Digital Commons Network^™

Msg-Fast: Metagenomic Shotgun Data Fast Annotation Using Microbial Gene Catalogs, Stuart M. Brown, Hao Chen, Yuhan Hao, Bobby P. Laungani, Thahmina A. Ali, Changsu Dong, Carlos Lijeron, Baekdoo Kim, Claudia Wultsch, Zhiheng Pei, Konstantinos Krampis

Publications and Research

Background: Current methods used for annotating metagenomics shotgun sequencing (MGS) data rely on a computationally intensive and low-stringency approach of mapping each read to a generic database of proteins or reference microbial genomes.

Results: We developed MGS-Fast, an analysis approach for shotgun whole-genome metagenomic data utilizing Bowtie2 DNA-DNA alignment of reads that is an alternative to using the integrated catalog of reference genes database of well-annotated genes compiled from human microbiome data. This method is rapid and provides high-stringency matches (>90% DNA sequence identity) of the metagenomics reads to genes with annotated functions. We demonstrate the use of this …

A Comparative Study Of Equine Gut Microbiomes Using 16s And 18s Rrna Sequencing, Jillian Jorgenson

Undergraduate Honors Thesis Projects

The gut microbiome of domestic horses (Equus ferus caballus) can be broken down into two primary divisions of interest: (1) prokaryotic composition, consisting of bacteria and archaea and (2) fungal composition. Within the gut, there are also eukaryotic parasite communities that may interact with the microbiome. While each has been the subject of various scientific explorations, in this study we analyze the potential interconnectedness of these categories. To determine the extent to which each component of the gut microbiome/parasitic communities influences the other, DNA was extracted and amplified from the fecal samples of eight horses. A combination of …

Temperamental! Prints In The Collection Of Bryn Mawr College

Books, pamphlets, catalogues, and scrapbooks

Brochure for an exhibition held at Bryn Mawr College March 22, 2019-June 2, 2019, organized by Tessa Haas (A.B./M.A. student), Anya Prussin (Class of 2019), Talia Shiroma (Class of 2019), and Maeve White (A.B./M.A. student): the students in a Fall 2018 exhibition seminar taught by Professor Christiane Hertel and Carrie Robbins (Bryn Mawr College Ph.D. 2013, Curator/Academic Liaison). Brochure design by Nathanael Roesch (Bryn Mawr College Ph.D. 2017).

Serological Proteomic Screening And Evaluation Of A Recombinant Egg Antigen For The Diagnosis Of Low-Intensity Schistosoma Mansoni Infections In Endemic Area In Brazil, Vanessa Silva-Moraes, Lisa Marie Shollenberger, William Castro-Borges, Ana Lucia Teles Rabello, Donald A. Harn, Lia Carolina Soares Medeiros, Wander De Jesus Jeremias, Liliane Maria Vidal Siqueira, Caroline Stephane Salviano Pereira, Maria Luysa Camargos Pedrosa, Nathalie Bonatti Franco Almeida, Aureo Almeida, Jose Roberto Lambertucci, Nidia Francisca De Figueiredo Carneiro, Paulo Marcos Zech Coelho, Refaella Fortini Queiroz Grenfell

Biological Sciences Faculty Publications

Background

Despite decades of use of control programs, schistosomiasis remains a global public health problem. To further reduce prevalence and intensity of infection, or to achieve the goal of elimination in low-endemic areas, there needs to be better diagnostic tools to detect low-intensity infections in low-endemic areas in Brazil. The rationale for development of new diagnostic tools is that the current standard test Kato-Katz (KK) is not sensitive enough to detect low-intensity infections in low-endemic areas. In order to develop new diagnostic tools, we employed a proteomics approach to identify biomarkers associated with schistosome-specific immune responses in hopes of developing …

Diagnosis Of Schistosoma Mansoni Infections: What Are The Choices In Brazilian Low-Endemic Areas?, Vanessa Silva-Moraes, Lisa M. Shollenberger, Liliane Maria Vidal Siqueira, William Castro-Borges, Donald A. Harn, Rafaella Fortini Queiroz E. Grenfell, Ana Lucia Teles Rabello, Paulo Marcos Zech Coelho

Biological Sciences Faculty Publications

The population of Brazil is currently characterised by many individuals harbouring low-intensity Schistosoma mansoni infections. The Kato-Katz technique is the diagnostic method recommended by the World Health Organization (WHO) to assess these infections, but this method is not sensitive enough in the context of low egg excretion. In this regard, potential alternatives are being employed to overcome the limits of the Kato-Katz technique. In the present review, we evaluated the performance of parasitological and immunological approaches adopted in Brazilian areas. Currently, the diagnostic choices involve a combination of strategies, including the utilisation of antibody methods to screen individuals and then …

His Friend Judas: Why Didn't He Betray His Messiah?, Trevan Hatch

Faculty Publications

A question that Christians might ask is, if Jesus was so entrenched within and embracive of Judaism, then why did he condemn Jewish leaders and why was he ultimately rejected and killed by his fellow Jews? In this and the next four chapters (chapters 6–10) we will challenge the assumptions of that very question and illustrate that “the Jews” did not reject and kill Jesus, and that Jesus did not reject and condemn “the Jews.” We will explore the relationship between Jesus and his peers. We start in this chapter by looking at Judas, whose story is perhaps Exhibit A …

The Effect Of Consumer Boycotting On The Stock Market, Anthony Levesque, Jouahn Nam

Honors College Theses

No abstract provided.

Differential Oviposition And Offspring Success Of Gray Treefrogs In The Presence Of An Invasive Fish, Geoffrey R. Smith, Johanna J. Harmon

Faculty Publications

No abstract provided.

Option Implied Volatility, Skewness, And Kurtosis And The Cross-Section Of Expected Stock Returns, Turan Bali, Jianfeng Hu, Murray Scott

Research Collection Lee Kong Chian School Of Business

We develop an ex-ante measure of expected stock returns based on analyst price targets. We then show that ex-ante measures of volatility, skewness, and kurtosis implied from stock option prices are positively related to the cross section of ex-ante expected stock returns. While expected returns are related to both the systematic and unsystematic components of volatility, only the unsystematic components of skewness and kurtosis are related to the cross section of expected stock returns after controlling for other variables known to be related to the cross section of expected stock returns or analyst forecast bias.

Care After Lymphoma (Caly) Trial: A Phase Ii Pilot Pragmatic Randomised Controlled Trial Of A Nurse-Led Model Of Survivorship Care, Karen Taylor, Paola Chivers, Caroline Bulsara, David Joske, Max Bulsara, Leanne Monterosso

Nursing Papers and Journal Articles

Purpose: Post-treatment follow-up for lymphoma potentially fails to address the supportive care needs of survivors. A nurse-led lymphoma survivorship model of care was developed and tested in a phase II pilot pragmatic randomised controlled trial (RCT). The intervention comprised three face-to-face appointments, delivery of tailored resources and an individualised survivorship care plan and treatment summary (SCPTS), shared with the general practitioner (GP).

Method: Three months’ post-treatment completion, eligible lymphoma patients were randomised 1:1 to usual care (control) or usual care plus intervention. Survivorship unmet needs (Short-Form Survivor Unmet Needs Survey), distress (Depression Anxiety Stress Scale 21), adjustment to cancer (Mini-Mental …

Induction Opioids For Caesarean Section Under General Anaesthesia: A Systematic Review And Meta-Analysis Of Randomised Controlled Trials, L D. White, A Hodsdon, G H. An, C Thang, T M. Melhuish, R Vlok

Medical Papers and Journal Articles

Introduction: The adverse effects of induction opioids on the neonate are poorly characterised. The study aim was to investigate whether induction opioids can be used in caesarean section without adversely affecting the neonate.

Methods: Six databases were systematically searched from inception until January 2019. Included studies compared induction opioids and placebo in caesarean section. Results were presented as odds ratios (95% confidence intervals) for dichotomous outcomes and weighted mean difference for continuous outcomes. An I² statistic of >50% was significant for heterogeneity. The primary outcome was Apgar score (1 and 5 min). Secondary outcomes included neonatal adverse events, cord …

Complementary Medicine Use And Health Literacy In Older Australians, Caroline A. Smith, Esther Chang, Gisselle Gallego

Medical Papers and Journal Articles

Objectives: To investigate whether complementary medicine (CAM) use is associated with health literacy levels and decision self-efficacy.

Design: A cross-sectional survey was distributed to men and women aged 65 years and older who participated in a randomised control trial (N = 153) in Sydney, Australia.

Results: One hundred and fifty-three people completed the survey of those 66% were females and the mean age was 76 years. Most participants used or were currently using CAM in the past 12 months (75%). The most common source of CAM information were GPs. Participants with higher levels of social support were found more likely …

The Impact Of Mandatory Iodine Fortification And Supplementation On Pregnant And Lactating Women In Australia, Stephen Hurley, Creswell J. Eastman, Gisselle Gallego

Medical Papers and Journal Articles

Background and Objectives: In Australia, two public health measures were introduced between 2009 and 2010 to reduce iodine deficiency. However there has been a shortage of information regarding their effectiveness and the ongoing prevalence of iodine deficiency in Australia. The primary aim of this study was to assess the extent to which these public health measures have reduced rates of iodine deficiency among pregnant and lactating women.

Methods and Study Design: A review was conducted to identify all studies published since January 2010 that quantitatively measured the iodine status of pregnant and/or lactating women in Australia.

Results: We found 25 …

Mortality Risk Reduction Differs According To Bisphosphonate Class: A 15-Year Observational Study, D Bliuc, T Tran, T Van Geel, J D. Adachi, C Berger, J Van Den Bergh, John A. Eisman, P Geusens, D Golzman, D A. Hanley, R G. Josse, S Kaiser, C S. Kovacs, L Langsetmo, J C. Prior, T V. Nguyen, J R. Center

Medical Papers and Journal Articles

Summary: In this prospective cohort of 6120 participants aged 50+, nitrogen-bisphosphonates but not non-nitrogen bisphosphonates were associated with a significant 34% mortality risk reduction compared to non-treated propensity score matched controls. These findings open new avenues for research into mechanistic pathways.

Introduction: Emerging evidence suggests that bisphosphonates (BP), first-line treatment of osteoporosis, are associated with reduced risks for all-cause mortality. This study aimed to determine the association between different BP types and mortality risk in participants with or without a fracture.

Methods: A prospective cohort study of users of different BPs matched to non-users by propensity score (age, gender, co-morbidities, …

Timing Of Palliative Care Referral And Aggressive Cancer Care Toward The End-Of-Life In Pancreatic Cancer: A Retrospective, Single-Center Observational Study, Natasha Michael, Greta Beale, Clare O'Callaghan, Adelaide Melia, William Desilva, Daniel Costa, David Kissane, Jeremy Shapiro, Richard Hiscock

Medical Papers and Journal Articles

Background: Pancreatic cancer is noted for its late presentation at diagnosis, limited prognosis and physical and psychosocial symptom burden. This study examined associations between timing of palliative care referral (PCR) and aggressive cancer care received by pancreatic cancer patients in the last 30 days of life through a single health service.

Method: A retrospective cohort analysis of end-of-life (EOL) care outcomes of patients with pancreatic cancer who died between 2012 and 2016. Key indicators of aggressive cancer care in the last 30 days of life used were: ≥1 emergency department (ED) presentations, acute inpatient/intensive care unit (ICU) admission, and chemotherapy …

Symptom Profile Of Patients Receiving Antibiotics For Upper Respiratory Tract Infections In General Practice: An Observational Study Using Smartphone Technology, Moyez Jiwa, Catherine Krejany, Epi Kanjo, Alan Leeb, Ian J. Peters

Medical Papers and Journal Articles

Background: Upper respiratory tract infections (URTIs) are a common presentation in general practice and are linked to high rates of inappropriate antibiotic prescription. There is limited information about the trajectory of patients with this condition who have been prescribed antibiotics.

Objective: To document the symptom profile of patients receiving antibiotics for URTIs in Australian general practice using smartphone technology and online surveys.

Methods: In total, 8218 patients received antibiotics after attending one of the 32 general practice clinics in Australia from June to October 2017: 4089 were identified as URTI presentations and were the cohort studied. Patients completed the Wisconsin …

Complex Structural Rearrangements Are Present In High-Grade Dysplastic Barrett's Oesophagus Samples, Felicity Newell, Kalpana Patel, Michael Gartside, Lutz Krause, Sandra Brosda, Lauren G. Aoude, Kelly A. Loffler, Vanessa F. Bonazzi, Ann-Marie Patch, Stephen H. Kazakoff, Oliver Holmes, Qinying Xu, Scott Wood, Conrad Leonard, Guy Lampe, Reginald V. Lord, David C. Whiteman, John V. Pearson, Katia Nones, Nicola Waddell, Andrew P. Barbour

Medical Papers and Journal Articles

Background: Oesophageal adenocarcinoma (EAC) incidence is increasing and has a poor survival rate. Barrett’s oesophagus (BE) is a precursor condition that is associated with EAC and often occurs in conjunction with chronic gastro-oesophageal reflux, however many individuals diagnosed with BE never progress to cancer. An understanding of the genomic features of BE and EAC may help with the early identification of at-risk individuals.

Methods: In this study, we assessed the genomic features of 16 BE samples using whole-genome sequencing. These included non-dysplastic samples collected at two time-points from two BE patients who had not progressed to EAC over several years. …

Metastatic Breast Cancer Incidence, Site And Survival In Australia, 2001-2016: A Population-Based Health Record Linkage Study Protocol, Sarah J. Lord, Belinda E. Kiely, Sally-Anne Pearson, Benjamin Daniels, Dianne L. O'Connell, Jane Beith, Max Bulsara, Nehmat Houssami

Medical Papers and Journal Articles

Introduction: Advances in systemic therapy for early and metastatic breast cancer (BC) over the last two decades have improved patients’ survival, but their impact on metastatic disease outcomes at a population level is not well described. The aim of this study is to investigate changes in the incidence, site and survival of metastatic disease for women with a first diagnosis of BC in 2001– 2002 vs 2006–2007.

Methods and analysis: Population-based retrospective cohort study of women with first primary invasive BC registered in the New South Wales (NSW) Cancer Registry in 2001–2002 and 2006–2007. We will use linked records from …

Microsimulation Model For The Health Economic Evaluation Of Osteoporosis Interventions: Study Protocol, Lei Si, John A. Eisman, Tania Winzenberg, Kerrie M. Sanders, Jacqueline R. Center, Tuan V. Nguyen, Andrew J. Palmer

Medical Papers and Journal Articles

Introduction: Osteoporosis is a systemic skeletal disease that is characterised by reduced bone strength and increased fracture risk. Osteoporosis-related fractures impose enormous disease and economic burden to the society. Although many treatments and health interventions are proven effective to prevent fractures, health economic evaluation adds evidence to their economic merits. Computer simulation modelling is a useful approach to extrapolate clinical and economic outcomes from clinical trials and it is increasingly used in health economic evaluation. Many osteoporosis health economic models have been developed in the past decades; however, they are limited to academic use and there are no publicly accessible …

Disability Patterns Over The First Year After A Diagnosis Of Epilepsy, Ying Xu, Dennis R. Neuen, Nick Glozier, Armin Nikpour, Ernest Somerville, Andrew Bleasel, Carol Ireland, Craig S. Anderson, Maree L. Hackett

Medical Papers and Journal Articles

Objective: To determine the patterns and predictors of disability over the first 12 months after a diagnosis of epilepsy.

Patients and methods: The Sydney Epilepsy Incidence Study to Measure Illness Consequences (SEISMIC) was a prospective, multicenter, community-based study of people with newly diagnosed epilepsy in Sydney, Australia. Disability was assessed using the World Health Organization’s, Disability Assessment Schedule (WHODAS) 2.0 12-item version, at baseline (i.e. within 28 days of diagnosis) and 12 months post-diagnosis. Demographic, socioeconomic, clinical and epilepsy-related data, obtained through structured interviews, were entered into multivariable linear regression and shift analysis to determine predictors of greater disability.

Results: …

Exploring Assessment Of Medical Students' Competencies In Pain Medicine - A Review, Elspeth Shipton, Carole Steketee, Frank Bate, Eric J. Visser

Medical Papers and Journal Articles

Introduction: Considering the continuing high prevalence and public health burden of pain, it is critical that medical students are equipped with competencies in the field of pain medicine. Robust assessment of student expertise is integral for effective implementation of competency-based medical education.

Objective: The aim of this review was to describe the literature regarding methods for assessing pain medicine competencies in medical students.

Method: PubMed, Medline, EMBASE, ERIC, and Google Scholar, and BEME data bases were searched for empirical studies primarily focusing on assessment of any domain of pain medicine competencies in medical students published between January 1997 and December …

The Art Of Clinical Supervision: Strategies To Assist With The Delivery Of Student Feedback, Kylie P. Russell

Medical Papers and Journal Articles

Objective: The Art of Clinical Supervision (ACS) seminar was developed to provide health professionals with the essential knowledge, skill and attitude to support student clinical learning. This paper provides an outline of the strategies provided to participants to support the delivery of feedback to students on clinical placement.

Setting: Western Australian health services

Primary argument: The provision of timely and descriptive feedback to students on clinical placement is essential for learning and achievement of competence. Health professionals working with students in the delivery of patient care, termed clinical supervisors, require effective strategies to support this communication technique.

Conclusion: ACS participant …

James Annesley Of Madras Medical Service (1800-1838) On Cholera In Madras Presidency In 1825, Ramya Raman, Anantanarayanan Raman

Medical Papers and Journal Articles

James Annesley from Ireland spent nearly four decades in Madras, first as an assistant and later as a senior surgeon attached to the Madras Medical Establishment. During this span of service he published the book in 1825 on the most prevalent diseases of India comprising a treatise on the epidemic cholera of the East. This paper recounts the epidemiology of cholera and the efforts made to manage it in the Madras Presidency in the 1820s, keeping in view the life of Annesley and the contents of his book.

Student Exposure To Cancer Patients: An Analysis Of Clinical Logbooks And Focus Groups In Clinical Year Medical Students, Darren L. Starmer, Caris L. House, Kristyn M. Langworthy

Medical Papers and Journal Articles

Despite cancer being the leading cause of mortality, cancer education and patient exposure are lacking in many medical schools. The aim of this study was to evaluate the nature of cancer patient exposure, relative to the clinical setting for medical students on placement and to explore their experiences. Participants were asked to maintain a logbook of cancer patient encounters and were invited to attend a structured focus group upon completion of the academic year. Eleven students submitted logbooks (rr = 6.15%) and eight participated in the focus groups (4.47%). A total of 247 cancer patient encounters were recorded. Third-year students …

Presumed Choroidal Metastasis From Soft Tissue Myoepithelial Carcinoma, Michelle M. Hui, Rohan Merani, Fiona Bonar, Angela M. Hong, Adrian T. Fung

Medical Papers and Journal Articles

Purpose: To report a case of presumed choroidal metastasis from soft tissue myoepithelial carcinoma and highlight challenges in its diagnosis.

Observations: A 52-year-old man was referred with a two-week history of photopsia in his left eye. His background medical history included known soft tissue myoepithelial carcinoma metastatic to his bone, lung, liver and chest wall. A large, raised, yellow choroidal lesion was identified nasal to and abutting the optic disc. This lesion demonstrated growth 1 month after presentation. The patient died with widespread metastatic disease 5 months after initial presentation.

Conclusion and importance: Soft tissue myoepithelial carcinoma can rarely metastasise …

Bioethics In The News: The Values At Stake. Why Are Conservative Values So Difficult To Communicate In The Public Square And Progressive Values So Easy?, Margaret Somerville

Medical Papers and Journal Articles

Bioethical issues are complex, often involve factual uncertainty, and have broad and long-term potential consequences for individuals, institutions and society. Simplification is a strategy used by so-called ‘progressive’ values advocates to promote acceptance of their values. It results from excluding consideration of complexity, uncertainty and potentiality in the values disputes around bio-ethical issues. In order to engage effectively in public debates of bioethics issues, it is necessary to understand the current societal values zeitgeist and how it differs from a traditional societal values zeitgeist. Since words are weapons in the values battles, it is necessary to identify how they are …

What Influences Chronic Pain Management? A Best–Worst Scaling Experiment With Final Year Medical Students And General Practitioners, Linda Rankin, Christopher J. Fowler, Britt-Marie Stålnacke, Gisselle Gallego

Medical Papers and Journal Articles

Background: Chronic pain education is an essential determinant for optimal chronic pain management. Given that attitudes and preferences are involved in making treatment decisions, identifying which factors are most influential to final year medical students’ and general practitioners’ (GPs) chronic pain management choices is of importance. This study investigates Swedish and Australian students’ preferences with respect to a chronic pain condition, using a best–worst scaling (BWS) experiment, which is designed to rank alternatives.

Methods: BWS, a stated-preference method grounded in random utility theory, was used to explore the importance of factors influencing chronic pain management.

Results: All three cohorts considered …

Kbg Syndrome Presenting With Brachydactyly Type E, Renata Libianto, Kathy H.C Wu, Sophie Devery, John A. Eisman, Jackie R. Center

Medical Papers and Journal Articles

We report the case of a young woman who presented at age 10 years with height on the tenth centile, brachydactyly type E and mild developmental delay. Biochemistry and hormonal profiles were normal. Differential diagnoses considered included Albright hereditary osteodystrophy without hormone resistance (a.k.a pseudopseudohypoparathyroidism), 2q37 microdeletion syndrome and acrodysostosis. She had a normal karyotype and normal FISH of 2q37. Whole genome sequencing (WGS) identified a mutation in the ANKRD11 gene associated with KBG syndrome. We review the clinical features of the genetic syndromes considered, and suggest KBG syndrome be considered in patients presenting with syndromic brachydactyly type E, especially …

Exploring Physicians, Nurses And Ward-Based Pharmacists Working Relationships In A Swedish Inpatient Setting: A Mixed Methods Study, Marcia H. Lindqvist, Maria Gustafsson, Gisselle Gallego

Medical Papers and Journal Articles

Background: In Sweden there has been limited work investigating the integration and nature of collaborative relationships between pharmacists and other healthcare practitioners.

Objective: To explore the working relationships of physicians, nurses and ward-based pharmacists in a rural hospital after the introduction of a clinical pharmacy service. Setting General medical ward in a rural hospital in northern Sweden.

Method: Mixed methods involving face-to-face semi-structured interviews with nurses, physicians and pharmacists, and a physician survey using the Physician-Pharmacist Collaboration Index to measure the extent of physician-reported collaborative working relationships.

Main outcome measure: Perceptions about collaborative working relationships between …

The Role Of Trauma And Partner Support In Perinatal Depression And Parenting Stress: An Australian Pregnancy Cohort Study, Megan Galbally, Stuart J. Watson, Phillip Boyce, Andrew J. Lewis

Medical Papers and Journal Articles

Background: Improving our understanding of the relationship between maternal depression and parenting stress is likely to lie in the range of additional factors that are associated with vulnerability to depression and also to parenting stress.

Objectives: To examine the role of trauma and partner support, in understanding the relationship between perinatal depression and parenting stress.

Methods: This study utilises data from 246 women in a pregnancy cohort study that followed women from early pregnancy until their infant was 12 months. Included were both women with a diagnosis of depression and those without depression. The measures included Structured Clinical Interview for …