Category: Statistics

Planta. 2024 Aug 17;260(3):74. doi: 10.1007/s00425-024-04507-x.

ABSTRACT

Transcriptome analysis in potato varieties revealed genes associated with tuber yield-related traits and developed gene expression markers. This study aimed to identify genes involved in high tuber yield and its component traits in test potato varieties (Kufri Frysona, Kufri Khyati, and Kufri Mohan) compared to control (Kufri Sutlej). The aeroponic evaluation showed significant differences in yield-related traits in the varieties. Total RNA sequencing was performed using tuber and leaf tissues on the Illumina platform. The high-quality reads (QV > 25) mapping with the reference potato genomes revealed statistically significant (P < 0.05) differentially expressed genes (DEGs) into two categories: up-regulated (> 2 Log₂ fold change) and down-regulated (< -2 Log₂ fold change). DEGs were characterized by Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. Collectively, we identified genes participating in sugar metabolism, stress response, transcription factors, phytohormones, kinase proteins, and other genes greatly affecting tuber yield and its related traits. A few selected genes were UDP-glucose glucosyltransferase, glutathion S-transferase, GDSL esterase/lipase, transcription factors (MYB, WRKY, bHLH63, and BURP), phytohormones (auxin-induced protein X10A, and GA20 oxidase), kinase proteins (Kunitz-type tuber invertase inhibitor, BRASSINOSTEROID INSENSITIVE 1-associated receptor kinase 1) and laccase. Based on the selected 17 peptide sequences representing 13 genes, a phylogeny tree and motifs were analyzed. Real time-quantitative polymerase chain reaction (RT-qPCR) analysis was used to validate the RNA-seq results. RT-qPCR based gene expression markers were developed for the genes such as 101 kDa heat shock protein, catechol oxidase B chloroplastic, cysteine protease inhibitor 1, Kunitz-type tuber invertase inhibitor, and laccase to identify high yielding potato genotypes. Thus, our study paved the path for potential genes associated with tuber yield traits in potato under aeroponics.

PMID:39153022 | DOI:10.1007/s00425-024-04507-x

Arch Dermatol Res. 2024 Aug 17;316(8):526. doi: 10.1007/s00403-024-03323-3.

NO ABSTRACT

PMID:39153021 | DOI:10.1007/s00403-024-03323-3

Vision Res. 2024 Aug 15;223:108464. doi: 10.1016/j.visres.2024.108464. Online ahead of print.

ABSTRACT

Exfoliation syndrome is a leading cause of secondary glaucoma worldwide. Among the risk-factors for exfoliation syndrome and exfoliation glaucoma that have been investigated, a genetic association with 15q24.1 is among the most striking. The leading candidates for the causal gene at this locus are LOXL1 and/or LOXL1-AS1, but studies have not yet coalesced in establishing, or ruling out, either candidate. Here, we contribute to studies of the 15q24.1 locus by making a partially humanized mouse model in which 166 kb of human genomic DNA from the 15q24.1 locus was introduced into the mouse genome via BAC transgenesis (B6-Tg(RP11-71M11)Andm). Transgenic expression of human genes in the BAC was only detectable for LOXL1-AS1. One cohort of 34 mice (21 experimental hemizygotes and 13 non-carrier control littermates) was assessed by slit-lamp exams and SD-OCT imaging at early (1-2 months) and mid (4-5 months) time points; fundus exams were performed at 5 months of age. A second smaller cohort (3 hemizygotes) were aged extensively (>12 months) to screen for overt abnormalities. Across all genotypes and ages, 136 slit-lamp exams, 128 SD-OCT exams, and 42 fundus exams detected no overt indices of exfoliation syndrome. Quantitatively, small, but statistically significant, age-related declines in ganglion cell complex thickness and total retinal thickness were detected in the hemizygotes at 4 months of age. Overall, this study demonstrates complexity in gene regulation from the 15q24.1 locus and suggests that LOXL1-AS1 is unlikely to be a monogenic cause of exfoliation syndrome but may contribute to glaucomatous retinal damage.

PMID:39151208 | DOI:10.1016/j.visres.2024.108464

Retina. 2024 Aug 14. doi: 10.1097/IAE.0000000000004249. Online ahead of print.

ABSTRACT

PURPOSE: To assess the longitudinal surgical outcomes of macular telangiectasia type 2 macular hole (MacTel-MH) and compare them with those of idiopathic MH.

METHODS: This retrospective, single-tertiary center study included patients who underwent MH surgery between January 2015 and September 2023. Patients with characteristic optical coherence tomography (OCT) findings of MacTel in both eyes or those who underwent fluorescence angiography were classified as having MacTel MH. Baseline and postoperative best-corrected visual acuity and OCT parameters were reviewed.

RESULTS: Totally, 27 and 243 eyes with MacTel and idiopathic MH, respectively, were included. MH closure rate was better achieved in idiopathic than in MacTel MH group at 2 years postoperatively. Temporal recovery of ellipsoid zone and external limiting membrane was more prominent in MacTel than in idiopathic MH group. Statistically significant visual acuity improvement was seen between 3 months and 2 years postoperatively in MacTel MH group.

CONCLUSION: To the best of our knowledge, this is the first study to analyze the surgical outcomes of MacTel MH in both anatomical and functional aspects and compare them with patients with idiopathic MH. Postoperative microglia change would have affected the restoration of outer retinal layer of patients; however, further studies are needed for clarification.

PMID:39151202 | DOI:10.1097/IAE.0000000000004249

J Neurosurg. 2024 Aug 16:1-7. doi: 10.3171/2024.4.JNS232119. Online ahead of print.

ABSTRACT

OBJECTIVE: The authors sought to quantify the role of social media-related academic activity through use of the Altmetric score (a composite score based on social media attention from a variety of sources) and investigate its potential impact on the number of citations received at 3 years postpublication (articles published between January 2019 and December 2019).

METHODS: Articles published in the top 12 neurosurgical journals according to Google Scholar (based on 5-year Web of Science impact factors, 2017-2021) were identified. Data collected included days since publication, Altmetric scores, and total number of tweets (posts), and 3-year citations were obtained from Google Scholar. A multiple linear regression model was created that featured a blocking method to stratify confounding variables from most to least contributing. Furthermore, the data were dichotomized by publications with ≥ 10 citations (top 25th percentile) and those with < 10 to analyze the impact of the score on total number of citations received at 3 years, using an independent-samples Mann-Whitney U-test.

RESULTS: Among 6721 included articles, the mean Altmetric score was 3.76 ± 15.69 and the mean number of citations received was 9.61 ± 22.16. When accounting for relevant control variables, the Altmetric score was a significant predictor of the total number of citations accumulated at 3 years (variability of 10.17%). On statistical testing, the Altmetric score was significantly higher in publications with ≥ 10 citations (p < 0.001).

CONCLUSIONS: The authors report a strong, statistically significant correlation between the Altmetric score and the number of citations received. To their knowledge, this is the first study to demonstrate the impact of social media academic activity on neurosurgery article citation dissemination, potentially influencing resident medical education.

PMID:39151198 | DOI:10.3171/2024.4.JNS232119

J Neurosurg. 2024 Aug 16:1-9. doi: 10.3171/2024.4.JNS232417. Online ahead of print.

ABSTRACT

OBJECTIVE: Stereo-electroencephalography (SEEG)-guided radiofrequency thermocoagulation (RFTC) is being used incrementally in the invasive diagnosis of epilepsy. There is currently a lack of information regarding the potential cognitive consequences of the extended use of this technique. This work describes, for the first time, the cognitive outcomes after RFTC in patients with temporal lobe epilepsy (TLE), evaluated longitudinally and using a control group.

METHODS: Forty-eight adult patients with drug-resistant unilateral TLE (30 RFTC-treated patients and 18 controls) were evaluated using a comprehensive neuropsychological protocol at baseline. In the RFTC group, two follow-up assessments were performed at 3 months and 1 year. The control group was reevaluated after 1 year. Two analyses were performed: 1) group-level analyses, in which linear mixed models were applied according to TLE lateralization (intragroup and intergroup [RFTC vs control] comparisons), and 2) individual-level analyses, in which the Reliable Change Index (RCI) algorithm was developed and a 90% CI (cutoff ± 1.64) was used to describe neuropsychological outcomes at 1 year post-RFTC. A memory subanalysis was performed in hippocampal RFTC patients (25/30). A Spearman coefficient study was conducted to determine the correlation between cognitive change and thermocoagulated contacts.

RESULTS: Left- and right-sided TLE patients treated with RFTC showed cognitive preservation at baseline. At a group level, the short-term evaluation, including verbal and visual memory, language, and executive functions, showed preservation in these domains and no significant differences compared with baseline. In the long-term follow-up assessment (1 year after RFTC), no significant intragroup changes were found, nor were significant changes found in comparison with the control group. The RCI algorithm showed that significant individual cognitive losses and gains were infrequent. Three patients presented with naming deficits, only 1 (3.3%) of whom showed a clinically significant deficit. Significant gains were more prevalent in executive function tests with a speed component (4/20 left-sided RFTC patients). Twenty-five of the 30 (83%) patients were treated with hippocampal RFTC. No patients experienced significant loss in verbal delayed memory in the left-sided RFTC sample or in visual delayed memory in the right-sided RFTC sample. The correlations between cognitive change and RFTC contacts were mostly nonsignificant.

CONCLUSIONS: In the group-level comparisons, discernible cognitive impairment following RFTC was not evidenced. The majority of patients did not exhibit significant individual declines during the 1-year follow-up period. Notably, the procedural intervention yielded no substantial repercussions on memory functioning following hippocampal RFTC. These findings underscore the evidence supporting the cognitive preservation associated with SEEG-guided RFTC.

PMID:39151196 | DOI:10.3171/2024.4.JNS232417

J Neurosurg Spine. 2024 Aug 16:1-8. doi: 10.3171/2024.5.SPINE231330. Online ahead of print.

ABSTRACT

OBJECTIVE: This study investigated the correlation between Hounsfield units (HU) of the cervical vertebrae and atrophy of the cervical deep paraspinal muscles, namely the multifidus and semispinalis cervicis (SCer), in patients diagnosed with degenerative cervical myelopathy (DCM).

METHODS: The authors retrospectively analyzed data from 136 patients aged 50-79 years (81 males and 55 females) who underwent surgical intervention for DCM. HU measurements of the cancellous bone in the C4 vertebra were acquired through standardized techniques. The authors evaluated fatty infiltration (FI); analyzed functional and vertebral cross-sectional area (CSA) of the multifidus and SCer at the C4-5, C5-6, and C6-7 levels; and analyzed the presence of Modic changes (MCs) and the incidence of axial neck pain.

RESULTS: Patients were categorized into group A (n = 56) with mean ± SD HU of 293.3 ± 15.6 and group B (n = 80) with mean ± SD HU of 389.5 ± 10.6. Both groups demonstrated significant improvements in postoperative clinical outcomes (p < 0.05); however, no statistically significant difference was observed (p > 0.05). Significant disparities in HU measurements and visual analog scale (VAS) scores for neck pain were observed between the groups (p < 0.05). The highest VAS score correlated with MCs-1 type (i.e., low signal on T1-weighted images and high signal on T2-weighted images). The functional CSA to vertebral CSA ratios of the multifidus and SCer in group A were markedly reduced compared to those of group B (p < 0.05). No significant difference was noted in functional CSA asymmetry between the groups for both muscles (p > 0.05). Lower HU measurements directly correlated with increased FI in the multifidus (p = 0.002) and SCer (p = 0.035). Furthermore, a strong positive association was found between the functional CSA to vertebral CSA ratio of the multifidus and HU values (p = 0.003), whereas HU measurements and VAS scores exhibited a negative correlation (p = 0.020).

CONCLUSIONS: Among those patients older than 50 years with DCM, those with decreased HU values demonstrated elevated FI levels in the multifidus and SCer muscles. Moreover, these patients presented with pronounced muscle atrophy, which correlated with axial neck pain. A significant relationship was also identified between MCs and diminished HU values.

PMID:39151195 | DOI:10.3171/2024.5.SPINE231330

J Neurosurg. 2024 Aug 16:1-9. doi: 10.3171/2024.4.JNS24205. Online ahead of print.

ABSTRACT

OBJECTIVE: To optimize surgical positioning for posterior fossa surgery (PFS) using the semisitting position (SSP) to avoid venous air embolism (VAE) and its possible life-threatening consequences, the authors evaluated their experiences with the SSP by analyzing a large cohort of PFS patients.

METHODS: A retrospective analysis of the charts of 202 consecutive PFS patients (median age 54 years, IQR 41-61 years; 121 females) with various tumor or vascular conditions who underwent surgery in an SSP between 2019 and 2022 was performed. Age, sex, weight, height, BMI, American Society of Anesthesiologists (ASA) class, histology, duration of surgery, and length of hospital stay were assessed. Transesophageal echocardiography was used pre- and intraoperatively to monitor for and assess the degree of VAE.

RESULTS: Altogether, VAE occurred in 30 of 202 (14.9%) patients, with clinically relevant VAE occurring in 14 of 202 (7%) patients. The grades of VAE were I, III, and IV in 16 (8%), 4 (2%), and 10 (5%) patients, respectively. Patient height (p = 0.04), ASA class (p = 0.03), and ASA class ≤ II (p = 0.02) remained the only preoperative statistically significant risk factors for intraoperative VAE, with a median height of 178 cm (IQR 172-184 cm) in patients with clinically relevant VAE compared with 170 cm (IQR 164-176 cm) in those without VAE.

CONCLUSIONS: In summary, the data demonstrate that SSP can be used safely for PFS when taking special care to optimize positioning in tall and lower-grade ASA patients intraoperatively.

PMID:39151192 | DOI:10.3171/2024.4.JNS24205

J Neurosurg Pediatr. 2024 Aug 16:1-6. doi: 10.3171/2024.6.PEDS24201. Online ahead of print.

ABSTRACT

OBJECTIVE: Sinogenic intracranial infections in children, such as subdural empyema or intracranial abscess, are a rare disease process with significant associated morbidity. Recent literature has suggested that there may have been an increase in frequency of these infections following the COVID-19 pandemic, but the literature has been conflicting, perhaps related to the heterogenous management of COVID-19 lockdowns in various states and differences in data capture between methods. The collection of statewide Australian data overcomes these limitations by capturing a comprehensive sample though the public healthcare system of patients who were subject to a homogeneous statewide approach to public health policy during the COVID-19 pandemic (population 5.6 million, including 1.3 million children). The objective of this study was to present population-level data to address the question of whether the incidence of intracranial infections changed in pediatric patients before and after the COVID-19 pandemic.

METHODS: The authors present a retrospective 10-year statewide description of sinogenic intracranial infections in Queensland, Australia. A comparison was made between the incidence and microbiological profile before and after the onset of COVID-19 lockdowns on March 22, 2020.

RESULTS: Forty-four pediatric intracranial infections undergoing neurosurgical intervention were identified within the review period. After exclusion of postsurgical and cardioembolic causes, 33 sinogenic intracranial infections were included (16 before and 17 after 2020, with a mean annualized incidence of 0.25 vs 0.37 cases per 100,000 children, respectively; p > 0.05). The most frequent organisms identified were Streptococcus milleri (n = 19), polymicrobial (n = 4), and S. aureus (n = 3). No significant differences in antimicrobial profile, susceptibility, parenchymal involvement, or clinical outcome were identified between the pre- and post-COVID-19 groups.

CONCLUSIONS: No statistically significant differences in the epidemiology of pediatric intracranial infection have occurred in the state of Queensland, Australia, before and after March 22, 2020, and the COVID-19 pandemic.

PMID:39151187 | DOI:10.3171/2024.6.PEDS24201