Digital Commons Network^™

Pathoscope: Species Identification And Strain Attribution With Unassembled Sequencing Data., Owen E Francis, Matthew Bendall, Solaiappan Manimaran, Changjin Hong, Nathan L Clement, Eduardo Castro-Nallar, Quinn Snell, G Bruce Schaalje, Mark J Clement, Keith A Crandall, W Evan Johnson

Computational Biology Institute

Emerging next-generation sequencing technologies have revolutionized the collection of genomic data for applications in bioforensics, biosurveillance, and for use in clinical settings. However, to make the most of these new data, new methodology needs to be developed that can accommodate large volumes of genetic data in a computationally efficient manner. We present a statistical framework to analyze raw next-generation sequence reads from purified or mixed environmental or targeted infected tissue samples for rapid species identification and strain attribution against a robust database of known biological agents. Our method, Pathoscope, capitalizes on a Bayesian statistical framework that accommodates information on sequence …

Outdated Dermatologic Drug Samples And Obligations To The Patient., Jordan Wang, Matthew Keller

Department of Dermatology and Cutaneous Biology Faculty Papers

CASE SCENARIO

A 37-year-old man with a slightly raised, red, scaly patch on his left arm is seen in the clinic of an academic teaching hospital by a young dermatologist. Following examination and biopsy, he is found to have squamous cell carcinoma in situ. The patient was recently laid off from work and had lost access to his health insurance. He is struggling to make ends meet for his family, so it would be difficult for him to cover any extraneous health-related expenses. Upon relaying this information to the dermatologist, the patient is provided with a full course of 5-fluorouracil …

Long-Term Outcomes Of Ranibizumab Therapy For Diabetic Macular Edema: The 36-Month Results From Two Phase Iii Trials: Rise And Ride., David M. Brown, Quan Dong Nguyen, Dennis M. Marcus, David S. Boyer, Sunil Patel, Leonard Feiner, Patricio G. Schlottmann, Amy Chen Rundle, Jiameng Zhang, Roman G. Rubio, Anthony P. Adamis, Jason S. Ehrlich, J. Jill Hopkins

Journal Articles: Ophthalmology

PURPOSE: To report 36-month outcomes of RIDE (NCT00473382) and RISE (NCT00473330), trials of ranibizumab in diabetic macular edema (DME).

DESIGN: Phase III, randomized, multicenter, double-masked, 3-year trials, sham injection-controlled for 2 years.

PARTICIPANTS: Adults with DME (n=759), baseline best-corrected visual acuity (BCVA) 20/40 to 20/320 Snellen equivalent, and central foveal thickness (CFT) ≥ 275 μm on optical coherence tomography.

METHODS: Patients were randomized equally (1 eye per patient) to monthly 0.5 mg or 0.3 mg ranibizumab or sham injection. In the third year, sham patients, while still masked, were eligible to cross over to monthly 0.5 mg ranibizumab. Macular laser …

Evidence-Based Practice In Occupational Therapy Curricula., Tina Angelis, Edd, Otr/L, Thomas G Dimarco, Susan Toth-Cohen, Edd, Otr/L

Department of Occupational Therapy Faculty Papers

The purpose of this study is to describe currently used educational strategies for teaching evidence-based practice (EBP) in entry-level master's degree occupational therapy programs in the United States. Fifty-eight entry-level occupational therapy program directors completed a survey. Results showed that occupational therapy programs consistently use a wide variety of EBP resources for teaching EBP including database searches, literature reviews, and the development of a research proposal. Less commonly used strategies include the use of case stories and journal clubs. The current study provides a baseline of existing strategies taught in entry level programs that may be built upon to gather …

A Population-Based Case–Control Study Of Urinary Arsenic Species And Squamous Cell Carcinoma In New Hampshire, Usa, Diane Gilbert-Diamond, Zhigang Li, Ann E. Perry, Steven K. Spencer, A Jay Gandolfi, Margaret R. Karagas

Dartmouth Scholarship

Background: Chronic high arsenic exposure is associated with squamous cell carcinoma (SCC) of the skin, and inorganic arsenic (iAs) metabolites may play an important role in this association. However, little is known about the carcinogenicity of arsenic at levels commonly observed in the United States.

Objective: We estimated associations between total urinary arsenic and arsenic species and SCC in a U.S. population.

Methods: We conducted a population-based case–control SCC study (470 cases, 447 controls) in a U.S. region with moderate arsenic exposure through private well water and diet. We measured urinary iAs, monomethylarsonic acid (MMA), and dimethylarsinic acid (DMA), and …

De Novo Frameshift Mutation In Asxl3 In A Patient With Global Developmental Delay, Microcephaly, And Craniofacial Anomalies., Darrell L. Dinwiddie, Sarah E. Soden, Carol J. Saunders, Neil A. Miller, Emily G. Farrow, Laurie D. Smith, Stephen F. Kingsmore

Manuscripts, Articles, Book Chapters and Other Papers

BACKGROUND: Currently, diagnosis of affected individuals with rare genetic disorders can be lengthy and costly, resulting in a diagnostic odyssey and in many patients a definitive molecular diagnosis is never achieved despite extensive clinical investigation. The recent advent and use of genomic medicine has resulted in a paradigm shift in the clinical molecular genetics of rare diseases and has provided insight into the causes of numerous rare genetic conditions. In particular, whole exome and genome sequencing of families has been particularly useful in discovering de novo germline mutations as the cause of both rare diseases and complex disorders.

CASE PRESENTATION: …

A Study On The Geophylogeny Of Clinical And Environmental Vibrio Cholerae In Kenya, J. Kiiru, A. Mutreja, A. A. Mohamed, R. W. Kimani, J. Mwituria, R. O. Sanaya, J. Muyodi, Gunturu Revathi, J. Parkhill, N. Thomson, G. Dougan, S. Kariuki

Pathology, East Africa

Cholera remains a significant public health challenge in many sub-Saharan countries including Kenya. We have performed a combination of phylogenetic and phenotypic analysis based on whole genome DNA sequences derived from 40 environmental and 57 clinical V. cholerae from different regions of Kenya isolated between 2005 and 2010. Some environmental and all clinical isolates mapped back onto wave three of the monophyletic seventh pandemic V. cholerae El Tor phylogeny but other environmental isolates were phylogenetically very distinct. Thus, the genomes of the Kenyan V. cholerae O1 El Tor isolates are clonally related to other El Tor V. cholerae isolated elsewhere …

The Flexible Fairness: Equality, Earned Entitlement, And Self-Interest, Chunliang Feng, Yi Luo, Ruolei Gu, Lucas S. Broster, Xueyi Shen, Tengxiang Tian, Yue-Jia Luo, Frank Krueger

Behavioral Science Faculty Publications

The current study explored whether earned entitlement modulated the perception of fairness in three experiments. A preliminary resource earning task was added before players decided how to allocate the resource they jointly earned. Participants' decision in allocation, their responses to equal or unequal offers, whether advantageous or disadvantageous, and subjective ratings of fairness were all assessed in the current study. Behavioral results revealed that participants proposed more generous offers and showed enhanced tolerance to disadvantageous unequal offers from others when they performed worse than their presumed "partners," while the reverse was true in the better-performance condition. The subjective ratings also …

Test Order Effects In Simultaneous Protocols, Abdulrazaq Imam, Timothy A. Warner

Psychology

Simultaneous protocols typically yield poorer stimulus equivalence outcomes than do other protocols commonly used in equivalence research. Two independent groups of three 3-member equivalence sets of stimuli were used in conditional discrimination procedures in two conditions, one using the standard simultaneous protocol and the other using a hybrid simultaneous training and simple-to-complex testing. Participants completed the two conditions in one long session in Experiment 1, but in separate sessions in Experiment 2. The same stimulus sets used in Experiment 1 were randomized for the two conditions in Experiment 2. Overall, accuracy was better with the hybrid than with the standard …

The Effect Of Malnutrition On Patients Undergoing Elective Joint Arthroplasty., Ronald Huang, Md, Max Greenky, Bs, Glenn J. Kerr, Md, Mathew S. Austin, Md, Javad Parvizi, Md, Frcs

Rothman Institute Papers

Malnutrition has been linked to serious complications in patients undergoing elective total joint arthroplasty (TJA). This study prospectively evaluated 2,161 patients undergoing elective TJA for malnutrition as defined by either an abnormal serum albumin or transferrin. The overall incidence of malnutrition was 8.5% (184 of 2,161) and the rate of overall complications in the malnourished group was 12% as compared to 2.9% in patients with normal parameters (P55years-old undergoing TJA and is associated with a significant increase in post-operative complications.

Conservation Of Structure And Mechanism By Trm5 Enzymes., Thomas Christian, Howard Gamper, Ya-Ming Hou

Department of Biochemistry and Molecular Biology Faculty Papers

Enzymes of the Trm5 family catalyze methyl transfer from S-adenosyl methionine (AdoMet) to the N¹ of G37 to synthesize m¹ G37-tRNA as a critical determinant to prevent ribosome frameshift errors. Trm5 is specific to eukaryotes and archaea, and it is unrelated in evolution from the bacterial counterpart TrmD, which is a leading anti-bacterial target. The successful targeting of TrmD requires detailed information on Trm5 to avoid cross-species inhibition. However, most information on Trm5 is derived from studies of the archaeal enzyme Methanococcus jannaschii (MjTrm5), whereas little information is available for eukaryotic enzymes. Here we use human Trm5 (Homo sapiens; HsTrm5) …

Equivalence Of Students' Scores On Timed And Untimed Anatomy Practical Examinations., Guiyan Zhang, Bruce Fenderson, Richard R Schmidt, J J. Veloski

Department of Pathology, Anatomy, and Cell Biology Faculty Papers

Untimed examinations are popular with students because there is a perception that first impressions may be incorrect, and that difficult questions require more time for reflection. In this report, we tested the hypothesis that timed anatomy practical examinations are inherently more difficult than untimed examinations. Students in the Doctor of Physical Therapy program at Thomas Jefferson University were assessed on their understanding of anatomic relationships using multiple-choice questions. For the class of 2012 (n = 46), students were allowed to circulate freely among 40 testing stations during the 40-minute testing session. For the class of 2013 (n = 46), students …

Self-Regulatory Depletion Increases Emotional Reactivity In The Amygdala, Dylan D. Wagner, Todd F. Heatherton

Dartmouth Scholarship

The ability to self-regulate can become impaired when people are required to engage in successive acts of effortful self-control, even when self-control occurs in different domains. Here, we used functional neuroimaging to test whether engaging in effortful inhibition in the cognitive domain would lead to putative dysfunction in the emotional domain. Forty-eight participants viewed images of emotional scenes during functional magnetic resonance imaging in two sessions that were separated by a challenging attention control task that required effortful inhibition (depletion group) or not (control group). Compared to the control group, depleted participants showed increased activity in the left amygdala to …

Regulation Of Cell Death By Transfer Rna., Ya-Ming Hou, Xiaolu Yang

Department of Biochemistry and Molecular Biology Faculty Papers

SIGNIFICANCE: Both transfer RNA (tRNA) and cytochrome c are essential molecules for the survival of cells. tRNA decodes mRNA codons into amino-acid-building blocks in protein in all organisms, whereas cytochrome c functions in the electron transport chain that powers ATP synthesis in mitochondrion-containing eukaryotes. Additionally, in vertebrates, cytochrome c that is released from mitochondria is a potent inducer of apoptosis, activating apoptotic proteins (caspases) in the cytoplasm to dismantle cells. A better understanding of both tRNA and cytochrome c is essential for an insight into the regulation of cell life and death.

RECENT ADVANCES: A recent study showed that the …

The Drug Facts Box: Improving The Communication Of Prescription Drug Information, Lisa M. Schwartz, Steven Woloshin

Dartmouth Scholarship

Communication about prescription drugs ought to be a paragon of public science communication. Unfortunately, it is not. Consumers see $4 billion of direct-to-consumer advertising annually, which typically fails to present data about how well drugs work. The professional label—the Food and Drug Administration's (FDA) mechanism to get physicians information needed for appropriate prescribing—may also fail to present benefit data. FDA labeling guidance, in fact, suggests that industry omit bene

Amyloid Β-Peptide (1–42)-Induced Oxidative Stress In Alzheimer Disease: Importance In Disease Pathogenesis And Progression, D. Allan Butterfield, Aaron M. Swomley, Rukhsana Sultana

Chemistry Faculty Publications

Significance: Alzheimer disease (AD) is an age-related neurodegenerative disease. AD is characterized by progressive cognitive impairment. One of the main histopathological hallmarks of AD brain is the presence of senile plaques (SPs) and another is elevated oxidative stress. The main component of SPs is amyloid beta-peptide (Aβ) that is derived from the proteolytic cleavage of amyloid precursor protein.

Recent Advances: Recent studies are consistent with the notion that methionine present at 35 position of Aβ is critical to Aβ-induced oxidative stress and neurotoxicity. Further, we also discuss the signatures of oxidatively modified brain proteins, identified using redox proteomics approaches, during …

Deficits In Retrospective And Prospective Components Underlying Prospective Memory Tasks In Amnestic Mild Cognitive Impairment, Ting Zhou, Lucas S. Broster, Yang Jiang, Feng Bao, Huali Wang, Juan Li

Behavioral Science Faculty Publications

OBJECTIVES: By use of purer indices of PM and RM components than previous studies and adoption of three PM task types, the present study aimed to investigate the deficits of these two components underlying global impairment at a PM task in individuals with amnestic mild cognitive impairment (aMCI).

METHODS: Nineteen aMCI patients and 22 normal controls were examined on event-, time- and activity-based PM tasks. Separate scores were obtained for initiation of intentions (i.e. PM component) and for the content of the intentions (i.e. RM component).

RESULTS: Individuals with aMCI achieved lower PM component (but not RM component) scores than …

Differential Dna Methylation In Umbilical Cord Blood Of Infants Exposed To Low Levels Of Arsenic In Utero, Devin C. Koestler, Michele Avissar-Whiting, E. Andres Houseman, Margaret R. Karagas, Carmen J. Marsit

Dartmouth Scholarship

Background: There is increasing epidemiologic evidence that arsenic exposure in utero, even at low levels found throughout much of the world, is associated with adverse reproductive outcomes and may contribute to long-term health effects. Animal models, in vitro studies, and human cancer data suggest that arsenic may induce epigenetic alterations, specifically by altering patterns of DNA methylation.

Objectives: In this study we aimed to identify differences in DNA methylation in cord blood samples of infants with in utero, low-level arsenic exposure.

Methods: DNA methylation of cord-blood derived DNA from 134 infants involved in a prospective birth cohort in …

Early Echocardiographic Changes After Percutaneous Implantation Of The Edwards Sapien Transcatheter Heart Valve In The Pulmonary Position., Shahryar M. Chowdhury, Ziyad M. Hijazi, John Rhodes, Saibal Kar, Raj Makkar, Michael Mullen, Qi-Ling Cao, Lydia King, Jodi Akin, Girish S. Shirali

Manuscripts, Articles, Book Chapters and Other Papers

OBJECTIVES: To evaluate echocardiographic changes after SAPIEN valve implantation in the pulmonary position.

BACKGROUND: The feasibility of the SAPIEN transcatheter pulmonary valve (TPV) has recently been demonstrated. We evaluated changes in pulmonary valve function and the right ventricle after SAPIEN TPV placement.

METHODS: We evaluated echocardiograms at baseline, discharge, 1 and 6 months after TPV placement in 33 patients from 4 centers. Pulmonary insufficiency severity was graded 0-4. TPV peak and mean gradients were measured. Right ventricular (RV) size and function were quantified using routine measures derived from color, spectral, and tissue Doppler indices and two-dimensional echocardiography.

RESULTS: At baseline, …

Body Mri Artifacts In Clinical Practice: A Physicist's And Radiologist's Perspective., Martin J Graves, Donald Mitchell

Department of Radiology Faculty Papers

The high information content of MRI exams brings with it unintended effects, which we call artifacts. The purpose of this review is to promote understanding of these artifacts, so they can be prevented or properly interpreted to optimize diagnostic effectiveness. We begin by addressing static magnetic field uniformity, which is essential for many techniques, such as fat saturation. Eddy currents, resulting from imperfect gradient pulses, are especially problematic for new techniques that depend on high performance gradient switching. Nonuniformity of the transmit radiofrequency system constitutes another source of artifacts, which are increasingly important as magnetic field strength increases. Defects in …

Hippocampal Functional Connectivity Patterns During Spatial Working Memory Differ In Right Versus Left Temporal Lobe Epilepsy., Gaelle Eve Doucet, Karol Osipowicz, Ashwini Sharan Md, Michael R Sperling, Joseph I Tracy

Department of Neurology Faculty Papers

Temporal lobe epilepsy (TLE), affecting the medial temporal lobe, is a disorder that affects not just episodic memory but also working memory (WM). However, the exact nature of hippocampal-related network activity in visuospatial WM remains unclear. To clarify this, we utilized a functional connectivity (FC) methodology to investigate hippocampal network involvement during the encoding phase of a functional magnetic resonance imaging (fMRI) visuospatial WM task in right and left TLE patients. Specifically, we assessed the relation between FC within right and left hippocampus-seeded networks, and patient performance (rate of correct responses) during the encoding phase of a block span WM …

An Integrated Clinico-Metabolomic Model Improves Prediction Of Death In Sepsis., Raymond J. Langley, Ephraim L. Tsalik, Jennifer C. Van Velkinburgh, Seth W. Glickman, Brandon J. Rice, Chunping Wang, Bo Chen, Lawrence Carin, Arturo Suarez, Robert P. Mohney, Debra H. Freeman, Mu Wang, Jinsam You, Jacob Wulff, J Will Thompson, M Arthur Moseley, Stephanie Reisinger, Brian T. Edmonds, Brian Grinnell, David R. Nelson, Darrell L. Dinwiddie, Neil A. Miller, Carol J. Saunders, Sarah Soden, Angela J. Rogers, Lee Gazourian, Laura E. Fredenburgh, Anthony F. Massaro, Rebecca M. Baron, Augustine M K Choi, G Ralph Corey, Geoffrey S. Ginsburg, Charles B. Cairns, Ronny M. Otero, Vance G. Fowler, Emanuel P. Rivers, Christopher W. Woods, Stephen F. Kingsmore

Manuscripts, Articles, Book Chapters and Other Papers

Sepsis is a common cause of death, but outcomes in individual patients are difficult to predict. Elucidating the molecular processes that differ between sepsis patients who survive and those who die may permit more appropriate treatments to be deployed. We examined the clinical features and the plasma metabolome and proteome of patients with and without community-acquired sepsis, upon their arrival at hospital emergency departments and 24 hours later. The metabolomes and proteomes of patients at hospital admittance who would ultimately die differed markedly from those of patients who would survive. The different profiles of proteins and metabolites clustered into the …

An Mll-Dependent Network Sustains Hematopoiesis, Erika L. Artinger, Bibhu P. Mishra, Kristin M. Zaffuto, Bin E. Li, Elaine K. Y. Chung, Adrian W. Moore, Yufei Chen, Chao Cheng, Patricia Ernst

Dartmouth Scholarship

The histone methyltransferase Mixed Lineage Leukemia (MLL) is essential to maintain hematopoietic stem cells and is a leukemia protooncogene. Although clustered homeobox genes are well-characterized targets of MLL and MLL fusion oncoproteins, the range of Mll-regulated genes in normal hematopoietic cells remains unknown. Here, we identify and characterize part of the Mll-dependent transcriptional network in hematopoietic stem cells with an integrated approach by using conditional loss-of-function models, genomewide expression analyses, chromatin immunoprecipitation, and functional rescue assays. The Mll-dependent transcriptional network extends well beyond the previously appreciated Hox targets, is comprised of many characterized regulators of self-renewal, and contains target genes …

Psychosocial Interventions For Patients With Head And Neck Cancer., Cherith Semple, Kader Parahoo, Alyson Norman, Eilis Mccaughan, Gerry Humphris, Moyra Mills

School of Psychology

BACKGROUND: A diagnosis of head and neck cancer, like many other cancers, can lead to significant psychosocial distress. Patients with head and neck cancer can have very specific needs, due to both the location of their disease and the impact of treatment, which can interfere with basic day-to-day activities such as eating, speaking and breathing. There is a lack of clarity on the effectiveness of the interventions developed to address the psychosocial distress experienced by patients living with head and neck cancer. OBJECTIVES: To assess the effectiveness of psychosocial interventions to improve quality of life and psychosocial well-being for patients …

Circulating Tumor Dna To Monitor Metastatic Breast Cancer., Massimo Cristofanilli, Paolo Fortina

Kimmel Cancer Center Faculty Papers

No abstract provided.

Counting Unstained, Confluent Cells By Modified Bright-Field Microscopy, L. Louis Drey, Michael Graber, Jan Bieschke

Open Access Publications

We present a very simple procedure yielding high-contrast images of adherent, confluent cells such as human neuroblastoma (SH-EP) cells by ordinary bright-field microscopy. Cells are illuminated through a color filter and a pinhole aperture placed between the condenser and the cell culture surface. Refraction by each cell body generates a sharp, bright spot when the image is defocused. The technique allows robust, automatic cell counting from a single bright-field image in a wide range of focal positions using free, readily available image-analysis tools. Contrast may be enhanced by swelling cell bodies with a brief incubation in PBS. The procedure was …

Dna Methylation Analysis Reveals Distinct Methylation Signatures In Pediatric Germ Cell Tumors, James F. Amatruda, Julie A. Ross, Brock Christensen, Nicholas J. Fustino, Kenneth S. Chen, Anthony J. Hooten, Heather Nelson, Jacquelyn K. Kuriger, Dinesh Rakheja, A. Lindsay Frazier, Jenny N. Poynter

Dartmouth Scholarship

Background: Aberrant DNA methylation is a prominent feature of many cancers, and may be especially relevant in germ cell tumors (GCTs) due to the extensive epigenetic reprogramming that occurs in the germ line during normal development. Methods: We used the Illumina GoldenGate Cancer Methylation Panel to compare DNA methylation in the three main histologic subtypes of pediatric GCTs (germinoma, teratoma and yolk sac tumor (YST); N = 51) and used recursively partitioned mixture models (RPMM) to test associations between methylation pattern and tumor and demographic characteristics. We identified genes and pathways that were differentially methylated using generalized linear models and …

Prevalence Of Rabies In Various Species In Yemen And Risk Factors Contributing To The Spread Of The Disease, Hassan A. Al-Shamahy, Ameera Sunhope, Khaled A.

Sultan Qaboos University Medical Journal

Objectives: This study aimed to describe for the first time the prevalence of the passively-reported rabies virus among different domestic and wild animals submitted to the Central Veterinary Laboratory from various areas in Yemen, and to study prevalence proportion ratios (PPR) that contributed to the spread of rabies among animals, and its transmission to humans. Methods: A brain sample was obtained from each of the 180 animals and tested for rabies virus by a direct fluorescent antibody test. Results: Out of the total number of animals involved in attacks on humans, 63.3 % were positive for rabies. Of these, dogs …

Id4 Deficiency Attenuates Prostate Development And Promotes Pin-Like Lesions By Regulating Androgen Receptor Activity And Expression Of Nkx3.1 And Pten, Pankaj Sharma, Ashley Knowell, Swathi Chinaranagari, Shravan Komaragiri, Peri Nagappan, Divya Patel, Mathew C. Havrda, Jaideep Chaudhary

Dartmouth Scholarship

Background: Inhibitor of differentiation 4 (Id4), a member of the helix-loop-helix family of transcriptional regulators has emerged as a tumor suppressor in prostate cancer. Id4 is expressed in the normal prostate where its expression is also regulated by androgens. In this study we investigated the effect of loss of Id4 (Id4-/-) on adult prostate morphology. Methods: Histological analysis was performed on prostates from 6-8 weeks old Id4-/-, Id4+/- and Id4+/+ mice. Expression of Id1, Sox9, Myc, androgen receptor, Akt, p-Akt, Pten and Nkx3.1 was investigated by immunohistochemistry. Androgen receptor binding on NKX3.1 promoter was studied by chromatin immuno-precipitation. Id4 was …

Post-Prandial Upright Exercise Echocardiography In Hypertrophic Cardiomyopathy, Ellina C. Feiner Md, Milla Arabadjian Fnp, Glenda Winson Rn, Bette Kim Md, Farooq Chaudhry Md, Mark V. Sherrid Md

Department of Medicine

No abstract provided.