Digital Commons Network^™

Truvari: Refined Structural Variant Comparison Preserves Allelic Diversity, Adam C English, Vipin K Menon, Richard A Gibbs, Ginger A Metcalf, Fritz J Sedlazeck

Faculty, Staff and Students Publications

The fundamental challenge of multi-sample structural variant (SV) analysis such as merging and benchmarking is identifying when two SVs are the same. Common approaches for comparing SVs were developed alongside technologies which produce ill-defined boundaries. As SV detection becomes more exact, algorithms to preserve this refined signal are needed. Here, we present Truvari-an SV comparison, annotation, and analysis toolkit-and demonstrate the effect of SV comparison choices by building population-level VCFs from 36 haplotype-resolved long-read assemblies. We observe over-merging from other SV merging approaches which cause up to a 2.2× inflation of allele frequency, relative to Truvari.

2022 Draft Final Butte Reduction Works (Brw) Smelter Area Mine Waste Remediation And Contaminated Groundwater Hydraulic Control Site Organic Pollutant Surface Water Sampling Quality Assurance Project Plan (Qapp), Pioneer Technical Services, Inc.

Silver Bow Creek/Butte Area Superfund Site

No abstract provided.

Method And System For Bi Cube Refresh Automation, Pradeep Kumar M K, Velkumar Thangavel, Abinaya Solaiyan, Chia-Chih Lu, Kumar Reddy

Defensive Publications Series

The present disclosure relates to a system for BI cube refresh automation. In the present disclosure, initially the status of the I-server 107 is determined. Once the I-server is active, the cube refresh automation system 103 may back-up the old workflow logs and deletes the old workflow logs from one or more data cubes 101. Further, the cube refresh automation system may split the insertion of new workflow logs into clustered server and then merges the insertion results from the clustered servers. The merger insertion results are further monitored. Upon successful insertion, the insertion trigger is deleted. When the insertion …

Politeness Strategies In Hotel Service Encounters In Jordan: Giving Directives, Mahmoud Rababah, Shatha Al Zoubi, Mohammed Al Masri, Mohammad Al-Abdulrazaq

Association of Arab Universities Journal for Arts مجلة اتحاد الجامعات العربية للآداب

This paper examines directive speech act performed by hotel service counters staff in Jordan. It investigates the politeness strategies employed by staff when they give their directives to hotel foreign guests. The data were collected through audiorecording interactions that occurred between the staff, who are nonnative speakers of English, and foreign guests. Findings from the study show that the directives issued by the staff are characterized by significant directness. The study argues that such directives can be perceived as blunt and discourteous and therefore capable of causing face-threat to the interactants. This principally refers to the fact that they appear …

The Jordanian Daily News Paper Coverage Of The Crisis Snow Storm "Jana": Analysis Study, Ghalib Shatnawi

Association of Arab Universities Journal for Arts مجلة اتحاد الجامعات العربية للآداب

This study aimed to know how the daily Jordanian newspapers covered the crisis of the snowstorm "jana". Using the content analysis as a method, the study analyzed materials about the crisis published in three main daily newspapers: Al-Rai , Addustour and Al-ghad through the period between 19 feb2015-22 feb of the same year. The study reached the following results: 1. News items came first with of the percentage of (17.8%) then the report with the percentage of (21.5%). 2. The Jordanian newspapers depended on several sources on its coverage.Its sources came first with the percentage of (63.6%) , then the …

New Worm On The Block: Planarians In (Neuro)Toxicology, Danielle Ireland, Eva-Maria S. Collins

Biology Faculty Works

Traditional mammalian testing is too time- and cost-intensive to keep up with the large number of environmental chemicals needing assessment. This has led to a dearth of information about the potential adverse effects of these chemicals, especially on the developing brain. Thus, there is an urgent need for rapid and cost-effective neurotoxicity and developmental neurotoxicity testing. Because of the complexity of the brain, metabolically competent organismal models are necessary to understand the effects of chemicals on nervous system development and function on a systems level. In this overview, we showcase asexual freshwater planarians as an alternative invertebrate (“non-animal”) organismal model …

Relationship Between Live-In Grandparents And Grandchild’S Health And Well-Being In Palestinian Refugees In Lebanon, Olfat B. Sheikomar, Hala Ghattas Ph.D., Nadine R. Sahyoun

Faculty Publications

Grandparents (GP) play influential roles in grandchildren’s health, behavior, and life. However, this relationship has not been examined in the Arab region. This study assesses whether the presence of GP in the household is associated with grandchildren’s health and wellbeing. Health status was determined by a child experiencing chronic health conditions or an acute illness, and wellbeing was determined based on school attendance and child labor. Data were collected through surveys conducted in 2010 and 2015 of representative samples of Palestinian refugees living in Lebanon. Multivariate logistic regression showed that, even after controlling for potential confounders, including the presence of …

Perampanel: A Monotherapy In Drug Resistant Epilepsy In Autism Spectrum Disorder, Saumya Mittal, Hompriya Issar

Manipal Journal of Medical Sciences

Autism Spectrum Disorder (ASD) is a neurodevelopmental condition. The patients of this disorder have impaired communication, and repetitive stereotypical atypical behavior with restricted interests and social behavior. Autism is not a single disease. It includes a spectrum of conditions. All types of seizures can be noted in epileptic seizures in people with ASD, the most common being focal seizures. Other types of seizures seen frequently include generalized seizures, absence seizures, etc. Commonly these children respond well to valproate, lamotrigine or levetiracetam. Perampanel (PER) is a noncompetitive antagonist of the a-amino-3-hydroxy-5-methyl-4-isoxazoleproprionic acid receptor. It is approved for the treatment of focal …

Hearing Loss And Cortical Atrophy: A Case Study, Nithin Anand Kottikkulam, Sinju P. Kandathil, Badarunisa Mohamad Basheer

Manipal Journal of Medical Sciences

Background Cerebral atrophy results from the loss of neurons and their connections with the brain. As dementia progresses, an increasing number of neural connections die off. Brain atrophy may potentially damage hearing capacity through the impairment of primary and secondary auditory centres which are located in the temporal lobe. While there is no proven evidence or definitive evidence that hearing loss results in cognitive decline and mental health issues, there is definitely some connection and several clues that experts are looking into.Through this case report, the occurrence of ARHL with a mild dementia is been highlighted. Documenting such cases would …

Diverse Monogenic Subforms Of Human Spermatogenic Failure, Liina Nagirnaja, Wu-Lin Charng, Christina A Gurnett, Kenan R Omurtag, Et Al.

2020-Current year OA Pubs

Non-obstructive azoospermia (NOA) is the most severe form of male infertility and typically incurable. Defining the genetic basis of NOA has proven challenging, and the most advanced classification of NOA subforms is not based on genetics, but simple description of testis histology. In this study, we exome-sequenced over 1000 clinically diagnosed NOA cases and identified a plausible recessive Mendelian cause in 20%. We find further support for 21 genes in a 2-stage burden test with 2072 cases and 11,587 fertile controls. The disrupted genes are primarily on the autosomes, enriched for undescribed human "knockouts", and, for the most part, have …

The New Venue Of ‘Manipal Journal Of Medical Sciences’, Murlimanju Bv, Krishnananda Prabhu

Manipal Journal of Medical Sciences

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Patient Factors Impacting Perioperative Outcomes For T1b-T2 Localized Renal Cell Carcinoma May Guide Decision For Partial Versus Radical Nephrectomy, Yash B Shah, Rishabh K Simhal, Kerith Wang, Hanan Goldberg, Costas D. Lallas, Thenappan Chandrasekar

Department of Urology Faculty Papers

There remains debate surrounding partial (PN) versus radical nephrectomy (RN) for T1b-T2 renal cell carcinoma (RCC). PN offers nephron-sparing benefits but involves increased perioperative complications. RN putatively maximizes oncologic benefit with complex tumors. We analyzed newly available nephrectomy-specific NSQIP data to elucidate predictors of perioperative outcomes in localized T1b-T2 RCC. We identified 2094 patients undergoing nephrectomy between 2019-2020. Captured variables include surgical procedure and approach, staging, comorbidities, prophylaxis, peri-operative complications, reoperations, and readmissions. 816 patients received PN while 1278 received RN. Reoperation rates were comparable; however, PN patients more commonly experienced 30-day readmissions (7.0% vs. 4.7%, p = 0.026), bleeds …

Anti-Cancer Mechanisms Of Action Of Therapeutic Alternating Electric Fields (Tumor Treating Fields [Ttfields]), Shadi Shams, Chirag B Patel

Faculty, Staff and Student Publications

Despite improved survival outcomes across many cancer types, the prognosis remains grim for certain solid organ cancers including glioblastoma and pancreatic cancer. Invariably in these cancers, the control achieved by time-limited interventions such as traditional surgical resection, radiation therapy, and chemotherapy is short-lived. A new form of anti-cancer therapy called therapeutic alternating electric fields (AEFs) or tumor treating fields (TTFields) has been shown, either by itself or in combination with chemotherapy, to have anti-cancer effects that translate to improved survival outcomes in patients. Although the pre-clinical and clinical data are promising, the mechanisms of TTFields are not fully elucidated. Many …

Feature Selection And Machine Learning Approach For Carotid Atherosclerosis In Asymptomatic Adults, Tao Liang, Qiao-Li Wang, Xiao-Qin Liu, Zhen Zhou, Scott Lowe, Zi-Heng Chen, Chenyu Sun

Student Publications

Objective: The presence of carotid atherosclerosis reflects the overall atherosclerotic load and may predict cardiovascular and cerebrovascular accidents. Studies have reported risk factors for carotid atherosclerosis. However, few practical models have been established to predict carotid atherosclerosis risk. Thus, this study was conducted to investigate important features of carotid atherosclerosis and to propose a machine learning-based method for predicting carotid atherosclerosis in asymptomatic adults.

Methods: Cross-sectional study was conducted using routine medical check-up data of individuals from January 2019 to January 2020. Pearson’s correlation analysis was performed to correlate the features. Then, features were selected by python’s feature-selection library and …

Kidney Proximal Tubule Glut2-More Than Meets The Eye, Majdoleen Ahmad, Ifat Abramovich, Bella Agranovich, Alina Nemirovski, Eyal Gottlieb, Liad Hinden, Joseph Tam

Faculty, Staff and Student Publications

Tubulopathy plays a central role in the pathophysiology of diabetic kidney disease (DKD). Under diabetic conditions, the kidney proximal tubule cells (KPTCs) are exposed to an extensive amount of nutrients, most notably glucose; these nutrients deteriorate KPTCs function and promote the development and progression of DKD. Recently, the facilitative glucose transporter 2 (GLUT2) in KPTCs has emerged as a central regulator in the pathogenesis of DKD. This has been demonstrated by identifying its specific role in enhancing glucose reabsorption and glucotoxicity, and by deciphering its effect in regulating the expression of the sodium-glucose transporter 2 (SGLT2) in KPTCs. Moreover, reduction/deletion …

The Diagnostic Performance Of Ultrasonography In The Evaluation Of Extrathyroidal Extension In Papillary Thyroid Carcinoma: A Systematic Review And Meta-Analysis, Peter P. Issa, Aaron L. Albuck, Eslam Hossam, Mohammad Hussein, Mohamed Aboueisha, Abdallah S. Attia, Mahmoud Omar, Seif Abdelrahman, Gehad Naser, Robert D.E. Clark, Eman Toraih, Emad Kandil

School of Medicine Faculty Publications

Extrathyroidal extension (ETE) in patients with papillary thyroid carcinoma (PTC) is an indication of disease progression and can influence treatment aggressiveness. This meta-analysis assesses the diagnostic accuracy of ultrasonography (US) in detecting ETE. A systematic review and meta-analysis were performed by searching PubMed, Embase, and Cochrane for studies published up to April 2022. The pooled sensitivity, specificity, and diagnostic odds ratio (DOR) were calculated. The areas under the curve (AUC) for summary receiver operating curves were compared. A total of 11 studies analyzed ETE in 3795 patients with PTC. The sensitivity of ETE detection was 76% (95%CI = 74–78%). The …

Management Of Transgender Patients In Critical Care, L Flower, A Cheung, S Connal, Et Al

Peninsula Medical School

As clinicians working in critical care, it is our duty to provide all of our patients with the high-quality care they deserve, regardless of their gender identity. The transgender community continues to suffer discrimination from the media, politicians and general public. As healthcare workers we often pride ourselves on our ability to safely care for all patients. However, there remains a distinct lack of understanding surrounding the care of critically ill transgender patients. This is likely in part because the specific care of transgender patients is not included in the Faculty of Intensive Care Medicine’s, Royal College of Anaesthetists’, Royal …

Saint Jude's, December 25, 2022

Saint Jude's

A newsletter published for Deaf Catholics in Waltham, MA

Saint Jude's Finding Aid

Association Of Smoking With Total Oxidant And Antioxidant Levels In Breast Milk, Nesibe Yildiz, Adnan Yilmaz

Makara Journal of Health Research

Background: Breast milk is a natural food that contains all the fluids, energy, and nutrients necessary for the optimum growth and development of newborns. Smoking is a public health problem that has harmful effects on the mother and baby. This study aimed to examine the association of exposure to smoking with total oxidant status (TOS) and total antioxidant status (TAS) in breast milk.

Methods: Healthy mothers without any health problems during their pregnancy and lactation periods were selected as subjects. Eighty-eight milk samples (44 in the smoking group and 44 in the nonsmoking group) were examined. TOS and …

Ratio Of Vascular Pedicle Width And Thoracic Diameter To Differentiate Cardiogenic And Non-Cardiogenic Pulmonary Edema, Rahmi Afifi, Achmad Fachri, Amir Sjarifuddin Madjid, Joedo Prihartono, Marcel Prasetyo, Andreas Christian

Makara Journal of Health Research

Background: Excess intravascular volume evaluation is essential in the intensive care unit (ICU); however, clinical information to differentiate cardiogenic and non-cardiogenic pulmonary edema has been proven ineffective. Thus, this study aimed to distinguish cardiogenic from non-cardiogenic pulmonary edema using the ratio of vascular pedicle width (VPW) to thoracic diameter (VPTR).

Methods: This cross-sectional study was conducted based on secondary data from chest radiographs of 100 patients with clinical symptoms of pulmonary edema in the ICU from January 2013 to December 2015. Cardiogenic and non-cardiogenic pulmonary edema were distinguished using VPW and cardiothoracic ratio measurements (CTR). VPTR was measured …

Daily Living Assistance Provided By Residents To Other Residents In Residential Aged Care Homes: Knowledge, Attitudes, And Practices, Siti Noraini Asmuri, Masne Kadar, Nor Afifi Razaob, Chai Siaw Chui, Hanif Farhan Mohd Rasdi

Makara Journal of Health Research

Background: The rise of the aged population in Malaysia has resulted in the increased need for services, especially in terms of healthcare. Hence, continuous support is crucial to managing the daily living activities of this group. This study aimed to identify the knowledge, attitudes, and practices of older adults residing in Malaysian aged care homes concerning daily living activities and their provision of assistance to other residents with more significant disabilities.

Methods: Semi-structured interviews were conducted on ten older adults and six staff members of two selected residential aged care homes. The interview session concerned the knowledge, attitudes, …

Potential Antihyperlipidemia Effect Of Lactoferrin In Hyperlipidemia-Induced Male Sprague–Dawley Rats, Louis Fabio Jonathan Jusni, Valencia Chandra, Tena Djuartina, Dion Notario, Zita Arieselia, Linawati Hananta

Makara Journal of Health Research

Background: Hyperlipidemia is a condition that is characterized as an increase in total cholesterol and triglyceride levels in the blood. Lactoferrin is a protein that can serve as an antioxidant. This study aims to determine whether lactoferrin can reduce total cholesterol and triglyceride levels.

Methods: This study used 24 Sprague–Dawley rat strains, which were divided into six groups: normal group; negative control; positive control; and dose groups 1, 2, and 3. The normal group was given standard feed, whereas the other group was given high cholesterol and fat. The positive control group and dose groups 1, 2, and …

Manuka Honey Reduces The Virulence Of Pectobacterium Brasiliense By Suppressing Genes That Encode Plant Cell Wall-Degrading Enzymes, Ava Sheila, Subandiyah Siti, Rohman Muhammad Saifur, Ogawa Naoto, Joko Tri

ASEAN Journal on Science and Technology for Development

The primary virulence of soft rot pectobacteria, including Pectobacterium brasiliense, is mainly determined by the massive production of plant cell wall-degrading enzymes (PCWDEs), which promote plant tissue maceration in many crops. The antibiotic treatment to treat bacterial soft rot causes environmental problems and potentially affects resistance. Antibiotic resistance is driving interest in antimicrobial treatments, and no organism has been reported to have acquired resistance to honey. However, the use of honey as a therapeutic agent for plant bacterial pathogens has rarely been studied. Therefore, this study was undertaken to determine the in vitro effect of Manuka honey against P. brasiliense …

Do Green Policies Produce Green Jobs?, Neal Woods, Jiyoon Kang, Morgan A. Lowder

Faculty Publications

Objective

We examine the relationship between clean energy policies and green job growth.

Methods

Using a set of meta-regression analyses, we assess the green job creation performance of a wide variety of policies in the American states.

Results

Our findings indicate that renewable portfolio standards and public benefit funds are systematically associated with increases in green jobs, although the effects of other policy tools are ambiguous at best. Effect estimates in the existing literature are significantly driven by how the dependent and core independent variables are measured.

Conclusion

Overall, our findings suggest that some policies may be an effective component …

Gender Dysphoria In Adolescents With Ehlers-Danlos Syndrome., Jordan T. Jones, William R. Black, Christine Moser, Eric T. Rush, Lindsey Malloy-Walton

Manuscripts, Articles, Book Chapters and Other Papers

OBJECTIVES: Ehlers-Danlos Syndrome represents a family of heritable connective tissue disorders that include joint hypermobility, tissue fragility, and skin hyperextensibility. Ehlers-Danlos Syndrome presents with clinical sequela across multiple body systems that require multidisciplinary care. Little is known about adolescents with Ehlers-Danlos Syndrome who are transgender and gender diverse. To date, there have been no reports of transgender and gender diverse youth in pediatric patients with Ehlers-Danlos Syndrome. The objective of this study was to characterize transgender and gender diverse adolescents with Ehlers-Danlos Syndrome seen in a pediatric multidisciplinary specialty clinic.

METHODS: A retrospective chart review was performed and it was …

Role Of Adenylyl Cyclase Type 7 In Functions Of Bv-2 Microglia, Yawen Hu, Rebecca A. Hill, Masami Yoshimura

School of Medicine Faculty Publications

To assess the role of adenylyl cyclase type 7 (AC7) in microglia’s immune function, we generated AC7 gene knockout (AC7 KO) clones from a mouse microglial cell line, BV-2, using the CRISPR-Cas9 gene editing system. The ability of BV-2 cells to generate cAMP and their innate immune functions were examined in the presence or absence of ethanol. The parental BV-2 cells showed robust cAMP production when stimulated with prostaglandin-E1 (PGE1) and ethanol increased cAMP production in a dose-dependent manner. AC7 KO clones of BV-2 cells showed diminished and ethanol-insensitive cAMP production. The phagocytic activity of the parental BV-2 cells was …

Mechanical Ventilation In Patients With Cardiogenic Pulmonary Edema: A Sub-Analysis Of The Lung Safe Study, Laura Amado-Rodríguez, Raquel Rodríguez-Garcia, Giacomo Bellani, Tài Pham, Eddy Fan, Fabiana Madotto, John G Laffey, Guillermo M Albaiceta, Lung Safe Investigators

Faculty, Staff and Student Publications

BACKGROUND: Patients with acute respiratory failure caused by cardiogenic pulmonary edema (CPE) may require mechanical ventilation that can cause further lung damage. Our aim was to determine the impact of ventilatory settings on CPE mortality.

METHODS: Patients from the LUNG SAFE cohort, a multicenter prospective cohort study of patients undergoing mechanical ventilation, were studied. Relationships between ventilatory parameters and outcomes (ICU discharge/hospital mortality) were assessed using latent mixture analysis and a marginal structural model.

RESULTS: From 4499 patients, 391 meeting CPE criteria (median age 70 [interquartile range 59-78], 40% female) were included. ICU and hospital mortality were 34% and 40%, …

Temporal Changes In Extracellular Vesicle Hemostatic Protein Composition Predict Favourable Left Ventricular Remodeling After Acute Myocardial Infarction, Xiong Chang Lim, Chenyuan Huang, Siti Maryam J.M. Yatim, Suet Yen Chong, Sock Hwee Tan, Xiaoxun Yang, Caryn L. Heidt, Jodi Pedersen, Michael Talanker, Harshvardhan Modh, Matthias G. Wacker, Giorgia Pastorin, Siew Pang Chan, A. Mark Richards, Chris J. Charles, Mark Y. Chan, Jiong Wei Wang

Michigan Tech Publications, Part 1

The subset of plasma extracellular vesicles (EVs) that coprecipitate with low-density lipoprotein (LDL-EVs) carry coagulation and fibrinolysis pathway proteins as cargo. We investigated the association between LDL-EV hemostatic/fibrinolysis protein ratios and post-acute myocardial infarction (post-AMI) left ventricular (LV) remodeling which precedes heart failure. Protein concentrations of von Willebrand factor (VWF), SerpinC1 and plasminogen were determined in LDL-EVs extracted from plasma samples obtained at baseline (within 72 h post-AMI), 1 month and 6 months post-AMI from 198 patients. Patients were categorized as exhibiting adverse (n = 98) or reverse (n = 100) LV remodeling based on changes in LV end-systolic volume …

Perceived Stress And Its Relationship To Moral Resilience Among Nurses In The Hail Region, Saudi Arabia, Hamdan Albaqawi, Maha Sanat Alrashidi

Makara Journal of Health Research

Background: This study aimed to determine the relationship between perceived stress and moral resilience among nurses.

Methods: The researcher used a quantitative–comparative correlational study design that utilized a self-administered questionnaire with 393 nurse participants in the Hail Region, Saudi Arabia. Adapted questionnaires were distributed through Google Form survey. Data collection was conducted between October and November 2021.

Results: The nurses were moderately stressed (21.69/30) but morally resilient (2.74/4). Perceived stress scale (p < 0.033) and moral resilience (p < 0.25) were found to be significantly associated with gender. The designated ward and age were not significantly associated with perceived stress and moral resilience. Conversely, the years of experience showed a significant association with perceived stress (p < 0.038) but not with moral resilience (p > 0.255). Finally, no relationship was observed between perceived stress and moral resilience (p > 0.248).

Conclusions: The nurses were perceived …

Caregivers Of Elderly With Moderate To Total Dependence In Activities Of Daily Living In Yogyakarta Indonesia: Correlation Of Burden And Quality Of Life, The Maria Meiwati Widagdo, Lise Insani Gulo, Herose Cendrasilvinia, Widya Christine Manus

Makara Journal of Health Research

Background: Aging is accompanied by a functional decline leading to the loss of independence in conducting activities of daily living. The dependence of the elderly can cause burden that affects the quality of life of caregivers. This study aimed to assess the correlation between the burden and quality of life of caregivers looking after moderately to totally dependent elderly.

Methods: This research is a cross-sectional study that used Zarit Burden Interview to assess caregiver burden and World Health Organization Quality of Life to measure the quality of life of people caring for elderly with moderate to total dependence …