Digital Commons Network^™

Gut Microbiome Metagenomics In Clinical Practice: Bridging The Gap Between Research And Precision Medicine, Henok Ayalew Tegegne, Tor C Savidge

Faculty, Staff and Students Publications

Gut microbiome metagenomics is emerging as a cornerstone of precision medicine, offering exceptional opportunities for improved diagnostics, risk stratification, and therapeutic development. Advances in high-throughput sequencing have uncovered robust microbial signatures linked to infectious, inflammatory, metabolic, and neoplastic diseases. Clinical applications now include pathogen detection, antimicrobial resistance profiling, microbiota-based therapies, and enterotype-guided patient stratification. However, translation into routine care is hindered by significant barriers including methodological variability, limited functional annotation, lack of bioinformatics standardization, and underrepresentation of global populations. This review synthesizes current translational strategies, emphasizing the need for hypothesis-driven designs, multi-omic integration, longitudinal and multi-center cohorts, and mechanistic validation. …

Coolies Of Shimla: Modern Slavery As Relic Of The British Raj, Priya Kapoor

Politics and Global Affairs Faculty Publications and Presentations

Coolie labor needs to be understood as a contemporary transnational practice rooted in local practices of feudal kings and the British Empire. When the British Raj established Shimla as its summer capital in 1864, they did not eliminate archaic labor practices; instead, they cleverly modified them to serve the Empire’s infrastructural needs. Under the guise of reform, the British introduced nominal pay to bypass anti-slavery laws, effectively rebranding the forced laborer as the "coolie"—a racialized linguistic construct that signified a state of permanent subalternity. This labor force was the veritable backbone of the Raj, manually carving the treacherous Hindustan-Tibet Road …

Us Drug Policy Does Not Align With Experts’ Rankings Of Drug Harms: A Multi-Criteria Decision Analysis, Michael Broman, Alan K Davis, Stacey Armstrong, Adam Levin, Kaltum Ahmed, Gustavo A Angarita, Brooke J Arterberry, Cecilia Bergeria, Mitch Earleywine, Kathryn S Gex, Tom Gregoire, Jamey J Lister, David S Mathai, Nicky J Mehtani, Nathan Menke, Charles D Nichols, Hillary Shaub, Alayna P Tackett, Brandon Weiss, Nefize Yalin, Lawrence D Phillips

Faculty, Staff and Students Publications

Background: United States drug policy is primarily based on the Controlled Substances Act of 1970 and largely contradicts scientific evidence about how to mitigate drugs’ harms. Expert consensus on drug harms could inform policy that improves the health of people who use drugs while reducing negative societal impacts of drug use. Therefore, this study adapted and extended the relevant 2010 United Kingdom multi-criteria decision analysis, rating drug harms by criteria comprising health and social impacts to people who use drugs and their families, communities, and society.

Methods: Seventeen experts on drug use in the US, including three with lived experience …

Nutrition Support Adequacy In Children With Biliary Atresia After Liver Transplant, Nicole Knebusch, Manpreet Virk, Moreshwar S Desai, Marwa Mansour, Stacey Beer, Brittany Pearo, Kelby Fuller, Krupa Mysore, John Goss, Thomas Fogarty, Fernando Stein, Jorge A Coss-Bu

Faculty, Staff and Students Publications

No abstract provided.

Going Nuclear: Exploring Mtor’S Transcriptional Role In Regulating Estrogen Receptor Positive Breast Cancer, Alek S. Torres

NYMC Student Theses and Dissertations

Global changes in gene expression are orchestrated by an array of transcription factors regulated by both extracellular and intracellular signals. The mechanistic target of rapamycin (mTOR) is a protein kinase that ubiquitously mediates signaling networks across every cell type, in two active complexes, mTORC1 and mTORC2. By phosphorylating its downstream targets, these classically cytosolic complexes regulate protein homeostasis, metabolism, cell growth, proliferation and survival. However, evidence from prostate cancer studies reveals mTOR and its partners can occupy the nucleus, where its interaction with chromatin (in complex with transcription factors) has been shown to regulate gene expression at the level of …

Personalized Postpartum Interventions And Their Impact On Working Mothers, Mey Elisa Safitri, Aniza Abd. Aziz, Nurulhuda Mat Hassan

Media Kesehatan Masyarakat Indonesia

Exclusive breastfeeding is a critical determinant in maintaining infant health and nutritional status. However, its coverage remains low, particularly among postpartum working mothers. Limited maternal knowledge, lack of family especially spousal support, and low maternal satisfaction are reported key factors contributing to suboptimal breastfeeding practices. This quasi-experimental study employed a non-equivalent control group pre-test and post-test design. It was conducted from January to October 2024 in the working area of the Darussalam Primary Health Center in Medan, Indonesia. A total of 140 postpartum working mothers were purposively selected and divided into two groups: intervention (n=70) and control (n=70). The intervention …

Developing The Community Outreach Effectiveness Model (Coem) For Hiv Prevention Among Key Populations In Indonesia: Evidence From The Ibbs, Lely Wahyuniar, Aang Sutrisna, Dimas Budi Wicaksana, Rizky Habsi

Media Kesehatan Masyarakat Indonesia

Indonesia continues to experience a concentrated HIV epidemic, with key populations female sex workers, men who have sex with men, transgender women, and people who inject drugs bearing a disproportionate burden, while uptake of HIV prevention services and sustained behavior change remain inadequate. Community outreach has been widely implemented to address these gaps; however, its effectiveness has not been comprehensively documented at the national level. This study aimed to assess the impact of community outreach interventions on HIV prevention uptake and behavioral outcomes among key populations in Indonesia using the Community Outreach Effectiveness Model (COEM). A quantitative retrospective study was …

Evaluation Of Anthropometric Data Quality For Children From Electronic-Based Nutrition Surveillance: A Case Study In Magelang Regency, Central Java, Indonesia, Slamet Riyanto, Digna Niken Purwaningrum, Lutfan Lazuardi

Media Kesehatan Masyarakat Indonesia

Data quality regarding the nutritional status of children under five is crucial for developing strategies to address nutritional issues. This study aims to develop indicators and assess the quality of anthropometric data from community-based nutrition surveillance using the EPPGBM application in Magelang Regency. The research employed an observational design with a quantitative approach. Data quality indicators were defined based on expert consensus using the Delphi method. These indicators were also used to construct an anthropometric data quality index (IKDA). The WPS Office spreadsheet was utilized to assess data quality and perform IKDA calculations. Nine data quality indicators were identified, categorized …

Eata Mediated Degradation Of Intestinal Mucus Is Species-Specific And Driven By Muc2 Structural Features, Sergio Trillo-Muyo, Brendan Dolan, Frida Svensson, Tim J Vickers, Liisa Arike, Maria-Jose García-Bonete, Jenny K Gustafsson, Mathias I Nielsen, Hans H Wandall, James M Fleckenstein, Gunnar C Hansson, Sjoerd Van Der Post

2020-Current year OA Pubs

Enterotoxigenic Escherichia coli (ETEC) infections are a leading cause of diarrheal illness, responsible for an estimated 100,000 deaths annually. ETEC pathogenesis is driven by various virulence factors, including toxins, adhesins, and noncanonical factors such as the protease EatA. The first line of host defense against intestinal pathogenic bacterial infections is the protective intestinal mucus layer. Here, we demonstrate the mechanism by which EatA degrades the core mucus component MUC2, thereby facilitating access to the epithelial cell surface and promoting infection. We identify the specific cleavage site region localized at the C-terminal of MUC2. EatA's protease activity depends on the interaction …

Membrane Il-18 Identifies A Human Macrophage Subset With Distinct Proteomic And Functional Traits, Chiara Vitale, Marco Colonna, Et Al.

2020-Current year OA Pubs

This study contributes to the characterization of human macrophages in normal and pathological conditions such as cancer. We characterized a macrophage population expressing membrane-associated IL-18 (mIL-18) that shows peculiar proteomic, phenotypic, ultrastructural, and functional properties. mIL-18+ macrophages exhibit increased levels of key proteins involved in pathogen recognition, activation, migration, and endocytosis. They also display specialized functions in vesicle and actin filament transport and lipid metabolism, and have typical mitochondrial traits. Importantly, mIL-18+ cells dominate the peritoneal fluid of adult cancer patients and are present in the bone marrow of children with neuroblastoma. They express high levels of TREM2 but display …

Harmonizing Self-Reported And Free Text Medication Data: A Reproducible Pipeline For Gerontological Research, Ramkrishna K Singh, Chen Chen, Semere Bekena, David C Brown, Kaylin Taylor, Matthew Blake, Yiqi Zhu, Kebede Beyene, David B Carr, Ganesh M Babulal

2020-Current year OA Pubs

BACKGROUND: Self-reported medication data collected as free text in gerontological and dementia research is often unstructured with inconsistent formatting. These circumstances pose a challenge for standardization and classification when preparing effective, reproducible analyses. Spelling variations, naming conventions, and reporting drug combinations can hinder mapping to standard pharmacologic vocabularies and compromise medication exposure assessments. We aimed to develop and implement a transparent, reproducible, and scalable data harmonization pipeline that ingests free-text medication records and classifies them according to American Hospital Formulary Service (AHFS) therapeutic categories. METHODS: A four-phase curation pipeline processed 30,062 Research Electronic Data Capture (REDCap) medication records collected over …

Ultrasound-Guided Diffuse Optical Tomography: An Adjunct To Ultrasound That Can Reduce Unnecessary Breast Biopsies, Quing Zhu, Debbie Bennett, Ian S Hagemann, Jaimee Mannix, Kimberly Wiele, Megan Luther, Jingqin Luo, Steven P Poplack

2020-Current year OA Pubs

BACKGROUND: Breast biopsy is recommended for any lesion in which the radiologist deems the likelihood of malignancy to be greater than 2% and more than 75% of biopsies return with benign results. This study assesses whether the total hemoglobin concentration (HbT) and blood oxygen saturation (%sO2) of malignant and benign breast lesions, obtained using Ultrasound-guided diffuse optical tomography (US-guided DOT), can help reduce benign breast biopsy rates. METHODS: 238 women consecutively recruited were examined with US-guided DOT before their US-guided biopsy. Three or four radiologists independently provided BI-RADS assessments using pre-procedure US and mammography (when available), first without and then …

Cost Of Illness Analysis In Total Knee Replacement At Public Hospital Jenderal Ahmad Yani, Lampung, Indonesia, Dina Fatma Alia, Dwi Endarti, Tri Murti Andayani

Jurnal Ekonomi Kesehatan Indonesia

Total knee replacement (TKR) is one of the most economical and frequently successful orthopedic procedures. Cost-of-illness studies of TKR in Indonesia are scarce and lack an analysis of the relationship between characteristics and costs. This study aims to examine the cost-of-illness of TKR from a social perspective and explore the relationship between the characteristics and the cost of TKR. This is an observational cross-sectional study of all patients who underwent TKR from 1st January 2022-31 st December 2023. The characteristics were collected from the medical records. Cost of illness was conducted from a social perspective with a bottom-up approach. Hospital …

Biomarker And Age At Onset Endophenotypes Offer New Insights Into The Genetic Etiology Of Alzheimer’S Disease, Joseph Bradley

Arts & Sciences Graduate Student Theses and Dissertations

Introduction: Alzheimer’s Disease (AD) remains among the top 10 causes of death in the United States and is projected to affect nearly 14 million people by 2050. To this point, studies of Alzheimer’s genetics and endophenotypes have yielded a bounty of results that culminated in the first disease-modifying drugs, lecanemab and donanemab, in 2022. Most of the genetic studies for Alzheimer’s disease to date have been focused on late-onset AD or Autosomal dominant AD, leaving a critical need for studying sporadic early-onset AD (EOAD; ~10% of cases). Furthermore, the demand for clinical portability has created a need for high-sensitivity proteomic …

Adaptive Retry Solutions For Recurrent Payment Decline Using Generative Artificial Intelligence, Alok Roy, Prajna Shetty, Vinay Sarda, Katyayani Kiranmayee Kolluru

Defensive Publications Series

The present disclosure provides a method and a system for adaptive retry solutions for recurrent payment transactions. The method comprises identifying the reason for decline of recurrent payment transactions, storing the declined transaction and subscribing to the issuer system based on the identified reason. The method further comprises predicting the future timestamp for successful retry attempts for declined recurrent payment transaction based on transaction history, and issuer rules. Furthermore, the method comprises transmitting the notification of predicted timestamp to the user devices and executing the retry attempt for declined recurrent payment transaction in the predicted timestamp. Further, transmitting the status …

Cycle-By-Cycle Current Limit Method For Unregulated Intermediate Bus Converters, N/A

Defensive Publications Series

This publication describes methods and circuits for limiting current in unregulated Intermediate Bus Converters (IBCs). The technology addresses issues related to parallel operation of low-impedance converters, where impedance mismatches can lead to significant current imbalances and transitory current spikes. By utilizing a cycle-by-cycle input charge control mechanism, the system can detect over-current conditions and temporarily increase the switching frequency to clamp the input current. This approach effectively uses the resonant capacitor voltage, which represents the integral of the input current, to trigger switching events. The system may further incorporate frequency compensation to ensure consistent current regulation across varying switching frequencies …

Diagnostic Significance Of Aspartate Transaminase And Alanine Transaminase In Hepatitis C Patients, Mohammed N. Fenjan, Ahmed Abdulhadi Jabbar

AUIQ Conference Proceedings

Background: Hepatitis C infection is spreading worldwide at an alarming rate. Hepatitis C is a viral infection that affects the liver. It is caused by the hepatitis C virus and can lead to liver damage, cirrhosis, and even liver cancer if left untreated. The virus is usually spread through contact with infected blood, such as through sharing needles or receiving a blood transfusion, antiviral medications can be used to treat the infection. AST (aspartate aminotransferase) and ALT (alanine aminotransferase) are enzymes that are primarily found in liver cells. The present study aimed to assess the relationship between liver enzymes aspartate …

Effects Of Different Chitosan Coated Tio2 Nanoparticles Concentrations On The Antibacterial Activities, Ali M. Ghazi, Murtadha H. Hashem, Hyder K. Abbood

AUIQ Conference Proceedings

This study aimed to determine how the composition and antibacterial properties of chitosan-based coating solution when treated with varying amounts of titanium dioxide (TiO2) nanoparticles (NPs). Scanning electron microscopy (SEM) analysis showed that the modified TiO2 NPs were evenly distributed throughout the chitosan matrix. UV-V_spectra, X-ray diffraction (XRD) and Fourier transform infrared spectroscopy (FTIR) analyses demonstrated that the chitosan interacted with TiO2 NPs and possessed good compatibility. When tested against Escherichia coli and Staphylococcus aureus, the chitosan-TiO2 nanocomposite proved to be an effective growth inhibitor. The inhibition zone for the antibacterial activity of the chitosan-TiO2 nanocomposites was (19.86 …

Nanomaterial Strategies For High-Performance Solid-State Batteries Beyond Lithium-Ion, Mahmoud Gharbavi, Salim Albukhaty

AUIQ Conference Proceedings

This is a comprehensive review of nanomaterial strategies for developing solid-state batteries in the future beyond lithium-ion technology. It discusses key challenges such as ionic conductivity, interfacial stability, and scalable manufacturing. Nanomaterials provide the ultimate means to control electrochemical processes at atomic scales, enabling solid-state systems with energy densities above 500 Wh/kg, enhanced safety from non-flammable electrolytes, and longer cycle life.

The review offers an in-depth analysis of advanced manufacturing methods, including suspension plasma spray (SPS), atomic layer deposition (ALD), and nano-level 3D printing for fabricating nanostructured components. Sulfide solid-state electrolytes demonstrate remarkable ionic conductivities of up to 10^{-2 …}

Nanotechnology-Based Non-Vaccine Prevention And Therapeutics: Advances In Antimicrobial Nanomaterials And Targeted Drug Delivery Systems, Yasmina Khane, Salim Albukhaty

AUIQ Conference Proceedings

Infectious diseases represent a massive one-health issue that needs concerted efforts. One of the most important of these efforts involves investing in nanotechnology and the physical, chemical, and biological properties of nanomaterials to contribute to the diagnosis, treatment, and prevention of infectious diseases. Non-vaccine nanotechnology approaches can enhance conventional methods by blocking infection pathways and bolstering the immune system. This review emphasizes two main aspects: nanomaterials with a natural capability to kill microorganisms—focusing on antimicrobial and antiviral actions—and nano-carrier systems for controlled drug delivery, immune modulation, and inflammation management. It details the functioning of these nanomaterials and their applications, before …

Rapid Detection Of Sheep-Specific Clostridium Perfringens Igg Using Silver Nanoparticle-Boosted Dot-Blot Assays, Ahmed Salam Jawad

AUIQ Conference Proceedings

Dot-blot immunoassay is a quick, simple, and low-cost technique for identifying target analytes in food, clinical diagnostics, and the environment with a visual inspection. For this purpose, silver nanoparticles (AgNPs) were synthesized using a sodium borohydride compound. Synthesized AgNPs were characterized using UV-Vs spectroscopy, scanning electron microscope (SEM), X-ray diffraction (XRD), dynamic light scattering (DLS), and zeta potential (ZP) tests. After that, SNPs were conjugated with anti-CLD N4-C. perfringens IgG. At the same time, the positive and negative C. perfringens samples have been determined using ELISA. Furthermore, PCR test was used for verification of C. perfringens. Consequently, dot-blot …

Utilization Of Biochar From Date Palm For Wastewater Treatment Technologies: Mini-Review, Atheel Alwash, Emad Yousif, Salam Mohammed

Al-Mustaqbal Journal of Sustainability in Engineering Sciences

Recently, recycling agricultural waste has gained great importance in the field of the biochar industry, as it is a sustainable and inexpensive material that can be used to get rid of environmentally polluting materials. Dates are one of the major agricultural wastes in Iraq and the Gulf countries, which include fronds, seeds, and trunks. The challenge of obtaining a green and clean environment is represented by the safe disposal of these residues. These wastes are promising materials for producing biochar products as efficient adsorbents with improved characteristic properties. The present article revises the synthesis of biochar derived from date palm …

Smart Universities And Digital Transformation Based On Artificial Intelligence: A Case Of Al-Mustaqbal University, Ahmed Rasol Hasson

Al-Mustaqbal Journal of Sustainability in Engineering Sciences

Artificial Intelligence (A.I) is a key facilitator of universities procedures. Although the performance of AI has stretch out superior levels in developed countries, it is remain in its insufficiency in a lot of the developing nations. In this state, there is an imperative need to determine the important of adopting AI everywhere on Iraqi universities, due to the continuous utilize of a management old-fashioned systems. This research sight to explore applications that may influence the acceptance and adoption of AI in the Iraqi universities. This is achieved based on a qualitative approach of thematic analysis. The AI applications that were …

Clinical Pathway Sebagai Solusi Keberlanjutan Jkn Di Indonesia: Systematic Review, Septiana Septiana, Siti Soekiswati, Burhannudin Ichsan

Jurnal Ekonomi Kesehatan Indonesia

The National Health Insurance (JKN) program is threatened with a deficit and potential default in 2026 due to inefficiency and the risk of fraud in healthcare facilities. In the context of JKN, which uses a package system (INA-CBG), Clinical Pathway (CP) is a strategic instrument within the JKN system that has dual benefits for both Payers (BPJS Kesehatan) and Providers (Hospitals). For BPJS Kesehatan, CP primarily functions to ensure service quality and prevent undertreatment fraud, the practice of reducing services to benefit hospitals. This prevention ultimately achieves cost efficiency in the JKN program by avoiding payment of complication claims and …

An Intrusion And Cyber-Attack Detection System Based On Ensemble Machine Learning Techniques, Zaed S. Mahdi, Rana M. Zaki, Negar Majma

The Journal of Engineering Research

In light of advancements in information technology, intrusion detection systems (IDS) and cybersecurity are two of the most pressing concerns confronting the world. Despite the fact that many academics have proposed intrusion detection models, the development of intrusion detection systems must be continuous due to the continual growth of cyber-attacks. This research presents a proposal for an intrusion detection model on the network, based on a machine learning ensemble. The first aim in this work is to reduce the number of features used in training the system to reduce the training time through the Double Feature Selection Method by using …

A New Approach For Key Generation Using Lorenz System And Henon Map, Bahaa Abdulwahid Hameed, Ekhlas K.Gbashi

The Journal of Engineering Research

To protect data transmission from theft and disclosure, encryption is necessary. Secure encryption requires a robust system. Often, this system’s strength depends on its key generation. Chaotic systems are used for the key generation process for some reasons, such as precise and random properties. This paper presents a new approach for key generation using two types of chaos theory: the 3D Henon map and the 3D Lorenz system, to enhance the security of a cryptographic system. The proposed algorithm aims to increase the security of cryptographic algorithms and the generation of random and secure key numbers. The results of the …

Detecting Interpolated Video Frames Based On Convolution Neural Networks, Ayat Razaq Abbas, Ekhlas Falih Naser

The Journal of Engineering Research

These days, films are exchanged often and have established themselves in daily lives due to the growing number of handheld video recording devices, social media, and messaging apps. But with a variety of user-friendly video editing programs available, anyone can manipulate videos. The spread of intentionally altered videos can have serious consequences, such as the propagation of false information. Video frames interpolation is detected in this research.The proposed methodology consists of three phases. In the first phase, the video stream is divided into a series of individual frames. Preprocessing follows, which involves resizing these video frames to fixed dimensions of …

Multi-Biometric Recognition System Based On A Specific Set Of Features, Zahraa Naji Razoqi, Raheem Ogla, Abdul Monem S. Rahma

The Journal of Engineering Research

Biometric techniques are replacing traditional passwords and Personal Identification Numbers since they are more dependable and secure. Unimodal biometric systems have various challenges, including non-universality and noisy data. The systems that use multiple modalities of biometrics can help overcome some of these restrictions, but retrieval and matching processes are time-consuming due to the high-dimensional nature of biometric data. This research proposes a serial multi-biometric recognition system using iris and face models based on only 16 features. Iris features are retrieved after splitting the region of interest into (2 × 2) blocks and computing the mean, standard deviation, and energy values …

Event Triggered Integral Sliding Mode Controller Design For Multi-Input Multi-Output Nonlinear System, Mohammed K. Hamzah, Safanah M. Raafat, Shibly A. Al- Samarraie

The Journal of Engineering Research

In this manuscript, the design of event based Integral Sliding Mode Controller Eb-ISMC is considered for a nonlinear system with perturbation. The proposed controller uses a novel triggering strategy which is established according to some stability requirements. The primary benefit of this strategy is the effective usage of the system resources by reducing the total amount of control computations as compared to the classical or periodic version of ISMC. Closed-loop system stability analysis has shown that the suggested controller achieves the practical sliding mode PSM using the developed triggering control scheme. Moreover, Zeno behaviour is circumvented by developing suitable expressions …

N-Queens Problem Solving Using Apiary Organizational-Based Optimization Algorithm, Mais A. Al-Sharqi, Ahmed T. Sadiq Al-Obaidi, Safaa O. Al-Mamory

The Journal of Engineering Research

Researchers have utilised nature-inspired metaheuristic algorithms to find solutions for complex combinatorial optimisation problems and Non-deterministic polynomial (NP) problems. The N-queens problem is categorised as an NP-Hard problem as it becomes insurmountable for large N. This paper proposed a solution for the N-queens problem based on the Apiary Organisational-Based Optimisation Algorithm (AOOA). AOOA is a nature-inspired metaheuristic optimisation algorithm for NP-Hard problems comprised of multiple beehives inside the apiary, each with its population. In contrast to the backtracking method, AOOA employs a fitness function and randomisation techniques through seven stages to approach the optimal distributions of queens so they don’t …