Category: Statistics

Methods Mol Biol. 2024;2818:249-270. doi: 10.1007/978-1-0716-3906-1_17.

ABSTRACT

Prophase I is a remarkable stage of meiotic division during which homologous chromosomes pair together and exchange DNA by meiotic recombination. Fluorescence microscopy of meiotic chromosome spreads is a central tool in the study of this process, with chromosome axis proteins being visualized as extended filaments upon which recombination proteins localize in focal patterns.Chromosome pairing and recombination are dynamic processes, and hundreds of recombination foci can be present in some meiotic nuclei. As meiotic nuclei can exhibit significant variations in staining patterns within and between nuclei, particularly in mutants, manual analysis of images presents challenges for consistency, documentation, and reproducibility. Here we share a combination of complementary computational tools that can be used to partially automate the quantitative analysis of meiotic images. (1) The segmentation of axial and focal staining patterns to automatically measure chromosome axis length and count axis-associated (and non-axis associated) recombination foci; (2) Quantification of focus position along chromosome axes to investigate spatial regulation; (3) Simulation of random distributions of foci within the nucleus or along the chromosome axes to statistically investigate observed foci-axis associations and foci-foci associations; (4) Quantification of chromosome axis proximity to investigate relationships with chromosome synapsis/asynapsis; (5) Quantification of and orientation of focus-axis distances. Together, these tools provide a framework to perform routine documentation and analysis of meiotic images, as well as opening up routes to build on this initial output and perform more detailed analyses.

PMID:39126480 | DOI:10.1007/978-1-0716-3906-1_17

J Gastroenterol. 2024 Aug 10. doi: 10.1007/s00535-024-02144-5. Online ahead of print.

ABSTRACT

BACKGROUND: Recent genome-wide association studies (GWASs) in liver diseases have generated some polygenic risk scores (PRSs), but their predictive effectiveness on hepatocellular carcinoma (HCC) risk assessment remains unclear.

METHODS: Here, we constructed a novel combined polygenic risk score and evaluated its increment to the well-established risk model. We used 15 HCC-associated genetic loci from two PRSs and FinnGen GWAS data to calculate a PRS-combined score and to fit the related PRS model in the UK Biobank cohort (N = 436,162). The PRS-combined score was further assessed for risk stratification for HCC integrating with the recommended clinical risk scores.

RESULTS: The PRS-combined model achieved a better AUC (0.657) than that of PRS-HFC (0.637) and PRS-cirrhosis (0.645). The top 20% of the PRS-combined distribution had a 3.25 increased risk of HCC vs. the middle decile (45-55%). At the population level, the addition of PRS-combined to the CLivD score significantly increased the C-statistic (from 0.716 to 0.746) and provided a remarkable improvement in reclassification (NRI = 0.088) at the 10-year risk threshold of 0.2%. In clinic, additional assessment of PRS-combined would reclassify 34,647 intermediate-risk participants as high genetic risk, corresponding to an increase of 63.92% (62/97) of the HCC events classified at high risk using the Fibrosis-4 alone.

CONCLUSIONS: The PRS may enhance HCC risk prediction effectiveness in the general population and refine risk stratification of the conventional clinical indicator.

PMID:39126459 | DOI:10.1007/s00535-024-02144-5

Urolithiasis. 2024 Aug 10;52(1):115. doi: 10.1007/s00240-024-01610-2.

ABSTRACT

The critical role of the human gut microbiota in kidney stone formation remains largely unknown, due to the low taxonomic resolution of previous sequencing technologies. Therefore, this study aimed to explore the gut microbiota using high-throughput sequencing to provide valuable insights and identify potential bacterial species and metabolite roles involved in kidney stone formation. The overall gut bacterial community and its potential functions in healthy participants and patients were examined using PacBio sequencing targeting the full-length 16S rRNA gene, coupled with stone and statistical analyses. Most kidney stones comprised calcium oxalate and calcium phosphate (75%), pure calcium oxalate (20%), and calcium phosphate and magnesium phosphate (5%), with higher content of Ca (130,510.5 ± 108,362.7 ppm) followed by P (18,746.4 ± 23,341.2 ppm). The microbial community structure was found to be weaker in patients’ kidney stone samples, followed by patients’ stool samples, than in healthy participants’ stool samples. The most abundant bacterial species in kidney stone samples was uncultured Morganella, whereas that in patient and healthy participant stool samples was Bacteroides vulgatus. Similarly, Akkermansia muciniphila was significantly enriched in patient stool samples at the species level, whereas Bacteroides plebeius was significantly enriched in kidney stone samples than that in healthy participant stool samples. Three microbial metabolic pathways, TCA cycle, fatty acid oxidation, and urea cycle, were significantly enriched in kidney stone patients compared to healthy participants. Inferring bacteria at the species level revealed key players in kidney stone formation, enhancing the clinical relevance of gut microbiota.

PMID:39126448 | DOI:10.1007/s00240-024-01610-2

J Anesth. 2024 Aug 10. doi: 10.1007/s00540-024-03389-3. Online ahead of print.

ABSTRACT

Lung resection surgery, which is performed as a treatment for lung cancer and metastatic lung tumors, is currently conducted via minimally invasive techniques such as video-assisted thoracoscopic surgery and robot-assisted methods. Postoperative complications related to this surgery, such as pulmonary vein thrombosis and cerebral and other organ infarctions, have been increasingly reported. The primary cause of these complications is thrombus formation in the pulmonary vein stump. Statistical data on the site of lung lobectomy have indicated that surgeries involving the left upper lobe are most frequently associated with embolic complications. Although this issue has not received considerable attention in anesthesiology, the importance of prevention and treatment in postoperative management is growing. The role of anesthesiologists in preventing these complications is critical. These roles involve careful fluid management to avoid hypercoagulable states, consideration of early postoperative anticoagulation therapy, assessment of the suitability of epidural anesthesia for postoperative anticoagulation, and improvement of hospital-wide safety systems and monitoring of high-risk patients. Anesthesiologists need to understand the pathology and risk factors involved and play an active role in preventing and treating these complications through effective collaboration with thoracic surgeons and the in-hospital stroke team.

PMID:39126427 | DOI:10.1007/s00540-024-03389-3

Avian Dis. 2023 Sep;67(3):237-244. doi: 10.1637/aviandiseases-D-22-00080.

ABSTRACT

Dust and ammonia gas (NH₃) are two of the most abundant pollutants suspended in the air of poultry houses. Chronic inhalation of poultry dust and NH₃ causes damage to the airways and reduces performance in broilers. Poultry dust is a mixture of organic and inorganic matter from feed, bedding material, manure, feathers, skin debris, and microorganisms. Thus, the composition and concentration of poultry dust vary among farms. This study proposes a model to assess the individual effect of a defined fraction of poultry dust derived from bedding material (wood dust) and its effects, alone or combined with NH₃, on the performance and respiratory integrity of broilers. Ninety-six, 1-day-old broilers were randomly divided into groups of 24 and placed into four controlled environment chambers to continuously receive one of four treatments: 1) negative control; 2) exposure to airborne red oak wood dust at a concentration of 7.5 × 10⁶ particles/m³ (particulate matter_5.0); 3) exposure to 50 parts per million (ppm) of NH₃; and 4) exposure to airborne red oak wood dust and 50 ppm of NH₃. On day 43, all birds were weighed and euthanized. Performance data were recorded. Tissue samples were collected from six birds per treatment. Histologic evaluations of the nasal turbinates, trachea, and lungs were conducted. Histologic lesion scores (0 to 3) were assigned, and tracheal mucosal thickness was measured. No significant differences among treatments were found in body weight (P = 0.066), tracheal mucosal thickness (P = 0.593), or tracheal lesion score (P = 0.07). The average nasal turbinate lesion scores were higher in the wood and wood + ammonia treatments compared with the control (P = 0.015). The lung lesion scores were higher (P = 0.004) in all treatment groups compared with the control. In conclusion, chronic exposure to red oak wood dust, alone or in combination with NH₃, induced important inflammatory damage to portions of the respiratory system of broilers; however, no significant effects on performance were observed.

PMID:39126410 | DOI:10.1637/aviandiseases-D-22-00080

J Psychosoc Oncol. 2024 Aug 10:1-16. doi: 10.1080/07347332.2024.2389094. Online ahead of print.

ABSTRACT

BACKGROUND: Traditional MBSR or MBTC programs do not delve deeply enough into emotional regulation, which is especially relevant in oncological patients. The aim of this study was to analyze the benefits of a mindfulness-based emotion regulation program in adult oncological patients.

METHOD: Psycho-oncologists from the AECC developed a mindfulness-based emotion regulation program. The Five Facet Mindfulness Questionnaire (FFMQ), Trait Meta-Mood Scale (TMMS), and Hospital Anxiety and Depression Scale (HADS) were administered before and after the program. A single-group pre-post test design with repeated measures was employed, utilizing the General Linear Model.

RESULTS: Ninety-seven adult cancer patients completed the pre- and post-program assessments. Statistically significant improvements were observed in all FFMQ subscales, increased clarity of emotional discrimination, mood repair, and statistically significant reductions in anxiety and depressive symptoms.

CONCLUSIONS: Regardless of the phase of the disease, the results of this study suggest that emotional regulation may improve and anxiety and depressive symptomatology decrease after a mindfulness-based emotion regulation program in oncological patients.

PMID:39126398 | DOI:10.1080/07347332.2024.2389094

J Bone Miner Res. 2024 Aug 10:zjae122. doi: 10.1093/jbmr/zjae122. Online ahead of print.

ABSTRACT

BACKGROUND: Several small genetic association studies have been conducted for atypical femur fracture (AFF) without replication of results. We assessed previously implicated and novel genes associated with AFFs in a larger set of unrelated AFF cases using whole exome sequencing (WES).

METHODS: We performed gene-based association analysis on 139 European AFF cases and 196 controls matched for bisphosphonate use. We tested all rare, protein-altering variants using both candidate gene and hypothesis-free approaches. In the latter, genes suggestively associated with AFFs (uncorrected P-values <0.01) were investigated in a Swedish whole-genome sequencing replication study and assessed in 46 non-European cases.

RESULTS: In the candidate gene analysis, PLOD2 showed a suggestive signal. The hypothesis-free approach revealed 10 tentative associations, with XRN2, SORD, and PLOD2 being the most likely candidates for AFF. XRN2 and PLOD2 showed consistent direction of effect estimates in the replication analysis, albeit not statistically significant. Three SNPs associated with SORD expression according to the GTEx portal, were in linkage disequilibrium (R2 ≥ 0.2) with a SNP previously reported in a genome-wide association study of AFF. The prevalence of carriers of variants for both PLOD2 and SORD was higher in Asian versus European cases.

CONCLUSIONS: While we did not identify genes enriched for damaging variants, we found suggestive evidence of a role for XRN2, PLOD2 and SORD, which requires further investigation. Our findings indicate that genetic factors responsible for AFFs are not widely shared among AFF cases. The study provides a stepping-stone for future larger genetic studies of AFF.

PMID:39126371 | DOI:10.1093/jbmr/zjae122

Clinics (Sao Paulo). 2024 Aug 8;79:100454. doi: 10.1016/j.clinsp.2024.100454. Online ahead of print.

ABSTRACT

OBJECTIVE: The aim of the study was to assess the impact of the Gamma coronavirus disease 2019 (COVID-19) variant on pregnant and postpartum women with Cardiovascular Disease (CVD).

METHODS: The Influenza Epidemiological Surveillance System database (SIVEP-Gripe), a compulsory notification system for cases of Severe Acute Respiratory Syndrome (SARS), was investigated for notified cases of pregnant and postpartum women with reported CVD and SARS due to COVID-19 between February 16, 2020 and May 1, 2021 (when vaccination began), was investigated. In this retrospective cohort, two groups were formed based on symptom onset date, according to the predominance of the variants: original (group 2020) and Gamma (group 2021). Cases with missing information on the presence or absence of CVD were excluded. The comparative analysis was controlled for confounding variables.

RESULTS: Among 703 COVID-19 cases notified with CVD (406 patients in 2020 and 297 patients in 2021), compared to 2020, cases in 2021 had more respiratory symptoms (90.6 % vs. 80.1 %, p < 0.001), greater ventilatory support need (75.3 % vs. 53.9 %, p < 0.001), more ICU admission (46.6 % vs. 34.3 %, p = 0.002), longer duration (20.59 ± 14.47 vs. 16.52 ± 12.98 days, p < 0.001), higher mortality (25.6 % vs. 15.5 %, p < 0.001), with more than two-times mortality likelihood in the third trimester (adjusted OR = 2.41, 95 % CI 1.50-3.88, p < 0.001) or puerperium periods (adjusted_OR = 2.15, 95 % CI 1.34-3.44, p = 0.001).

CONCLUSIONS: In Brazil, pregnant and postpartum women with CVDs in the Gamma variant phase have higher morbidity and mortality than those affected by the original variant of Coronavirus-19.

PMID:39121513 | DOI:10.1016/j.clinsp.2024.100454

J Anxiety Disord. 2024 Jul 26;106:102895. doi: 10.1016/j.janxdis.2024.102895. Online ahead of print.

ABSTRACT

PURPOSE: This study examined the relationship between structural brain networks and long-term treatment outcomes in patients with panic disorder (PD) using machine learning methods.

METHOD: The study involved 80 participants (53 PD patients and 27 healthy controls) and included clinical assessments and MRI scans at baseline and after two years (160 MRIs). Patients were categorized based on their response to two-year pharmacotherapy. Brain networks were analyzed using white matter tractography and network-based statistics.

RESULTS: Results showed structural network changes in PD patients, particularly in the extended fear network, including frontal regions, thalamus, and cingulate gyrus. Longitudinal analysis revealed that increased connections to the amygdala, hippocampus, and insula were associated with better treatment response. Conversely, overconnectivity in the amygdala and insula at baseline was associated with poor response, and similar patterns were found in the insula and parieto-occipital cortex related to non-remission. This study found that SVM and CPM could effectively predict treatment outcomes based on network pattern changes in PD.

CONCLUSIONS: These findings suggest that monitoring structural connectome changes in limbic and paralimbic regions is critical for understanding PD and tailoring treatment. The study highlights the potential of using personalized biomarkers to develop individualized treatment strategies for PD.

PMID:39121510 | DOI:10.1016/j.janxdis.2024.102895

Retina. 2024 Aug 9. doi: 10.1097/IAE.0000000000004240. Online ahead of print.

ABSTRACT

PURPOSE: To determine the validity, accuracy and acceptability of the Image Warping Test (IWT), a novel test for the measurement of visual distortion in the central visual field.

METHODS: 25 volunteers with metamorphopsia secondary to vitreoretinal pathology were recruited at a tertiary referral center. All subjects underwent ophthalmological examination and measurement of metamorphopsia via Amsler grid, Morphision, M-CHARTS and the IWT. Construct validity was determined through assessment of the association between symptoms, pathology, visual acuity, established metamorphopsia test results and IWT results.

RESULTS: There was close association between subjective estimation of metamorphopsia severity and IWT score (p=0.005), between Morphision result and IWT score (p=0.015), and between the nature of vitreoretinal pathology and IWT score (p=0.007). There was no statistically significant correlation between best corrected distance visual acuity and IWT score, and between M-CHARTS score and IWT score.

CONCLUSION: The IWT allows the creation of a digital map of subjective metamorphopsia which effectively measures its severity and nature, and opens the possibility to its non-invasive correction in future through inverse mapping of the distortion map onto live images.

PMID:39121494 | DOI:10.1097/IAE.0000000000004240