Category: Nevin Manimala

Bioinformatics. 2023 Apr 2:btad149. doi: 10.1093/bioinformatics/btad149. Online ahead of print.

ABSTRACT

MOTIVATION: Elucidating functionally similar orthologous regulatory regions for human and model organism genomes is critical for exploiting model organism research and advancing our understanding of results from genome-wide association studies. Sequence conservation is the de facto approach for finding orthologous non-coding regions between human and model organism genomes. However, existing methods for mapping non-coding genomic regions across species are challenged by the multi-mapping, low precision, and low mapping rate issues.

RESULTS: We develop Adaptive liftOver (AdaLiftOver), a large-scale computational tool for identifying functionally similar orthologous non-coding regions across species. AdaLiftOver builds on the UCSC liftOver framework to extend the query regions and prioritizes the resulting candidate target regions based on the conservation of the epigenomic and the sequence grammar features. Evaluations of AdaLiftOver with multiple case studies, spanning both genomic intervals from epigenome datasets across a wide range of model organisms and GWAS SNPs yield AdaLiftOver as a versatile method for deriving hard-to-obtain human epigenome datasets as well as reliably identifying orthologous loci for GWAS SNPs.

AVAILABILITY: The R package AdaLiftOver is available from https://github.com/ThomasDCY/AdaLiftOver.

SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

PMID:37004197 | DOI:10.1093/bioinformatics/btad149

Am J Ind Med. 2023 Apr 2. doi: 10.1002/ajim.23473. Online ahead of print.

ABSTRACT

INTRODUCTION: Growth of e-commerce has caused a vast increase in parcel delivery, which raises concern for safety of drivers and other road users as more deliveries take place.

METHODS: This project analyzes injury/illness and fatality trends among workers with delivery-related NAICS codes using three major sources of occupational hazard data in the United States: the Survey of Occupational Illnesses and Injuries, the Census of Fatal Occupational Injuries, and the Industrial Tracking Application. Descriptive statistics were employed to illustrate trends over time as well as to highlight opportunities for improved data collection and dissemination.

RESULTS: The number of injuries to drivers has risen sharply over the past decade. Some of this increase appears due to growth of this industry, but increasing overall rates suggest the industry is becoming more hazardous. While nonfatal injuries were typically caused by continuous workplace exposures (e.g., repetitive strain, contact with object/equipment), fatalities were almost exclusively caused by transportation incidents. Additionally, crucial aspects of these trends are difficult or impossible to analyze given the current data landscape.

CONCLUSIONS: Observed trends reinforce earlier calls for additional scrutiny of working conditions that threaten drivers. Injuries caused by transportation incidents are likely more severe than others and highlight the danger the transportation system poses to drivers and others. Current data collection and dissemination processes offer room to improve in terms of understanding how to prevent future injuries.

PMID:37004194 | DOI:10.1002/ajim.23473

Med J Aust. 2023 Apr 3;218 Suppl 6:S13-S18. doi: 10.5694/mja2.51873.

ABSTRACT

OBJECTIVES: To estimate the prevalence in Australia of each type of child maltreatment; to identify gender- and age group-related differences in prevalence.

DESIGN, SETTING: Cross-sectional national survey; mobile telephone interviews using random digit dialling (computer-generated), Australia, 9 April – 11 October 2021. Retrospective self-report data using validated questionnaire (Juvenile Victimisation Questionnaire-R2 Adapted Version (Australian Child Maltreatment Study).

PARTICIPANTS: People aged 16 years or more. The target sample size was 8500 respondents: 3500 people aged 16-24 years and 1000 respondents each from five further age groups (25-34, 35-44, 45-54, 55-64, 65 years or more).

MAIN OUTCOME MEASURES: Proportions of respondents reporting physical abuse, sexual abuse, emotional abuse, neglect, and exposure to domestic violence to age 18 years, assessed with the Juvenile Victimization Questionnaire-R2 Adapted Version (Australian Child Maltreatment Study), overall and by gender and age group, and weighted to reflect characteristics of the Australian population aged 16 years or more in 2016.

RESULTS: Complete survey data were available for 8503 eligible participants (14% response rate). Physical abuse was reported by 32.0% of respondents (95% confidence interval [CI], 30.7-33.3%), sexual abuse by 28.5% (95% CI, 27.3-29.8%), emotional abuse by 30.9% (95% CI, 29.7-32.2%), neglect by 8.9% (95% CI, 8.1-9.7%), and exposure to domestic violence by 39.6% (95% CI, 38.3-40.9%). The proportions of respondents who reported sexual abuse, emotional abuse, or neglect were each statistically significantly larger for women than men. The reported prevalence of physical abuse by respondents aged 16-24 years was lower than for those aged 25-34 years, and that of sexual abuse was lower than for those aged 35-44 years, suggesting recent declines in the prevalence of these maltreatment types.

CONCLUSIONS: Child maltreatment is common in Australia, and larger proportions of women than men report having experienced sexual abuse, emotional abuse, and neglect during childhood. As physical and sexual abuse may have declined recently, public health policy and practice may have positive effects, justifying continued monitoring and prevention activities.

PMID:37004184 | DOI:10.5694/mja2.51873

Med J Aust. 2023 Apr 3;218 Suppl 6:S5-S12. doi: 10.5694/mja2.51869.

ABSTRACT

OBJECTIVES: To describe the aims, design, methodology, and respondent sample representativeness of the Australian Child Maltreatment Study (ACMS).

DESIGN, SETTING: Cross-sectional, retrospective survey; computer-assisted mobile telephone interviewing using random digit dialling (computer-generated), Australia, 9 April – 11 October 2021.

PARTICIPANTS: People aged 16 years or more. The target sample size was 8500 respondents: 3500 people aged 16-24 years and 1000 respondents each from five further age groups (25-34, 35-44, 45-54, 55-64, 65 years or more).

MAIN OUTCOME MEASURES: Primary outcomes: Emotional abuse, neglect, physical abuse, sexual abuse, exposure to domestic violence during childhood, assessed with the Juvenile Victimization Questionnaire-R2 Adapted Version (Australian Child Maltreatment Study).

SECONDARY OUTCOMES: selected mental disorder diagnoses (Mini International Neuropsychiatric Interview, MINI), selected physical health conditions, health risk behaviours, health service use.

RESULTS: The demographic characteristics of the ACMS sample were similar to those of the Australian population in 2016 with respect to gender, Indigenous status, region and remoteness category of residence, and marital status, but larger proportions of participants were born in Australia, lived in areas of higher socio-economic status, had tertiary qualifications, and had income greater than $1250 per week. Population weights were derived to adjust for these differences. Associations between the number of calls required to recruit participants and maltreatment rates and health outcomes were not statistically significant.

CONCLUSIONS: The ACMS provides the first reliable estimates of the prevalence of each type of child maltreatment in Australia. These estimates, and those of associated mental health and health risk behaviours reported in this supplement can inform policy and practice initiatives for reducing the prevalence of child maltreatment and its consequences. Our benchmark study also provides baseline data for repeated waves of the ACMS that will assess the effectiveness of these initiatives.

PMID:37004182 | DOI:10.5694/mja2.51869

JNCI Cancer Spectr. 2023 Apr 2:pkad022. doi: 10.1093/jncics/pkad022. Online ahead of print.

ABSTRACT

BACKGROUND: Cognitive effects of tamoxifen have been described. We augment data from a previous short-term (ST) follow-up study with long-term (LT) data to evaluate ST and LT cognitive effects of tamoxifen followed by exemestane and exemestane in breast cancer patients.

METHODS: Patients from the Tamoxifen and Exemestane Adjuvant Multinational trial received 5 years exemestane (exemestane group, n = 114) or 2.5 years tamoxifen followed by 2.5 years exemestane (sequential group, n = 92). Neuropsychological performance was assessed pre-endocrine therapy, after 1 year (ST follow-up) and at 5 years (LT follow-up). Controls (n = 120) were assessed with parallel intervals. With random effects modeling we evaluated cognitive changes from baseline to ST and LT follow-up. Statistical tests were 2-sided.

RESULTS: After controlling for age, intelligence quotient, attrition, menopausal symptoms, anxiety and/or depression, and/or fatigue, the sequential group showed ST and LT decline compared with controls on verbal memory (effect size [ES] = 0.26, P = .01; ES = 0.34, p = .003) and executive function (ES = 0.27, p = .007; ES = 0.38, p = .002). Compared with the exemestane group, the sequential group demonstrated ST decline on information processing speed (ES = 0.33; p = .01) and executive function (ES = 0.32; p = .01) and LT decline on verbal memory (ES = 0.33; p = .02). The exemestane group showed no cognitive decline compared with controls.

CONCLUSION(S): Cognitive adverse effects of tamoxifen alone and after switching to exemestane were observed, suggestive of a carryover effect of tamoxifen. Our results underline the need for well-controlled, prospective trials studying cognitive effects of endocrine therapy.

PMID:37004168 | DOI:10.1093/jncics/pkad022

Acta Otolaryngol. 2023 Apr 2:1-6. doi: 10.1080/00016489.2023.2191646. Online ahead of print.

ABSTRACT

BACKGROUND AND OBJECTIVES: Carcinomas of the minor salivary glands are rare with a heterogeneous pathology. This study explored the demographics, histology, treatment and survival in the Swedish population over 11 years.

MATERIAL AND METHODS: Cases of salivary gland carcinomas in the oral cavity were extracted from the ‘Swedish Head and Neck Cancer Register’ (2008-2018). Statistical analyses with cross tabulation, age grouping, chi-square, the Kaplan-Meier method and log-rank tests were performed.

RESULTS: Three hundred thirty cases were included (62% female; mean age 60 years; 83% were WHO Performance Status 0). The carcinomas were mostly stage I (57%), and the most common site was the palate with 165 tumours (50%). The most common histology was mucoepidermoid carcinoma (30%), followed by polymorphous low-grade adenocarcinoma (25%) and adenoid cystic carcinoma (24%). The distribution of histology differed between age groups. The five-year predicted overall survival rate was 83%. Most patients (89%) were treated with primary surgery.

CONCLUSION AND SIGNIFICANCE: The demographics, histology, and survival of minor salivary gland carcinomas in the oral cavity in the Swedish population correspond well with previously published material. The demographics and histology differ from carcinomas of the major salivary glands in the same population.

PMID:37004167 | DOI:10.1080/00016489.2023.2191646

Neurosurg Focus. 2023 Apr;54(4):E2. doi: 10.3171/2023.1.FOCUS22637.

ABSTRACT

OBJECTIVE: The management of excess CSF in patients with hydrocephalus typically requires using a shunt to divert CSF. Unfortunately, there is a high rate of shunt failure despite improvements in device components and insertion techniques. Reoperation is frequently necessary, which contributes to patient harm and increased healthcare costs. While factors affecting shunt failure are well defined in the pediatric population, information regarding adults is lacking. The authors undertook a systematic review and meta-analysis to determine how shunt failure in the adult population is reported and investigated the etiologies of shunt failure.

METHODS: This review is reported according to PRIMSA and utilized the MEDLINE, Embase, and Google Scholar databases. Abstracts were screened by two independent reviewers, and data were extracted in duplicate by two independent reviewers. Statistical analyses were performed using SPSS and Stata.

RESULTS: The pooled rates of shunt failure were 10% (95% CI 5%-15%) in studies with a mean follow-up time of less than 1 year, 12% (95% CI 8%-14%) with a follow-up time between 1 and 2 years, and 32% in studies with a follow-up time of 2 years or greater (95% CI 19%-43%). The pooled rate of failure was 17% across all studies. The most common cause of shunt failure was obstruction at 3.0% (95% CI 2%-4%), accounting for 23.2% of shunt failures. Infection was the second most common at 2.8% (95% CI 2%-3%), accounting for 22.5% of shunt failures. The most common location of shunt failure was the distal catheter, with a failure rate of 4.0% (95% CI 3%-5%), accounting for 33.4% of shunt failures. The definition of shunt failure was heterogeneous and varied depending on institutional practices. The combination of symptoms with either CT or MRI was the most frequently reported method for assessing shunt failure.

CONCLUSIONS: Important variation regarding how to define, investigate, and report shunt failure was identified. The overall shunt failure rate in adults is at least 32% after 2 years, which, while lower than that typically reported in the pediatric population, is significant. The most common causes of shunt failure in adults are infection and obstruction. The most common site of failure occurred at the distal catheter, highlighting the need to develop strategies to both report and mitigate distal shunt failure in adult shunt patients.

PMID:37004137 | DOI:10.3171/2023.1.FOCUS22637

Neurosurg Focus. 2023 Apr;54(4):E6. doi: 10.3171/2023.1.FOCUS22640.

ABSTRACT

OBJECTIVE: Idiopathic normal pressure hydrocephalus (iNPH) results in significant morbidity in the elderly with symptoms of dementia, gait instability, and urinary incontinence. In well-selected patients, ventriculoperitoneal shunt (VPS) placement often results in clinical improvement. Most postshunt assessments of patients rely on subjective scales. The goal of this study was to assess the utility of remote activity monitoring to provide objective evidence of gait improvement following VPS placement for iNPH.

METHODS: Patients with iNPH were prospectively enrolled and fitted with 5 activity monitors (on the hip and bilateral thighs and ankles) that they wore for 4 days preoperatively within 30 days of surgery and for 4 days within 30 days postoperatively. Monitors collected continuous data for number of steps, cadence, body position (upright, prone, supine, and lateral decubitus), gait entropy, and the proportion of each day spent active or static. Data were retrieved from the devices and a comparison of pre- and postoperative movement assessment was performed. The gait data were also correlated with formal clinical gait assessments before and after lumbar puncture and with motion analysis laboratory testing at baseline and 1 month and 1 year after VPS placement.

RESULTS: Twenty patients fulfilled the inclusion and exclusion criteria (median age 76 years). The baseline median number of daily steps was 1929, the median percentage of the day spent inactive was 70%, the median percentage of the day with a static posture was 95%, the median gait velocity was 0.49 m/sec, and the median number of steps required to turn was 8. There was objective improvement in median entropy from pre- to postoperatively, increasing from 0.6 to 0.8 (p = 0.002). There were no statistically significant differences for any of the remaining variables measured by the activity monitors when comparing the preoperative to the 1-month postoperative time point. All variables from motion analysis testing showed statistically significant differences or a trend toward significance at 1 year after VPS placement. Among the significantly correlated variables at baseline, cadence was inversely correlated with percentage of gait cycle spent in the support phase (contact with ground vs swing phase).

CONCLUSIONS: This pilot study suggests that activity monitoring provides an early objective measure of improvement in gait entropy after VPS placement among patients with iNPH, although a more significant improvement was noted on the detailed clinical gait assessments. Further long-term studies are needed to determine the utility of remote monitoring for assessing gait improvement following VPS placement.

PMID:37004136 | DOI:10.3171/2023.1.FOCUS22640

Neurosurg Focus. 2023 Apr;54(4):E8. doi: 10.3171/2023.1.FOCUS22642.

ABSTRACT

OBJECTIVE: Long-standing overt ventriculomegaly in adults (LOVA) is a form of chronic hydrocephalus and its pathophysiology and treatment remain debated. An analysis of CSF dynamics in this condition has rarely been reported. The aim of this study was to analyze hydrodynamic characteristics of patients with suspected LOVA to discuss its pathophysiological mechanisms and the importance of CSF dynamics analysis for diagnosis and treatment of these patients.

METHODS: This retrospective cohort study, conducted between May 2018 and October 2022, included adult patients aged > 18 years investigated in a department of neurosurgery through a lumbar infusion study for suspicion of LOVA (n = 23). These patients were then compared with a control cohort explored for suspicion of idiopathic normal pressure hydrocephalus (iNPH; n = 30). Clinical symptoms, radiological findings, and hydrodynamic parameters were analyzed. The authors specifically compared two hydrodynamic parameters: resistance to CSF outflow, or Rout, which relies on CSF resorption, and pressure-volume index (PVI), which reflect overall craniospinal compliance. The lumbar infusion study was considered pathological (confirming the diagnosis of chronic hydrocephalus) when at least one of these two parameters was altered.

RESULTS: Rout was significantly less frequently increased (cutoff ≥ 12 mm Hg/ml/min) in patients with LOVA (52%) than in those with iNPH (97%; p < 0.001). In contrast, PVI was impaired (cutoff ≤ 25 ml) in both cohorts, i.e., in 61% of patients with LOVA and in 83% of patients with iNPH. Overall, the rate of pathological lumbar infusion study in LOVA (87%) was not statistically different than in iNPH (100%). However, PVI was the only impaired parameter most frequently found in those with LOVA (35%) compared with those with iNPH (3%; p = 0.002).

CONCLUSIONS: This study suggests that there is a differential CSF dynamics pattern when comparing patients with LOVA versus those with iNPH. A higher proportion of patients with LOVA showed isolated compliance impairment. These findings highlight the utility of CSF dynamics analysis for the evaluation of patients with suspected chronic obstructive hydrocephalus such as LOVA. Future research with larger case series may help define diagnosis and treatment algorithms of chronic obstructive hydrocephalus based on CSF dynamics analysis, in addition to clinical and radiological criteria.

PMID:37004133 | DOI:10.3171/2023.1.FOCUS22642

Chin Neurosurg J. 2023 Apr 1;9(1):8. doi: 10.1186/s41016-023-00322-7.

ABSTRACT

INTRODUCTION: In the present letter we share the results of an analysis of more than 140,000 non traumatic arterial subarachnoid hemorrhages whereas the majority of them is expected to be after aneurysm rupture, in which we investigate a possible correlation of climatic changes and emotional bursts as correlating factors for such a rupture.

METHODS: We obtained the daily number of SAH from 2006 to 2018 for males and females from the German National statistics agency. The ICD codes provided to us were I60.1-I60.7, which are SAHs originating from intracranial arteries and excluding traumatic SAH and other not specified SAH.

RESULTS: An increase of mean SAH per day could be seen in winter compared to summer and family events seemed to have a protective effect against aneurysmal SAH. Additionally 6.55 more women per day suffer an SAH compared to men.

CONCLUSION: There is a statistical significant higher risk of aneurysm ruptures in winter and in females, and a statistical lower number in Mother’s day.

PMID:37004110 | DOI:10.1186/s41016-023-00322-7