Subject and Academic Setting of Pre-residency Publications as Potential Predictors of Post-residency Academic Productivity in a Cohort of Ophthalmology Residents

Objective This study aimed to determine if there is any association between the subject of pre-residency research publications (PRPs) and the academic settings in which they are produced with post-residency academic productivity among graduates from an academic ophthalmology residency program.

Design, Setting, Participants This is a cross-sectional study involving graduates of the Wilmer Eye Institute Residency Training Program from 1990 to 1999. An electronic survey was conducted and each participant was asked to submit his/her curriculum vitae, including a list of peer-reviewed publications. Publications were validated and then classified according to the academic setting in which the research was performed, and whether or not the research was related to ophthalmology.

Outcome Measures The primary outcome measure was the post-residency academic productivity score. The secondary outcome measures were the relationships of academic productivity with the settings in which PRPs were performed and the topics of the PRPs.

Results Fifty-one individuals were included. Regression analysis showed a positive association between the number of PRPs generated during undergraduate studies and medical school and the academic productivity score (ratio = 1.17, p = 0.006) but not during an advanced degree program, research fellowship, or a year off to perform research. Regardless of the setting in which it was performed, the subject of a PRP was not associated with academic productivity.

Conclusion It may be appropriate for ophthalmology residency programs whose mission is to train future academicians to place increased weight on applicants who have published articles related to projects performed during undergraduate years or in medical school and less weight on publications related to research performed during a more structured research period, such as an advanced degree program, regardless of the subject(s) of the publication(s).

Hypotonia and intellectual disability without dysmorphic features in a patient with PIGN-related disease

Background

Defects in the human glycosylphosphatidylinositol anchor biosynthetic pathway are associated with inherited glycosylphosphatidylinositol (GPI)-deficiencies characterized by a broad range of clinical phenotypes including multiple congenital anomalies, dysmorphic faces, developmental delay, hypotonia, and epilepsy. Biallelic variants in PIGN, encoding phosphatidylinositol-glycan biosynthesis class N have been recently associated with multiple congenital anomalies hypotonia seizure syndrome.

Case presentation

Our patient is a 2 year old male with hypotonia, global developmental delay, and focal epilepsy. Trio whole-exome sequencing revealed heterozygous variants in PIGN, c.181G > T (p.Glu61*) and c.284G > A (p.Arg95Gln). Analysis of FLAER and anti-CD59 by flow-cytometry demonstrated a shift in this patient’s granulocytes, confirming a glycosylphosphatidylinositol-biosynthesis defect, consistent with PIGN-related disease.

Conclusions

To date, a total of 18 patients have been reported, all but 2 of whom have congenital anomalies and/or obvious dysmorphic features. Our patient has no significant dysmorphic features or multiple congenital anomalies, which is consistent with recent reports linking non-truncating variants with a milder phenotype, highlighting the importance of functional studies in interpreting sequence variants.

Electronic supplementary material

The online version of this article (10.1186/s12881-017-0481-9) contains supplementary material, which is available to authorized users.

Minimising variation in aspalathin content of aqueous green rooibos extract: optimising extraction and identifying critical material attributes

BACKGROUND

High levels of aspalathin, an antidiabetic dihydrochalcone, in green rooibos underpins interest in the production of a standardised extract. Elements of a quality-by-design approach were applied to optimise extraction conditions, aiming at the delivery of a dry matter yield (DMY) ≥ 160 g kg^-1 and an extract with an aspalathin content (AC) ≥ 80 g kg^-1 .

RESULTS

Hot water extraction parameters, namely extraction time, extraction temperature and water-to-plant material ratio, were optimised for DMY and aspalathin extraction efficiency (AEE) using Design of Experiments. Good polynomial prediction models were obtained and multiresponse desirability plots indicated 37 min, 93 °C and 23:1 as optimal conditions. Even when using 30 min and 10:1 instead for practical reasons, the target DMY and AC values could be achieved with the caveat that plant material with an AC ≥ 30 g kg^-1 is used. Particle size distribution and stem content were identified as contributing to variation in the AC of raw material.

CONCLUSION

By setting raw material specifications in terms of AC, as well as applying practical optimum extraction conditions, 160 g kg^-1 extract with an AC ≥ 80 g kg^-1 could be consistently achieved from green rooibos plant material. © 2017 Society of Chemical Industry.

Investigating the association of rs2910164 with cancer predisposition in an Irish cohort

INTRODUCTION

MicroRNAs (miRNAs) are small noncoding RNA molecules that exert post-transcriptional effects on gene expression by binding with cis-regulatory regions in target messenger RNA (mRNA). Polymorphisms in genes encoding miRNAs or in miRNA-mRNA binding sites confer deleterious epigenetic effects on cancer risk. miR-146a has a role in inflammation and may have a role as a tumour suppressor. The polymorphism rs2910164 in the MIR146A gene encoding pre-miR-146a has been implicated in several inflammatory pathologies, including cancers of the breast and thyroid, although evidence for the associations has been conflicting in different populations. We aimed to further investigate the association of this variant with these two cancers in an Irish cohort.

METHODS

The study group comprised patients with breast cancer (BC), patients with differentiated thyroid cancer (DTC) and unaffected controls. Germline DNA was extracted from blood or from saliva collected using the DNA Genotek Oragene 575 collection kit, using crystallisation precipitation, and genotyped using TaqMan-based PCR. Data were analysed using SPSS, v22.

RESULTS

The total study group included 1516 participants. This comprised 1386 Irish participants; 724 unaffected individuals (controls), 523 patients with breast cancer (BC), 136 patients with differentiated thyroid cancer (DTC) and three patients with dual primary breast and thyroid cancer. An additional cohort of 130 patients with DTC from the South of France was also genotyped for the variant. The variant was detected with a minor allele frequency (MAF) of 0.19 in controls, 0.22 in BC and 0.27 and 0.26 in DTC cases from Ireland and France, respectively. The variant was not significantly associated with BC (per allele odds ratio = 1.20 (0.98-1.46), P  = 0.07), but was associated with DTC in Irish patients (per allele OR = 1.59 (1.18-2.14), P = 0.002).

CONCLUSION

The rs2910164 variant in MIR146A is significantly associated with DTC, but is not significantly associated with BC in this cohort.

Abstract 2416: Transcriptome and cluster analysis of infant acute lymphoblastic leukemia cases with and without MLL (KMT2A) rearrangement

Background: Infant acute lymphoblastic leukemia (ALL) is a high-risk cancer with poor survival due to treatment failure and relapse. The majority of infant ALL cases possess an MLL (KMT2A) translocation (MLL-R), where MLL joins with AF4 (AFF1), ENL (MLLT1), or another partner gene to create a novel fusion gene. A subset of infant ALL cases do not involve an MLL rearrangement (non-MLL-R). Gene expression profiling delineates MLL-R from non-MLL-R cases. Here, we describe transcriptome profiling and cluster analysis of MLL-R and non-MLL-R cases and compare between partner genes.

Methods: We performed RNA sequencing (RNA-seq) on diagnostic blood or bone marrow samples from 40 infants with ALL. Cohort A included 16 patients with MLL-R ALL known to have relapsed; cohort B, 10 patients with MLL-R ALL not known to have relapsed; and cohort C, 14 patients with non-MLL-R ALL whom to date have also not relapsed. RNA-seq was performed to an average of 8.8Gb and analyzed using Bowtie2, RSEM, and limma-voom. Multiple different groups of cases (e.g. cohort A versus B) were compared for differential gene expression; the resulting genes were ranked by adjusted P value with a significance cutoff of 0.01 and further evaluated for pathway analysis with Ingenuity software. Hierarchical clustering of samples was conducted using distance measures computed from normalized gene expression.

Results: Transcriptome analysis of MLL-R versus non-MLL-R cases found 2,334 differentially expressed genes. Ingenuity pathway analysis of these genes showed enrichment in specific gene sets, such as those involved in PTEN, EGF, and NF-κB signaling. Ingenuity predicted increased PTEN signaling and diminished EGF and NF-κB signaling in MLL-R cases relative to non-MLL-R cases. Transcriptome analysis of relapsed versus non-relapsed MLL-R cases found no differentially expressed genes meeting significance criteria, while analysis of MLL fusion partners identified 46 differentially expressed genes including BMI1 and MYC. Cluster analysis demonstrated a distinct grouping of non-MLL-R cases relative to MLL-R cases. Additionally, MLL-R samples sub-clustered according to their MLL fusion gene partners. However, no difference in clustering was appreciated between MLL-R cases that later went on to relapse versus those that did not.

Conclusions: Our findings show that MLL-R infant ALL has a distinct gene expression signature at diagnosis that correlates with the type of MLL translocation present. This is important because it suggests treatment strategies could be tailored to the MLL partner gene. Risk of relapse in MLL-R cases could not be predicted by this signature due to a paucity of differentially expressed genes between relapsed and non-relapsed groups at diagnosis. Similar to prior profiling studies, we find that non-MLL-R cases independently cluster together and have a gene expression signature distinct from MLL-R cases.[B.Y. and M.F. contributed equally to this work.]

Citation Format: Byunggil Yoo, Midhat S. Farooqi, Rumen Kostadinov, Neil Miller, Jeff Johnston, Emily Farrow, Shannon Kelley, Margaret Gibson, Patrick Brown, Erin Guest. Transcriptome and cluster analysis of infant acute lymphoblastic leukemia cases with and without MLL (KMT2A) rearrangement [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 2416. doi:10.1158/1538-7445.AM2017-2416

Abstract P3-17-01: Long-term rates of breast preservation after breast-conserving therapy for ductal carcinoma in situ

Background: Despite evidence that radiotherapy (RT) after breast-conserving surgery (BCS) for ductal carcinoma in situ (DCIS) halves the risk of recurrence, the benefit of RT in the management of DCIS continues to be a matter of controversy. One argument against the use of RT after BCS is that patients who develop ipsilateral local recurrence (LR) can be salvaged with further breast-conserving surgery such that the omission of RT will lead to high rates of breast preservation while minimizing exposure to RT. Breast preservation is an important determinant of quality of life for women with early stage breast cancer and DCIS. Yet the management of LR and the impact of RT on the resultant long-term risks of bilateral breast preservation in a population of women with DCIS are unclear. We assessed the treatment of LR, the impact of RT on the use of salvage mastectomy and the long-term risks of bilateral breast preservation achieved in a population of women with DCIS treated with BCS alone or BCS+RT.

Methods: A population-based analysis of women diagnosed with DCIS from 1994-2003 treated with BCS alone or BCS+RT with pathology review. Treatment and outcomes, including the development of LR and contralateral breast events, were determined by administrative databases with validation by review of operative or pathology reports. Median follow-up was 10.2 years for cases treated by BCS alone, 11.6 years for those treated by BCS+RT. We used a propensity-adjusted Cox proportional hazards model to evaluate factors associated with the use of salvage mastectomy for LR and to evaluate factors associated with any mastectomy. We assessed the risk of long-term breast preservation by calculating the KM 10-year risk of ipsilateral mastectomy and any mastectomy.

Results: The population cohort includes 3303 women with pure DCIS;1649 (50%) were treated by BCS alone, 1654 (50%) received BCS+RT. Women treated with RT had more high risk features of DCIS than those treated by BCS alone. LR developed in 343 (21%) women treated by BCS alone and in 257 (15.5%) women treated by BCS+RT (p<0.01). Most women who developed LR received salvage mastectomy, irrespective of age at diagnosis and histology. Salvage mastectomy was used in 57.4% (197/343) of cases that recurred after BCS alone and in 67.6% (173/257) that recurred after BCS+RT. The likelihood of receiving salvage mastectomy for LR was similar in patients initially treated by BCS+RT vs. those initially treated BCS alone. Most (90%) of mastectomies were performed for a LR. Overall, individuals initially treated by BCS+RT had a 29% lower probability of having a mastectomy at 10 years compared to those treated by BCS alone (HR=0.71, 95%CI: 0.60,0.84,p<0.0001). The 10 year mastectomy-free survival rates are 82.7% for women initially treated by BCS alone and 87.3% for those treated by BCS+RT (p=0.0096).

Conclusion: Women who received RT after BCS for DCIS experience a greater likelihood of long-term bilateral breast preservation. This is attributable to the lower risks of LR and that most local recurrences after breast-conserving therapy are treated by salvage mastectomy. Long-term breast preservation should be considered in discussions weighing the benefits and risks of RT after conservative surgery for DCIS.

Citation Format: Rakovitch E, Nofech-Mozes S, Hanna W, Gu S, Fong C, Tuck A, Sengupta S, Elavathil L, Jani P, Done S, Miller N, Youngson B, Bonin M, Chang M, Paszat L. Long-term rates of breast preservation after breast-conserving therapy for ductal carcinoma in situ [abstract]. In: Proceedings of the 2016 San Antonio Breast Cancer Symposium; 2016 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2017;77(4 Suppl):Abstract nr P3-17-01.

Functional validation of novel compound heterozygous variants in B3GAT3 resulting in severe osteopenia and fractures: expanding the disease phenotype

Background

A new disease class of syndromes, described as linkeropathies, which are derived from defects in the glycosaminoglycan-linker region as well as glycosaminoglycan-side chains of proteoglycans is increasingly being recognized as a cause of human disease. Proteoglycans are an essential component of the extracellular matrix. Defects in the enzymatic process of proteoglycan synthesis broadly occur due to the incorrect addition of side chains. Previously, homozygous missense variants within the B3GAT3 gene encoding beta 1,3 glucuronyltransferase 3(GlcAT-I) responsible for the biosynthesis of glycosaminoglycans have been described in 7 individuals.

Case presentation

In this study, a 4-year-old patient with a severe phenotype of osteoporosis, hypotonia, joint laxity, fractures, scoliosis, biscuspid aortic valve and myopia was referred for next generation sequencing after extensive negative clinical testing. Whole exome sequencing was performed on the proband and his unaffected parents to identify the molecular basis of his disease. Sequencing revealed compound heterozygous variants in B3GAT3: c.1A > G (p.Met1?) and c.671 T > A (p.L224Q). Clinical and in vitro functional studies were then completed to verify the pathogenicity of the genotype and further characterize the functional basis of the patient’s disease demonstrating the patient had a decrease both in the protein level of B3GAT3 and in the glucuronyltransferase activity when compared to control samples. Independent in vitro assessment of each variant confirmed the B3GAT3: c.1A > G (p.Met1?) variant is functionally null and the c.671 T > A (p.L224Q) missense variant has significantly reduced glucuronyltransferase activity (~3% of control).

Conclusions

This is the first report of a patient with compound heterozygosity for a null variant in trans with a missense in B3GAT3 resulting in a severe phenotype, expanding both the genotypic and phenotypic spectrum of B3GAT3-related disease.

Electronic supplementary material

The online version of this article (doi:10.1186/s12881-016-0344-9) contains supplementary material, which is available to authorized users.

A novel epileptic encephalopathy mutation in KCNB1 disrupts Kv2.1 ion selectivity, expression, and localization

A missense mutation in the pore-forming α subunit of a delayed rectifier Kv channel is associated with epileptic encephalopathy, alters the cation selectivity of voltage-gated currents, and disrupts channel expression and localization.

The epileptic encephalopathies are a group of highly heterogeneous genetic disorders. The majority of disease-causing mutations alter genes encoding voltage-gated ion channels, neurotransmitter receptors, or synaptic proteins. We have identified a novel de novo pathogenic K⁺ channel variant in an idiopathic epileptic encephalopathy family. Here, we report the effects of this mutation on channel function and heterologous expression in cell lines. We present a case report of infantile epileptic encephalopathy in a young girl, and trio-exome sequencing to determine the genetic etiology of her disorder. The patient was heterozygous for a de novo missense variant in the coding region of the KCNB1 gene, c.1133T>C. The variant encodes a V378A mutation in the α subunit of the Kv2.1 voltage-gated K⁺ channel, which is expressed at high levels in central neurons and is an important regulator of neuronal excitability. We found that expression of the V378A variant results in voltage-activated currents that are sensitive to the selective Kv2 channel blocker guangxitoxin-1E. These voltage-activated Kv2.1 V378A currents were nonselective among monovalent cations. Striking cell background–dependent differences in expression and subcellular localization of the V378A mutation were observed in heterologous cells. Further, coexpression of V378A subunits and wild-type Kv2.1 subunits reciprocally affects their respective trafficking characteristics. A recent study reported epileptic encephalopathy-linked missense variants that render Kv2.1 a tonically activated, nonselective cation channel that is not voltage activated. Our findings strengthen the correlation between mutations that result in loss of Kv2.1 ion selectivity and development of epileptic encephalopathy. However, the strong voltage sensitivity of currents from the V378A mutant indicates that the loss of voltage-sensitive gating seen in all other reported disease mutants is not required for an epileptic encephalopathy phenotype. In addition to electrophysiological differences, we suggest that defects in expression and subcellular localization of Kv2.1 V378A channels could contribute to the pathophysiology of this KCNB1 variant.

The effects of a stroke unit on activities of daily living

Objective: To determine whether specific daily activities are improved more by treatment in a specialized stroke unit for patients seen after stroke.

Design: Randomized controlled study allocating patients to management in a stroke unit or on conventional hospital wards.

Setting: District general hospital medical or geriatric wards, or a hospital stroke unit.

Subjects: Patients who within five weeks of acute stroke were considered suitable for intensive stroke unit rehabilitation (if so randomized).

Interventions: Standard rehabilitation as delivered in the medical/geriatric wards or as delivered in the stroke unit.

Outcome measures: All individual items from the Barthel activities of daily living (ADL) scale, all items from the Rivermead ADL scales (self-care and household sections) and all items from the Nottingham Extended ADL scale were analysed.

Results: One hundred and seventy-six patients were seen in the stroke unit and 139 on the conventional wards. At entry the stroke unit had more women and stroke unit patients had less good arm function; otherwise the groups were comparable. The main differences were in the areas of feeding, dressing and household activities.

Conclusions: Stroke unit rehabilitation seems to improve feeding, dressing and household activities more than occurs on conventional wards; mobility was improved equally in both settings.

Intracytoplasmic morphologically selected sperm injection and congenital birth defects: a retrospective cohort study

Our objective was to study the birth defect rates in intracytoplasmic morphologically selected sperm injection (IMSI) pregnancies. A cohort of couples presenting male factor infertility between January 2006 and January 2014 was retrospectively analyzed. Discharge letters and a telephone interview were performed for assessing pregnancy outcome. All clinical data were reviewed by a board certified medical geneticist. Main outcomes were fetal/birth defect and chromosomal abnormality rates. Two thousand two hundred and fifty-eight pregnancies were available for analysis, of them, 1669 (73.9%) resulting from ICSI and 2258 (26.1%) achieved by IMSI. Pregnancy outcome distribution did not show a significant difference. For the fresh embryo transfer cohort, fetal/birth defect rate was 4.5%, chromosomal aberration rate was 1.0%, and structural malformation rate was 3.5%. IMSI vs. ICSI pregnancies were less likely to involve a fetal/birth defect: 3.5% vs. 4.8%, respectively, but did not reach a statistical significance OR 0.71 (95% CI 0.39-1.22). Split by multiplicity, this trend existed only for singleton pregnancies; 1.4% structural malformations rate vs. 3.8%, respectively, OR 0.35 (95% CI 0.11-0.9). The frozen cohort demonstrated a significantly lower birth defect rate (OR 0.25, 95% CI 0.09-0.58). We conclude that IMSI procedure does not involve an increased malformation rate and may offer a reduced anomaly incidence. Further studies are required.

Breast Cancer in the Bahamas in 2009-2011

BACKGROUND

Breast cancer is the most common form of cancer affecting women in the Bahamas, which consists of many islands. This is the first attempt to identify which island has the highest occurrence of breast cancer.

OBJECTIVE

The aim of this study was to describe the sociodemographical and spatial features of breast cancer in the Bahamas in 2009-2011.

METHODS

A review of the medical records of all women with a confirmed diagnosis of breast cancer during the period January 1, 2009-December 31, 2011, was undertaken. Data were first obtained from the National Oncology Board of the Bahamas and validated by a review of the medical records. The patient address was geocoded and mapped using ArcGIS 10.0 Environmental Systems Research Institute (ESRI) to satellite images obtained from The Nature Conservancy in the Bahamas.

RESULTS

We recruited 270 patients who satisfied the entry criteria. The cumulative incidences of breast cancer for the years 2009-2011 were 51.4, 45.4, and 51.4, respectively. Breast cancer occurred most often in women of African origin with a mean age at diagnosis of 56.6 ± 13.8 years. Ductal carcinoma was the most common histological type observed with most cancers occurring in Grade II or higher and presenting as late stage (≥ Stage II). Surgery was the preferred method of treatment with modified radical mastectomy being the procedure of choice. Spatial distribution of cases across the Bahamas revealed one cluster, which is present on the island of New Providence. Further analysis of New Providence showed a consistently skewed kernel density in the central and eastern regions, compared with a scattered distribution in the southern and western regions.

CONCLUSION

The island of New Providence had the highest occurrence of breast cancer among all the islands of the Bahamas. The increasing incidence of breast cancer in young women is likely to impose a significant burden on the future of Bahamian health care.

A 6-month telephone-based weight loss intervention in overweight and obese subjects with idiopathic intracranial hypertension

Objectives

The purpose of this paper is to measure the change in body weight after a 6‐month telephone‐based weight loss intervention in overweight and obese subjects with idiopathic intracranial hypertension (IIH) and mild visual loss randomized to receive either acetazolamide or placebo.

Methods

One hundred sixty‐five subjects with IIH, aged 29.1 ± 7.5 (mean ± SD) and BMI 39.9 + 8.3 kg/m², enrolled at 38 academic and private practice sites in North America, participated in this trial. This was a randomized, double‐masked, placebo‐controlled trial of acetazolamide in subjects with IIH and mild visual loss. All participants received a reduced‐sodium, weight‐reduction diet and a 6‐month telephone‐based weight loss intervention. Six‐month changes from baseline in body weight, perimetric mean deviation as assessed by automated perimetry and quality of life using the National Eye Institute Visual Function Questionnaire 25 and the 36‐item Short Form Health Survey were measured.

Results

Mean percent weight change at 6 months was −5.9% ± 6.7% of initial body weight overall, −3.5% ± 5.9% in the placebo group and −7.8% ± 6.8% in the acetazolamide group. Weight change was not associated with changes in either mean deviation or quality of life scores.

Conclusion

Patients with IIH and mild visual loss assigned to either acetazolamide or placebo, all of whom received a 6‐month telephone‐based weight loss intervention, lost an average of 5.9% of initial body weight, consistent with NHLBI guidelines of 5% to 10% of body weight loss for clinically significant health benefit.