Tag: statistics

Funct Integr Genomics. 2023 May 3;23(2):144. doi: 10.1007/s10142-023-01066-4.

ABSTRACT

Vigna mungo, a highly consumed crop in the pan-Asian countries, is vulnerable to several biotic and abiotic stresses. Understanding the post-transcriptional gene regulatory cascades, especially alternative splicing (AS), may underpin large-scale genetic improvements to develop stress-resilient varieties. Herein, a transcriptome based approach was undertaken to decipher the genome-wide AS landscape and splicing dynamics in order to establish the intricacies of their functional interactions in various tissues and stresses. RNA sequencing followed by high-throughput computational analyses identified 54,526 AS events involving 15,506 AS genes that generated 57,405 transcripts isoforms. Enrichment analysis revealed their involvement in diverse regulatory functions and demonstrated that transcription factors are splicing-intensive, splice variants of which are expressed differentially across tissues and environmental cues. Increased expression of a splicing regulator NHP2L1/SNU13 was found to co-occur with lower intron retention events. The host transcriptome is significantly impacted by differential isoform expression of 1172 and 765 AS genes that resulted in 1227 (46.8% up and 53.2% downregulated) and 831 (47.5% up and 52.5% downregulated) transcript isoforms under viral pathogenesis and Fe²⁺ stressed condition, respectively. However, genes experiencing AS operate differently from the differentially expressed genes, suggesting AS is a unique and independent mode of regulatory mechanism. Therefore, it can be inferred that AS mediates a crucial regulatory role across tissues and stressful situations and the results would provide an invaluable resource for future endeavours in V. mungo genomics.

PMID:37133618 | DOI:10.1007/s10142-023-01066-4

J Autism Dev Disord. 2023 May 3. doi: 10.1007/s10803-023-06000-y. Online ahead of print.

ABSTRACT

We examined the use of filled pauses in conversations between homogeneous pairs of autistic and non-autistic adults. A corpus of semi-spontaneous speech was used to analyse the rate, lexical type (nasal “uhm” or non-nasal “uh”), and prosodic realisation (rising, level or falling) of filled pauses. We used Bayesian modelling for statistical analysis. We found an identical rate of filled pauses and an equivalent preference of “uhm” over “uh” across groups, but also a robust group-level difference regarding the intonational realisation of filled pauses: non-autistic controls produced a considerably higher proportion of filled pause tokens realised with the canonical level pitch contour than autistic speakers. Despite the fact that filled pauses are a frequent and impactful part of speech, previous work on their conversational use in autism spectrum disorder (ASD) is limited. Our account is the first to analyse the intonational realisation of filled pauses in ASD and the first to investigate conversations between autistic adults in this context. Our results on rate and lexical type can help to contextualise previous research, while the novel findings on intonational realisation set the stage for future investigations.

PMID:37133610 | DOI:10.1007/s10803-023-06000-y

Faraday Discuss. 2023 May 3. doi: 10.1039/d2fd00176d. Online ahead of print.

ABSTRACT

The photoinduced ring-conversion reaction when cyclopentadiene (CP) is excited at 5.10 eV is simulated using surface-hopping semiclassical trajectories with XMS(3)-CASPT2(4,4)/cc-pVDZ electronic structure theory. In addition, PBE0/def2-SV(P) is employed for ground state propagation of the trajectories. The dynamics is propagated for 10 ps, mapping both the nonadiabatic short-time dynamics (<300 fs) and the increasingly statistical dynamics on the electronic ground state. The short-time dynamics yields a mixture of hot CP and bicyclo[2.1.0]pentene (BP), with the two products reached via different regions of the same conical intersection seam. On the ground state, we observe slow conversion from BP to CP which is modelled by RRKM theory with a transition state determined using PBE0/def2-TZVP. The CP products are furthermore associated with ground state hydrogen shifts and some H-atom dissociation. Finally, the prospects for detailed experimental mapping using novel ultrafast X-ray scattering experiments are discussed and observables for such experiments are predicted. In particular, we assess the possibility of retrieving electronic states and their populations alongside the structural dynamics.

PMID:37132432 | DOI:10.1039/d2fd00176d

Am J Transplant. 2023 Feb;23(2S1):S12-S20. doi: 10.1016/j.ajt.2023.02.003.

ABSTRACT

The OPTN/SRTR 2021 Annual Data Report presents the status of the solid organ transplantation system in the United States from 2010 through 2021. Organ-specific chapters are presented for kidney, pancreas, liver, intestine, heart, and lung transplant. Each organ-specific chapter is organized to present waitlist information, donor information (both deceased and living, as appropriate), transplant information, and patient outcomes. Data pertaining to pediatric patients are generally presented separately from the adult data. In addition to the organ-specific chapters, you will find chapters dedicated to deceased organ donation, vascularized composite allograft, and the COVID-19 pandemic. The data presented in the Annual Data Report are descriptive in nature. In other words, most tables and figures present raw data without statistical adjustment for possible confounding or changes over time. Therefore, the reader should keep in mind the observational nature of the data when attempting to draw inferences before trying to ascribe a cause to any observed patterns or trends. This introduction provides a brief overview of trends in waitlist and transplant activity. More detailed descriptions can be found in the respective organ-specific chapters.

PMID:37132351 | DOI:10.1016/j.ajt.2023.02.003

Int J Geriatr Psychiatry. 2023 May;38(5):e5916. doi: 10.1002/gps.5916.

ABSTRACT

OBJECTIVES: The study aims to describe people with dementia and informal caregivers’ respective experiences of support after diagnosis and compares these experiences. Additionally, we determine how people with dementia and informal caregivers who are satisfied with support differ from those dissatisfied.

METHODS: A cross-sectional survey study in Australia, Canada, the Netherlands, Poland, and United Kingdom was carried out to examine people with dementia and informal caregivers experience with support (satisfaction with information, access to care, health literacy, and confidence in ability to live well with dementia). The separate surveys contained closed questions. Analysis consisted of descriptive statistics and Chi-square tests.

RESULTS: Ninety people with dementia and 300 informal caregivers participated, and 69% of people with dementia and 67% of informal caregivers said support after diagnosis helped them deal more efficiently with their concerns. Up to one-third of people with dementia and informal caregivers were dissatisfied with information about management, prognosis, and strategies for living positively. Few people with dementia (22%) and informal caregivers (35%) received a care plan. People with dementia were more often satisfied with information, had more often confidence in their ability to live well with dementia, and were less often satisfied with access to care compared to informal caregivers. Informal caregivers who were satisfied with support were more satisfied with information and access to care compared to informal caregivers not satisfied with support.

CONCLUSIONS: Experience of dementia support can be improved and people with dementia and informal caregiver differ in their experiences of support.

PMID:37132330 | DOI:10.1002/gps.5916

Curr Med Imaging. 2023 Apr 28. doi: 10.2174/1573405620666230428123541. Online ahead of print.

ABSTRACT

BACKGROUND: Strain echocardiography (SE) is a procedure for analyzing myocardial dysfunction that is known to be less dependent on preload and afterload of heart function. Unlike dimension-based parameters, like ejection fraction (EF) and fractional shortening (FS), SE measures cardiac function by tracking cardiac tissue deformation and anomalies throughout the cardiac cycle. Although SE is proven to locate myocardial ailments in various heart diseases, few studies exist regarding using SE relevant to sepsis pathophysiology.

OBJECTIVE: The study aimed to calculate the myocardial strain and strain rates, like longitudianl strain (LS), global radial strain (GRS), and global longitudinal strain (GLS), and to show these to be reduced earlier in cecal ligation and puncture (CLP) and lipopolysaccharide (LPS)-induced sepsis in coordination with an elevation of pro-inflammatory cytokines Methodology: Wild-type mice C57BL/6J (WT) were taken in this study and classified as CLP, LPS, and control groups. CLP surgery and LPS injection were given to induce sepsis. Endotoxemic septic shock was induced by intraperitoneal (IP) injection of LPS Escherichia coli. Echocardiography short axis views (SAX), longitudinal strain (LS), global circumferential strain (GCS), and global radial strain (GRS) were measured from the anterior and posterior positions of the septal and lateral walls of the heart. Real-time polymerase chain reaction (RT-PCR) was performed to evaluate post-CLP and LPS to analyze cardiac pro-inflammatory cytokines expressions. Inter- and intra-observer variables were tested by Bland-Altman analyses (BA). All data analysis was performed by GraphPad Prism 6 software. p<0.05 was taken as statistically significant.

RESULT: After 48 hours following CLP and LPS-induced sepsis, a significant declination in both longitudinal strain and strain rate (LS and LSR) was identified in the CLP and LPS groups compared to the control group. Strain depression in sepsis was linked with the up-regulation of pro-inflammatory cytokines in RT-PCR analysis.

CONCLUSION: In the present study, we found myocardial strain and strain rate parameters, like LS, GRS, and GLS, to be reduced after CLP and LPS-induced sepsis in coordination with the elevation of pro-inflammatory cytokines.

PMID:37132319 | DOI:10.2174/1573405620666230428123541

J Sports Med Phys Fitness. 2023 May;63(5):674-684. doi: 10.23736/S0022-4707.22.14376-8.

ABSTRACT

BACKGROUND: Supraspinatus tendinopathy is a significant cause of pain and function loss. It has been suggested that platelet-rich plasma (PRP) and prolotherapy are effective treatments for this condition. This study was done to assess and compare the effects of PRP and prolotherapy on shoulder function and pain. The secondary aim was to evaluate the effect of the treatment on shoulder range of motion, supraspinatus tendon thickness, patient satisfaction, and adverse effects.

METHODS: This was a randomized, double-blind clinical trial. The study included 64 patients over the age of 18 who had supraspinatus tendinopathy and had not responded to at least three months of conventional treatment. Patients were assigned to either receive 2 mL of PRP (N.=32) or prolotherapy (N.=32). The Shoulder Pain and Disability Index (SPADI) and the Numerical Rating Scale (NRS) were the primary outcomes. Secondary outcomes included shoulder range of motion (ROM), supraspinatus tendon thickness, and adverse effects, which were measured at baseline, 3, 6, and 6 months after injection. At six months, patient satisfaction was assessed.

RESULTS: Repeated measures ANOVA showed there was a statistically significant effect of time on total SPADI scores (F [2.75, 151.11], = 2.85, P=0.040) and the NRS (F [2.69, 147.86], = 4.32, P=0.008) within each group. There were no other significant changes over time or between groups. Significantly more patients in the PRP group experienced increased pain lasting less than two weeks after injection (χ²=11.94, P=0.030).

CONCLUSIONS: PRP and prolotherapy resulted in improved shoulder function and pain for patients with chronic supraspinatus tendinopathy who did not response to conventional treatment.

PMID:37132278 | DOI:10.23736/S0022-4707.22.14376-8

Biometrics. 2023 May 3. doi: 10.1111/biom.13873. Online ahead of print.

ABSTRACT

Gene-environment (G-E) interactions have important implications for cancer outcomes and phenotypes beyond the main G and E effects. Compared to main-effect-only analysis, G-E interaction analysis more seriously suffers from a lack of information caused by higher dimensionality, weaker signals, and other factors. It is also uniquely challenged by the “main effects, interactions” variable selection hierarchy. Effort has been made to bring in additional information to assist cancer G-E interaction analysis. In this study, we take a strategy different from the existing literature and borrow information from pathological imaging data. Such data is a “byproduct” of biopsy, enjoys broad availability and low cost, and has been shown as informative for modeling prognosis and other cancer outcomes/phenotypes in recent studies. Building on penalization, we develop an assisted estimation and variable selection approach for G-E interaction analysis. The approach is intuitive, can be effectively realized, and has competitive performance in simulation. We further analyze The Cancer Genome Atlas (TCGA) data on lung adenocarcinoma (LUAD). The outcome of interest is overall survival, and for G variables, we analyze gene expressions. Assisted by pathological imaging data, our G-E interaction analysis leads to different findings with competitive prediction performance and stability. This article is protected by copyright. All rights reserved.

PMID:37132273 | DOI:10.1111/biom.13873

Nucl Med Commun. 2023 May 3. doi: 10.1097/MNM.0000000000001703. Online ahead of print.

ABSTRACT

In this pilot study, we investigated the feasibility of response prediction using digital [18F]FDG PET/computed tomography (CT) and multiparametric MRI before, during, and after neoadjuvant chemoradiation therapy in locally advanced rectal cancer (LARC) patients and aimed to select the most promising imaging modalities and timepoints for further investigation in a larger trial. Rectal cancer patients scheduled to undergo neoadjuvant chemoradiation therapy were prospectively included in this trial, and underwent multiparametric MRI and [18F]FDG PET/CT before, 2 weeks into, and 6-8 weeks after chemoradiation therapy. Two groups were created based on pathological tumor regression grade, that is, good responders (TRG1-2) and poor responders (TRG3-5). Using binary logistic regression analysis with a cutoff value of P ≤ 0.2, promising predictive features for response were selected. Nineteen patients were included. Of these, five were good responders, and 14 were poor responders. Patient characteristics of these groups were similar at baseline. Fifty-seven features were extracted, of which 13 were found to be promising predictors of response. Baseline [T2: volume, diffusion-weighted imaging (DWI): apparent diffusion coefficient (ADC) mean, DWI: difference entropy], early response (T2: volume change, DWI: ADC mean change) and end-of-treatment presurgical evaluation MRI (T2: gray level nonuniformity, DWI: inverse difference normalized, DWI: gray level nonuniformity normalized), as well as baseline (metabolic tumor volume, total lesion glycolysis) and early response PET/CT (Δ maximum standardized uptake value, Δ peak standardized uptake value corrected for lean body mass), were promising features. Both multiparametric MRI and [18F]FDG PET/CT contain promising imaging features to predict response to neoadjuvant chemoradiotherapy in LARC patients. A future larger trial should investigate baseline, early response, and end-of-treatment presurgical evaluation MRI and baseline and early response PET/CT.

PMID:37132268 | DOI:10.1097/MNM.0000000000001703

Nurs Open. 2023 May 3. doi: 10.1002/nop2.1773. Online ahead of print.

ABSTRACT

AIMS: To report on the engagement of Swiss nursing homes and of nurses in expanded roles in quality improvement.

DESIGN: A cross-sectional study (2018-2019).

METHODS: Survey data from a sample of 115 Swiss nursing homes and 104 nurses in expanded roles. Descriptive statistics were used.

RESULTS: Most participating nursing homes reported carrying several quality improvement activities (median of eight out of 10 activities surveyed) but some were only engaged in five activities or less. Nursing homes working with nurses in expanded roles (n = 83) showed greater engagement in quality improvement than those working with none. Nurses with more advanced qualifications (Bachelor’s or Master’s degree) engaged more in quality improvement than nurses with standard training. Specifically, higher educated nurses were more involved in data-focused activities. Using nurses in expanded roles can be a way forward for nursing homes seeking to actively carry out quality improvement in their facilities.

CONCLUSION: Although a large proportion of nurses in expanded roles surveyed were implementing quality activities, their level of engagement depended on their educational level. Our findings support the principle that higher level competencies are a key aspect of data-based quality improvement in nursing homes. However, as Advance Practice Registered Nurses will remain difficult to recruit in nursing homes, using nurses in expanded roles might contribute to quality improvement.

PMID:37132255 | DOI:10.1002/nop2.1773