Haptools: a toolkit for admixture and haplotype analysis.

SUMMARY: Leveraging local ancestry and haplotype information in genome-wide association studies and downstream analyses can improve the utility of genomics for individuals from diverse and recently admixed ancestries. However, most existing simulation, visualization and variant analysis frameworks are based on variant-level analysis and do not automatically handle these features. We present haptools, an open-source toolkit for performing local ancestry aware and haplotype-based analysis of complex traits. Haptools supports fast simulation of admixed genomes, visualization of admixture tracks, simulation of haplotype- and local ancestry-specific phenotype effects and a variety of file operations and statistics computed in a haplotype-aware manner. AVAILABILITY AND IMPLEMENTATION: Haptools is freely available at https://github.com/cast-genomics/haptools. DOCUMENTATION: Detailed documentation is available at https://haptools.readthedocs.io. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Discovering single nucleotide variants and indels from bulk and single-cell ATAC-seq.

Genetic variants and de novo mutations in regulatory regions of the genome are typically discovered by whole-genome sequencing (WGS), however WGS is expensive and most WGS reads come from non-regulatory regions. The Assay for Transposase-Accessible Chromatin (ATAC-seq) generates reads from regulatory sequences and could potentially be used as a low-cost 'capture' method for regulatory variant discovery, but its use for this purpose has not been systematically evaluated. Here we apply seven variant callers to bulk and single-cell ATAC-seq data and evaluate their ability to identify single nucleotide variants (SNVs) and insertions/deletions (indels). In addition, we develop an ensemble classifier, VarCA, which combines features from individual variant callers to predict variants. The Genome Analysis Toolkit (GATK) is the best-performing individual caller with precision/recall on a bulk ATAC test dataset of 0.92/0.97 for SNVs and 0.87/0.82 for indels within ATAC-seq peak regions with at least 10 reads. On bulk ATAC-seq reads, VarCA achieves superior performance with precision/recall of 0.99/0.95 for SNVs and 0.93/0.80 for indels. On single-cell ATAC-seq reads, VarCA attains precision/recall of 0.98/0.94 for SNVs and 0.82/0.82 for indels. In summary, ATAC-seq reads can be used to accurately discover non-coding regulatory variants in the absence of whole-genome sequencing data and our ensemble method, VarCA, has the best overall performance.

Letrozole treatment of adult female mice results in a similar reproductive phenotype but distinct changes in metabolism and the gut microbiome compared to pubertal mice.

BACKGROUND: A majority of women with polycystic ovary syndrome (PCOS) have metabolic dysfunction that results in an increased risk of type 2 diabetes. We previously developed a pubertal mouse model using the aromatase inhibitor, letrozole, which recapitulates many of the reproductive and metabolic features of PCOS. To further our understanding of the effects of androgen excess, we compared the effects of letrozole treatment initiated in puberty versus adulthood on reproductive and metabolic phenotypes as well as on the gut microbiome. RESULTS: Letrozole treatment of both pubertal and adult female mice resulted in reproductive hallmarks of PCOS, including hyperandrogenemia, anovulation and polycystic ovaries. However, unlike pubertal mice, treatment of adult female mice resulted in modest weight gain and abdominal adiposity, minimal elevation in fasting blood glucose and insulin levels, and no detectable insulin resistance. In addition, letrozole treatment of adult mice was associated with a distinct shift in gut microbial diversity compared to letrozole treatment of pubertal mice. CONCLUSIONS: Our results indicate that dysregulation of metabolism and the gut microbiome in PCOS may be influenced by the timing of androgen exposure. In addition, the minimal weight gain and lack of insulin resistance in adult female mice after letrozole treatment indicates that this model may be useful for investigating the effects of hyperandrogenemia on the hypothalamic-pituitary-gonadal axis and the periphery without the influence of substantial metabolic dysregulation.

Anticancer activity studies of cubebin isolated from Piper cubeba and its synthetic derivatives.

(-)-Cubebin, isolated from the seeds of Piper cubeba, and its five different types of derivatives (a total of 17), with varying functionalities, were tested for their in vitro anticancer activity against six human cancer cell lines (A549, K562, SiHa, KB, HCT116 and HT29) using MTT assay. Cubebin as well as its derivatives containing lactone and amide groups showed significant anticancer activity. In some of the tested cell lines, the amide derivatives showed higher activity. Morphological analysis indicated that these compounds act through apoptosis mediated pathway of cell death and we expect that these results will pave new paths in the development of novel anticancer agents by the derivatization of (-)-cubebin.

Comparative study of multiple cancellous screws versus sliding hip screws in femoral neck fractures of young adults.

PURPOSE: Both cannulated cancellous screw (CCS) and sliding hip screw (SHS) are used in femoral neck fracture fixations, but which is superior is yet to be determined. This study was aimed to compare the clinicoradiological outcome of femoral neck fracture treated with SHS or CCS in young adults. METHODS: Adults (16e60 years) with femoral neck fracture were divided into Group 1 fixed with SHS and Group 2 fixed with three CCS after closed reduction. Pain relief, functional recovery and postoperative radiographs at 6 weeks, 3 months, 6 months and then yearly for upto 4 years were analyzed. RESULTS: Group 1 (n=40) achieved radiological union at mean of 7.6 months, with the union rate of 87.5% (n=35), avascular necrosis (AVN) rate of 7.5% (n=3) and mean Harris Hip Score (HHS) of 86.15 at the end of 4 years. In Group 2 (n=45) these parameters were union at 7.1 months, union rate of 82.22% (n=37), AVN rate of 6.67% (n=3) and HHS of 88.65. Comparative results were statistically insignificant. CONCLUSION: There is no significant difference in clinicoradiological outcome between the two implants.

Metabolic perturbations associated with hIAPP-induced insulin resistance in skeletal muscles: Implications to the development of type 2 diabetes.

The human islet amyloid polypeptide (hIAPP) tends to misfold and self-assemble to form amyloid fibrils, which has been associated with the loss of function and viability of pancreatic ß-cells in type 2 diabetes mellitus (T2DM). The role of hIAPP in the development of insulin resistance (a hallmark of T2DM) in skeletal muscles - the major sites for glucose utilization - needs further investigation. Even though, insulin-resistant conditions have been known to stimulate hIAPP aggregation, the events that lead to the development of insulin resistance due to hIAPP aggregation in skeletal muscles remain unidentified. Here, we have attempted to identify metabolic perturbations in L6 myotubes that were exposed to increasing concentrations of recombinant hIAPP for different time durations. It was observed that hIAPP exposure was associated with increased mitochondrial and cellular ROS levels, loss in mitochondrial membrane potential and viability of the myotubes. Metabolomic investigations of hIAPP-treated myotubes revealed significant perturbations in o-phosphocholine, sn-glycero-3-phosphocholine and dimethylamine levels (p < 0.05). Therefore, we anticipate that defects in glycerophospholipid metabolism and the associated oxidative stress and membrane damage may play key roles in the development of insulin resistance due to protein misfolding in skeletal muscles. In summary, the perturbed metabolites and their pathways have not only the potential to be used as early biomarkers to predict the onset of insulin resistance and T2DM but also as therapeutic targets for the effective management of the same.

BDNF augmentation reverses cranial radiation therapy-induced cognitive decline and neurodegenerative consequences.

Cranial radiation therapy (RT) for brain cancers is often associated with the development of radiation-induced cognitive dysfunction (RICD). RICD significantly impacts the quality of life for cancer survivors, highlighting an unmet medical need. Previous human studies revealed a marked reduction in plasma brain-derived neurotrophic factor (BDNF) post-chronic chemotherapy, linking this decline to a substantial cognitive dysfunction among cancer survivors. Moreover, riluzole (RZ)-mediated increased BDNF in vivo in the chemotherapy-exposed mice reversed cognitive decline. RZ is an FDA-approved medication for ALS known to increase BDNF in vivo . In an effort to mitigate the detrimental effects of RT-induced BDNF decline in RICD, we tested the efficacy of RZ in a cranially irradiated (9 Gy) adult mouse model. Notably, RT-exposed mice exhibited significantly reduced hippocampal BDNF, accompanied by increased neuroinflammation, loss of neuronal plasticity-related immediate early gene product, cFos, and synaptic density. Spatial transcriptomic profiling comparing the RT+Veh with the RT+RZ group showed gene expression signatures of neuroprotection of hippocampal excitatory neurons post-RZ. RT-exposed mice performed poorly on learning and memory, and memory consolidation tasks. However, irradiated mice receiving RZ (13 mg/kg, drinking water) for 6-7 weeks showed a significant improvement in cognitive function compared to RT-exposed mice receiving vehicle. Dual-immunofluorescence staining, spatial transcriptomics, and biochemical assessment of RZ-treated irradiated brains demonstrated preservation of synaptic integrity and neuronal plasticity but not neurogenesis and reduced neuroinflammation concurrent with elevated BDNF levels and transcripts compared to vehicle-treated irradiated brains. In summary, oral administration of RZ represents a viable and translationally feasible neuroprotective approach against RICD.

Complement C5a receptor 1 blockade reverses cognitive deficits following cranial radiation therapy for brain cancer.

Cranial radiation therapy (RT) for brain cancers leads to an irreversible decline in cognitive function without an available remedy. Radiation-induced cognitive deficits (RICD) are particularly a pressing problem for the survivors of pediatric and low grade glioma (LGG) patients who often live long post-RT. Radiation-induced elevated neuroinflammation and gliosis, triggered by the detrimental CNS complement cascade, lead to excessive synaptic and cognitive loss. Using intact and brain cancer-bearing mouse models, we now show that targeting anaphylatoxin complement C5a receptor (C5aR1) is neuroprotective against RICD. We used a genetic knockout, C5aR1 KO mouse, and a pharmacologic approach, employing the orally active, brain penetrant C5aR1 antagonist PMX205, to reverse RICD. Irradiated C5aR1 KO and WT mice receiving PMX205 showed significant neurocognitive improvements in object recognition memory and memory consolidation tasks. C5aR1 inhibition reduced microglial activation, astrogliosis, and synaptic loss in the irradiated brain. Importantly, C5aR1 inhibition in the syngeneic, orthotopic astrocytoma, and glioblastoma-bearing mice protected against RICD without interfering with the therapeutic efficacy of RT to reduce tumor volume in vivo . PMX205 is currently in clinical trials for amyotrophic lateral sclerosis (ALS). Thus, C5aR1 inhibition is a translationally feasible approach to address RICD, an unmet medical need.

Localization of a major susceptibility locus influencing preterm birth.

Preterm birth (PTB) is a complex trait, but little is known regarding its major genetic determinants. The objective of this study is to localize genes that influence susceptibility to PTB in Mexican Americans (MAs), a minority population in the USA, using predominantly microfilmed birth certificate-based data obtained from the San Antonio Family Birth Weight Study. Only 1302 singleton births from 288 families with information on PTB and significant covariates were considered for genetic analysis. PTB is defined as a childbirth that occurs at <37 completed weeks of gestation, and the prevalence of PTB in this sample was 6.4%. An ∼10 cM genetic map was used to conduct a genome-wide linkage analysis using the program SOLAR. The heritability of PTB was high (h(2) ± SE: 0.75 ± 0.20) and significant (P = 4.5 × 10(-5)), after adjusting for the significant effects of birthweight and birth order. We found significant evidence for linkage of PTB (LOD = 3.6; nominal P = 2.3 × 10(-5); empirical P = 1.0 × 10(-5)) on chromosome 18q between markers D18S1364 and D18S541. Several other chromosomal regions (2q, 9p, 16q and 20q) were also potentially linked with PTB. A strong positional candidate gene in the 18q linked region is SERPINB2 or PAI-2, a member of the plasminogen activator system that is associated with various reproductive processes. In conclusion, to our knowledge, perhaps for the first time in MAs or US populations, we have localized a major susceptibility locus for PTB on chromosome 18q21.33-q23.

A convenient way to do valgus osteotomy for neglected fracture neck of femur.

BACKGROUND: Neglected fracture of neck of femur in young adults is a major problem in developing countries. Existing treatment options varies from osteotomy to various graft techniques (muscle pedicle, vascularized and nonvascularized fibula etc.). There is paucity of literature regarding the use of double angle barrel plate and hip screw in such cases. We conducted a prospective longitudinal observational study with displaced, neglected fracture neck of femur in young adults and compared the results with literature. OBJECTIVES: The aim of this study was to determine feasibility and effectiveness of 120° double angle barrel plate and hip screw fixation in neglected fracture neck of femur. Effectiveness of fixed 30 degree closed wedge osteotomy in neglected fracture neck of femur. METHODS: Thirty cases of neglected (more than three weeks) femoral neck fracture (Pauwel II and III) of age 20-60 years were included in the study conducted at Postgraduate Institute Of Medical Education and Research, Dr. Ram Manohar Lohia Hospital, New Delhi, India in year 2004-06. Average age of the patient was 35.4 years (range, 22yrs-55yrs). In all cases internal fixation was done by 120° double angle barrel plate and hip Screw. At the end of follow-up, results were evaluated according to Askin Bryan Criteria and Harris-hip score. RESULTS: Union was achieved in 28 of 30 patients. Two patients that went into nonunion were later treated with hemireplacement arthroplasty. According to Askin Bryan Criteria at the end of study, 35% patients had excellent results, 50% patients had good results. Minimum follow-up in our study was 12 months and maximum was five years. CONCLUSION: This study validates the use of double angled screw plate configuration for successful outcome in patients with neglected fracture neck of femur. Valgus osteotomy is also technically easy operation in hands of average trauma surgeon with the use of a fixed angle plate and hip screw.

Justifying the implementation of intraoperative computed tomography for midface fracture treatment in improving outcomes.

Intraoperative CT scanning is the international standard for treating midface fractures as it allows intraoperative assessment of reduction and fixation. To our knowledge, no NHS hospital in the UK has this facility yet due to the financial and logistical burden of its implementation. The aim of this study was to determine if complications including the requirement for a return to theatre (RTT) could have been predicted from the post-fixation CT scan. All treated midface fractures that had presented to a regionalised major trauma centre within two years (01 January 2020 - 31 December 2021) were identified. Those developing complications including RTT were determined. All postoperative CT scans (including those without complication or RTT) were re-analysed with the clinicians blinded to the outcomes to determine the positive predictive value (PPV) and negative predictive value (NPV) of requiring RTT to alter plate position intraoperatively based on CT scan alone. In all, there were eight episodes of unplanned return to theatre, resulting in an overall RTT rate of 8/119 (6.7%). When only analysing patients treated for orbital fractures this RTT rises to 8/40 (20%). Of those eight patients who had a postoperative CT and required RTT, this could have been predicted in 7/8 (87.5%). A total of 16/44 (36.4%) patients that did not have RTT would have additionally been recommended to have the plate position altered based on CT alone. Based upon those that had a CT, the PPV of CT alone being able to predict those requiring RTT was 40.6% and the NPV 96.2%. Our results would suggest intraoperative CT would likely have prevented eight patients requiring RTT in two years and could have improved outcomes in 16 cases. In preventing RTT as well as potentially improving the outcomes of a further 16 cases in maxillofacial surgery, the purchase of an intraoperative CT scanner could yield net savings of £75534-£114990 over two years.

Erratum: Author Correction: Telemedicine-Rehabilitation and Virtual Reality in Orthopaedics and Sports Medicine.

[This corrects the article DOI: 10.1007/s43465-022-00766-6.].

Telemedicine-Rehabilitation and Virtual Reality in Orthopaedics and Sports Medicine.

Introduction: Tele-rehabilitation is a method of delivering rehabilitation services using information, technology and communication to everyone, irrespective of their geographic location. National zeal for competitive sports and COVID pandemic has led to an increase in its demand and popularity worldwide. The athletes need immediate treatment and correct rehabilitation to keep them in their game. This review aims to bring into perspective the importance of telemedicine and telerehabilitation in orthopaedics and sports medicine with a focus on virtual reality. Methods: Articles were searched based on suitable keywords 'telemedicine', 'telerehabilitation' 'orthopedics', 'orthopaedics', 'sports' and 'India*' which were combined using suitable boolean operators in PubMed, Scopus and Web of Science. Government guidelines and laws were also reviewed in view of telehealth and telemedicine. Conclusion: Tele-rehabilitation and virtual physical therapy are innovative and cost-effective ways to provide the best rehabilitative services to the patients at their doorstep. Virtual reality should be incorporated into the Indian telehealth delivering system with a special focus on the remote athlete population.

Early pregnancy imaging predicts ischemic placental disease.

INTRODUCTION: To characterize early-gestation changes in placental structure, perfusion, and oxygenation in the context of ischemic placental disease (IPD) as a composite outcome and in individual sub-groups. METHODS: In a single-center prospective cohort study, 199 women were recruited from antenatal clinics between February 2017 and February 2019. Maternal magnetic resonance imaging (MRI) studies of the placenta were temporally conducted at two timepoints: 14-16 weeks gestational age (GA) and 19-24 weeks GA. The pregnancy was monitored via four additional study visits, including at delivery. Placental volume, perfusion, and oxygenation were assessed at both MRI timepoints. The primary outcome was defined as pregnancy complicated by IPD, with group assignment confirmed after delivery. RESULTS: In early gestation, mothers with IPD who subsequently developed fetal growth restriction (FGR) and/or delivered small-for gestational age (SGA) infants showed significantly decreased MRI indices of placental volume, perfusion, and oxygenation compared to controls. The prediction of FGR or SGA by multiple logistic regression using placental volume, perfusion, and oxygenation revealed receiver operator characteristic curves with areas under the curve of 0.81 (Positive predictive value (PPV) = 0.84, negative predictive value (NPV) = 0.75) at 14-16 weeks GA and 0.66 (PPV = 0.78, NPV = 0.60) at 19-24 weeks GA. DISCUSSION: MRI indices showing decreased placental volume, perfusion and oxygenation in early pregnancy were associated with subsequent onset of IPD, with the greatest deviation evident in subjects with FGR and/or SGA. These early-gestation MRI changes may be predictive of the subsequent development of FGR and/or SGA.

Plasma sphingolipids, lung function and COPD: the Cardiovascular Health Study.

Rationale: COPD is the third leading cause of death in the United States. Sphingolipids, structural membrane constituents that play a role in cellular stress and apoptosis signalling, may be involved in lung function. Methods: In the Cardiovascular Health Study, a prospective cohort of older adults, we cross-sectionally examined the association of plasma levels of 17 sphingolipid species with lung function and COPD. Multivariable linear regression and logistic regression were used to evaluate associations of sphingolipid concentrations with forced expiratory volume in 1 s (FEV1) and odds of COPD, respectively. Results: Of the 17 sphingolipids evaluated, ceramide-18 (Cer-18) and sphingomyelin-18 (SM-18) were associated with lower FEV1 values (-0.061 L per two-fold higher Cer-18, p=0.001; -0.092 L per two-fold higher SM-18, p=0.002) after correction for multiple testing. Several other associations were significant at a 0.05 level, but did not reach statistical significance after correction for multiple testing. Specifically, Cer-18 and SM-18 were associated with higher odds of COPD (odds ratio per two-fold higher Cer-18 1.29, p=0.03 and SM-18 1.73, p=0.008). Additionally, Cer-16 and SM-16 were associated with lower FEV1 values, and Cer-14, SM-14 and SM-16 with a higher odds of COPD. Conclusion: In this large cross-sectional study, specific ceramides and sphingomyelins were associated with reduced lung function in a population-based study. Future studies are needed to examine whether these biomarkers are associated with longitudinal change in FEV1 within individuals or with incident COPD.

Phenytoin-induced gingival overgrowth.

Gingival overgrowth is a common adverse effect of therapy with Phenytoin, having important medical and cosmetic implications. Poor periodontal hygiene is an important risk factor for severity of Phenytoin-induced gingival overgrowth (PIGO), which is a time-dependent process. There is complex interplay of altered fibroblast biology, connective tissue turnover, inflammatory processes, and growth factors on a background of genetic susceptibility to produce increase in various components of interstitial matrix in PIGO tissue. Treatment options have included change of PHT to another anti-seizure drug, measures to improve periodontal hygiene and gingivectomy. There is conclusive evidence that folic acid supplementation significantly decreases the incidence of PIGO.

Renal Salt-Wasting Syndrome Induced by Neoadjuvant Chemotherapy Containing Cisplatin - A Case Report.

Hyponatremia is one of the most common electrolyte abnormality seen in oncology practice. The underlying pathogenetic mechanism for chemotherapy-induced hyponatremia is renal salt-wasting syndrome (RSWS) and syndrome of inappropriate antidiuretic hormone secretion (SIADH). Fluid restriction is the treatment of choice in SIADH, whereas salt supplements is the mode of treatment in RSWS. Hence, differentiation between RSWS and SIADH is very important though difficult. Case reports of cisplatin (cis-dichloro-diammine-platinum-2)-induced RSWS and SIADH are rare in the literature. We report about a patient who developed hyponatremia, hypokalemia with excessive urinary excretion of sodium and potassium, renal glycosuria, and aminoaciduria on the third day of the first cycle of cisplatin-containing chemotherapy.