringency of operon calls depending on whether your priority is high recall or high specificity. In addition, we provide the code so that users can retrain the algorithm and re-establish hyperparameters based on any data they choose, allowing for this method to be expanded as additional data is generated. We show that our approach detects operon pairs that are missed by current methods by comparing our predictions to publicly available long-read sequencing data. OperonSEQer therefore improves on existing methods in terms of accuracy, flexibility, and adaptability.

PMID:34986143 | DOI:10.1371/journal.pcbi.1009731

J Pediatr Hematol Oncol. 2022 Jan 1;44(1):e199-e203. doi: 10.1097/MPH.0000000000002306.

ABSTRACT

BACKGROUND AND AIM: Oral mucositis (OM) is a common side effect of systemic chemotherapy (CT) in cancer patients. The aim was to evaluate the effect of low-level laser therapy (LLLT) for the treatment of CT-induced OM children.

PATIENTS AND METHODS: The study was carried out in 40 pediatric patients 3 to 18 years of age, who were hospitalized for the diagnosis of leukemia and underwent CT between June 1, 2019, and December 31, 2019. They were randomly divided into 2 groups with 20 cases in each group. The LLLT group was treated with GaAlAs diode laser (l): 830 nm (infrared), power: 150 mW, dose: 4.5 J/cm2 and the control group underwent bicarbonate treatment. Patients received intervention for 3 days. The grade of OM was clinically assessed by the World Health Organization (WHO) Common Toxicity Criteria Scale. Visual Analog Scale was used on the same days with OM grade to evaluate the pain status.

RESULTS: While there was no significant difference between the groups in terms of OM grade at the beginning of the treatment and on the first, second, fourth, and 11th days of the treatment, the average OM grade of the LLLT group was found to be statistically significantly lower on the third, fifth, sixth, and seventh days of the treatment. The Visual Analog Scale score of the LLLT group was statistically significantly lower compared with the control group at all examinations starting from the first day of treatment (P<0.05).

CONCLUSION: In the treatment of oral OM that occurs in children after CT, both standard care and LLLT treatment improve the grade and pain of OM.

PMID:34986132 | DOI:10.1097/MPH.0000000000002306

Acta Med Port. 2021 Nov 2;34(11):761-766. doi: 10.20344/amp.16209. Epub 2021 Nov 2.

ABSTRACT

INTRODUCTION: In March 2020, the World Health Organization declared COVID-19 as a pandemic, and Portugal reported its initial cases. In this study, we aimed to determine the impact of COVID-19 on Portuguese individuals aged over 60 years old.

MATERIAL AND METHODS: We performed a cross-sectional study using data from the Survey of Health, Ageing and Retirement in Europe (SHARE 8: COVID-19 Survey). We selected a sample of 1080 noninstitutional Portuguese individuals aged ≥ 60 years.

RESULTS: The study sample consisted of 605 (56%) women and 475 (44%) men, with a mean age of 70 ± 9.1 years. In total, 80% of the participants experienced higher levels of anxiety, 73% felt more depressed and 30% experienced additional sleep problems comparedto the period before the pandemic. Interestingly, there were no statistically significant differences between the sexes or the two selected age groups (60 – 74 and over 75 years old) regarding the incidence of these changes. Only 23%, of those that were interviewed maintained their walking routines. In addition, only 8% of the participants continued visiting family members as frequently as before. While 8% of the participants were refused some form of medical treatment, 56% claimed that they experienced healthcare delays. However,only 15% of the participants reported that their health status worsened during the pandemic.

DISCUSSION: The pandemic has had a significant impact on Portuguese individuals aged ≥ 60 years; which is in agreement with the findings of previous international studies. It changed the participants’ routines and increased their anxiety and depression levels. Despite the deterioration of healthcare services, most participants did not experience worsening of their health status.

CONCLUSION: In conclusion, a COVID-19 pandemic had a significant impact on the elderly population, particularly regarding their mental health.

PMID:34986084 | DOI:10.20344/amp.16209

IEEE J Biomed Health Inform. 2022 Jan 5;PP. doi: 10.1109/JBHI.2022.3140531. Online ahead of print.

ABSTRACT

Functional near-infrared spectroscopy (fNIRS) is a promising neuroimaging technology. The fNIRS classification problem has always been the focus of the brain-computer interface (BCI). Inspired by the success of Transformer based on self-attention mechanism in the fields of natural language processing and computer vision, we propose an fNIRS classification network based on Transformer, named fNIRS-T. We explore the spatial-level and channel-level representation of fNIRS signals to improve data utilization and network representation capacity. Besides, a preprocessing module, which consists of one-dimensional average pooling and layer normalization, is designed to replace filtering and baseline correction of data preprocessing. It makes fNIRS-T an end-to-end network, called fNIRS-PreT. Compared with traditional machine learning classifiers, convolutional neural network (CNN), and long short-term memory (LSTM), the proposed models obtain the best accuracy on three open-access datasets. Specifically, in the most extensive ternary classification task (30 subjects) that includes three types of overt movements, fNIRS-T, CNN, and LSTM obtain 75.49%, 72.89%, and 61.94% on test sets, respectively. Compared to traditional classifiers, fNIRS-T is at least 27.41% higher than statistical features and 6.79% higher than well-designed features. In the individual subject experiment of the ternary classification task, fNIRS-T achieves an average subject accuracy of 78.22% and surpasses CNN and LSTM by a large margin of +4.75% and +11.33%. fNIRS-PreT using raw data also achieves competitive performance to fNIRS-T. Therefore, the proposed models improve the performance of fNIRS-based BCI significantly.

PMID:34986110 | DOI:10.1109/JBHI.2022.3140531

Comput Methods Biomech Biomed Engin. 2022 Jan 5:1-13. doi: 10.1080/10255842.2021.2021194. Online ahead of print.

ABSTRACT

The hydrothermal features of unsteady, incompressible, and laminar hybrid nanofluid motion through a porous capillary are analytically studied in the magnetic field presence. The hybrid nanofluid (GO + ZnO + Blood) is synthesized by blending nanomaterials of graphene oxide and zinc oxide with blood acting as the host fluid. The mathematical model of the flow comprises of a coupled nonlinear set of partial differential equations (PDEs) satisfying appropriate boundary conditions. These equations are reduced to ordinary differential equations (ODEs) by using similarity transformations and then solved with homotopy analysis method (HAM). The impacts of various pertinent physical parameters over the hybrid nanofluid state functions are examined by displaying 2 D graphs. It has been observed that the fluid velocity mitigates with the varying strength of M, A₀, N₀, and N₁. The enhancing buoyancy parameter ϵ augments the fluid velocity. The increasing Prandtl number causes to reduce, while the enhancing A₀, B, and N₂ augment the hybrid nanofluid temperature. The fluid concentration mitigates with the higher Schmidt number values and A₀, and augments with the increasing Soret number strength. The augmenting magnetic field strength causes to enhance the fluid friction, whereas the convective heat transfer increases with the Prandtl number rising values. The rising Sherwood number drops the mass transfer rate of the fluid. The achieved results are validated due to the agreement with the published results. The results of this computation will find applications in biomedicine, nanotechnology, and fluid dynamics.

PMID:34986079 | DOI:10.1080/10255842.2021.2021194

Acta Med Port. 2021 Nov 2;34(11):724-732. doi: 10.20344/amp.14004. Epub 2021 Nov 2.

ABSTRACT

INTRODUCTION: Urinary incontinence affects up to one third of women in Portugal. Exercise can be a precipitating/aggravating factor but also protective, if appropriate. The aim of this study was to determine the prevalence of urinary incontinence in women who practice recreational exercise, to assess its relationship with the type of exercise and other coexisting risk factors, and assess whether the topic is addressed in gyms.

MATERIAL AND METHODS: Cross-sectional study using self-reported questionnaires in gyms in Porto and Vila Nova de Gaia, Portugal.

RESULTS: Two hundred and ninety women completed the questionnaires. From these, 67.6% were under 40 years old, 25.2% reported incontinence, and 53.4% had at least one risk factor unrelated to exercise. There was a statistically significant association (p < 0.05) between incontinence, obesity and constipation. High impact exercises were included in the training of 62.1% continent and 50.9% incontinent women. The topic of incontinence and strengthening of the pelvic floor muscles was addressed in only 5.5% in the initial assessment, 9.7% in collective training, and in 13.5% of the 37 women with individualized training.

DISCUSSION: The higher proportion of continent women – compared to incontinent – who practiced strenuous exercise suggests that this might be a provocative factor for some, although there was no statistically significant association between incontinence and type of exercise.

CONCLUSION: Urinary incontinence affects women who practice recreational exercise, regardless of age and exercise characteristics. It is rarely addressed in gyms, and it is necessary to raise the awareness of professionals to enhance the preventive/therapeutic effects of exercise on the function of the pelvic floor and in the control of modifiable risk factors.

PMID:34986083 | DOI:10.20344/amp.14004

Physiol Biochem Zool. 2022 Mar-Apr;95(2):113-121. doi: 10.1086/717938.

ABSTRACT

AbstractAlthough climate warming poses a grave threat to amphibians, little is known about the capacity of this group to evolve in response to warming. The capacity of key traits to evolve depends on the presence of genetic variation on which selection can act. Here, we use repeatability estimates to estimate the potential upper bounds of heritable genetic variation in voluntary and critical thermal maxima of gray-cheeked salamanders (Plethodon metcalfi). Increases in thermal tolerance may also require concordant increases in resistance to water loss because hotter temperatures incur greater evaporative risk. Therefore, we also tested for a correlation between voluntary thermal maxima and resistance to water loss and conducted an acclimation study to test for covariation between these traits in response to warming. Voluntary thermal maxima exhibited low to moderate levels of repeatability (R=0.32, P=0.045), while critical thermal maxima exhibited no statistically significant repeatability (R=0.10, P=0.57). Voluntary thermal maxima also correlated positively with resistance to water loss (R=0.31, P=0.025) but only when controlling for body mass. Voluntary thermal maxima and resistance to water loss also exhibited different acclimatory responses across control (12°C-18°C) and warm (18°C-24°C) temperature regimes, indicating a potential decoupling of traits in different thermal environments. By addressing the repeatability of thermal tolerance and the potential for covariation with resistance to water loss, we begin to address some of the key requirements of amphibians to evolve in warming climates.

PMID:34986078 | DOI:10.1086/717938

Birth Defects Res. 2022 Jan 4. doi: 10.1002/bdr2.1973. Online ahead of print.

ABSTRACT

BACKGROUND: In 2016, Zika virus (ZIKV) was recognized as a human teratogen. North Carolina (NC) had no local transmission of ZIKV but infants with relevant birth defects, including severe brain anomalies, microcephaly, and eye abnormalities, require specialized care and services, the costs of which have not yet been quantified. The objective of this study is to examine NC Medicaid healthcare expenditures for infants with defects potentially related to ZIKV compared to infants with no reported defects.

METHODS: Data sources for this retrospective cohort study include NC birth certificates, Birth Defects Monitoring Program data, and Medicaid enrollment and paid claims files. Infants with relevant defects were identified and expenditure ratios were calculated to compare distributions of estimated expenditures during the first year of life for infants with relevant defects and infants with no reported defects.

RESULTS: This analysis included 551 infants with relevant defects and 365,318 infants with no reported defects born 2011-2016. Mean total expenditure per infant with defects was $69,244 (median $30,544) for the first year. The ratio of these expenditures relative to infants with no reported defects was 14.5. Expenditures for infants with select brain anomalies were greater than those for infants with select eye abnormalities only.

CONCLUSIONS: Infants with defects potentially related to ZIKV had substantially higher Medicaid expenditures than infants with no reported defects. These results may be informative in the event of a future outbreak and are a resource for program planning related to care for infants in NC.

PMID:34984857 | DOI:10.1002/bdr2.1973

Dermatol Ther. 2022 Jan 4:e15303. doi: 10.1111/dth.15303. Online ahead of print.

ABSTRACT

Chronic spontaneous urticaria (CSU) is characterized by the spontaneous development of wheals, itching, and/or angioedema, for ≥6 weeks. In China, non-sedating H1-antihistamines (H1AH) are the recommended first-line treatment, with escalation up to 4× the standard dose in symptomatic patients to achieve control. Treatment options for Chinese patients who remain symptomatic on H1AH treatment are limited. This 20-week randomized, double-blind, placebo-controlled, parallel-group study investigated the efficacy and safety of omalizumab as an add-on therapy for the treatment of patients with CSU who remained symptomatic despite H1AH treatment in China. Adult patients (N = 418) diagnosed with refractory CSU for ≥6 months were randomized (2:2:1) to receive omalizumab 300 mg (OMA300), omalizumab 150 mg (OMA150) or placebo, subcutaneously, every 4 weeks. Primary outcome was change from baseline to Week 12 in weekly itch severity score (ISS7). Safety was assessed by rates of adverse events (AEs). Demographic and disease characteristics at baseline were comparable across treatment groups. At week 12, statistically significant greater decreases from baseline were observed in ISS7 with OMA300 (least square mean difference [LSM]: -4.23; 95% confidence interval [CI]: -5.70, -2.77; P < 0.001) and OMA150 (LSM: -3.79; 95% CI: -5.24, -2.33; P < 0.001) vs. placebo. Incidence of treatment-emergent AEs over 20 weeks was slightly higher with OMA300 (71.3%) compared to OMA150 and placebo groups (64.7% and 63.9%, respectively). The incidences of serious AEs were balanced between groups. This study demonstrated the efficacy and safety of omalizumab in Chinese adult patients with CSU who remained symptomatic despite H1AH therapy. Trials registered at clinicaltrials.gov NCT03328897 Date of registration: 1 November 2017.

PMID:34984792 | DOI:10.1111/dth.15303

ANZ J Surg. 2022 Jan 4. doi: 10.1111/ans.17448. Online ahead of print.

ABSTRACT

BACKGROUND: Maxillofacial trauma accounts for ~10% of trauma presentations to most centres, with massive haemorrhage occurring in 1.2-4.5% of cases. Despite its infrequent presentation, there is significant associated morbidity and mortality. Transcatheter arterial embolization (TAE) is playing an increasingly prominent role in trauma presentations. The aim of this article was to compare outcomes of TAE with more traditional management methods for the treatment of massive facial haemorrhage following maxillofacial trauma.

METHODS: A database and Google Scholar search was performed, with articles discussing massive facial haemorrhage secondary to maxillofacial trauma and its management included.

RESULTS: Twenty-seven articles were found that met inclusion criteria, encompassing 384 patients. Statistical testing comparing mortality between TAE and non-TAE groups did not find a significant difference, with a mortality rate of 30.2% in the TAE group and 38.9% in the non-TAE group. Assessment of morbidity directly related to interventions was difficult, as many of the included participants had significant associated injuries which contributed an indeterminate degree to morbidity. There was a 10% rate of adverse events associated with TAE, most commonly puncture site haematomas and soft tissue swelling, with more significant adverse events including cerebrovascular accidents and blindness.

CONCLUSION: Embolization was correlated with increased rates of haemorrhage control when compared with other interventions. Overall, despite no significant impact on mortality, embolization is recommended in the management of massive haemorrhage following maxillofacial trauma due to improved success rates at haemorrhage control and a low rate of significant adverse events.

PMID:34984779 | DOI:10.1111/ans.17448