Digital Commons Network^™

Sigma Leverages Protein Structural Information To Predict The Pathogenicity Of Missense Variants, Hengqiang Zhao, Huakang Du, Sen Zhao, Zefu Chen, Yaqi Li, Kexin Xu, Bowen Liu, Xi Cheng, Wen Wen, Guozhuang Li, Guilin Chen, Zhengye Zhao, Guixing Qiu, Deciphering Disorders Involving Scoliosis & Comorbidities (Disco) Study, Pengfei Liu, Terry Jianguo Zhang, Zhihong Wu, Nan Wu

Faculty, Staff and Students Publications

Leveraging protein structural information to evaluate pathogenicity has been hindered by the scarcity of experimentally determined 3D protein. With the aid of AlphaFold2 predictions, we developed the structure-informed genetic missense mutation assessor (SIGMA) to predict missense variant pathogenicity. In comparison with existing predictors across labeled variant datasets and experimental datasets, SIGMA demonstrates superior performance in predicting missense variant pathogenicity (AUC = 0.933). We found that the relative solvent accessibility of the mutated residue contributed greatly to the predictive ability of SIGMA. We further explored combining SIGMA with other top-tier predictors to create SIGMA+, proving highly effective for variant pathogenicity prediction …

Crispr-Dipoff: An Interpretable Deep Learning Approach For Crispr Cas-9 Off-Target Prediction, Md Toufikuzzaman, Md Abul Hassan Samee, M Sohel Rahman

Faculty, Staff and Students Publications

CRISPR Cas-9 is a groundbreaking genome-editing tool that harnesses bacterial defense systems to alter DNA sequences accurately. This innovative technology holds vast promise in multiple domains like biotechnology, agriculture and medicine. However, such power does not come without its own peril, and one such issue is the potential for unintended modifications (Off-Target), which highlights the need for accurate prediction and mitigation strategies. Though previous studies have demonstrated improvement in Off-Target prediction capability with the application of deep learning, they often struggle with the precision-recall trade-off, limiting their effectiveness and do not provide proper interpretation of the complex decision-making process of …

Unexpected Inhibition Of The Lipid Kinase Pikfyve Reveals An Epistatic Role For P38 Mapks In Endolysosomal Fission And Volume Control, Daric J Wible, Zalak Parikh, Eun Jeong Cho, Miao-Der Chen, Collene R Jeter, Somshuvra Mukhopadhyay, Kevin N Dalby, Shankar Varadarajan, Shawn B Bratton

Faculty, Staff and Student Publications

p38 mitogen-activated protein kinases (MAPKs) participate in autophagic signaling; and previous reports suggest that pyridinyl imidazole p38 MAPK inhibitors, including SB203580 and SB202190, induce cell death in some cancer cell-types through unrestrained autophagy. Subsequent studies, however, have suggested that the associated cytoplasmic vacuolation resulted from off-target inhibition of an unidentified enzyme. Herein, we report that SB203580-induced vacuolation is rapid, reversible, and relies on the class III phosphatidylinositol 3-kinase (PIK3C3) complex and the production of phosphatidylinositol 3-phosphate [PI(3)P] but not on autophagy per se. Rather, vacuolation resulted from the accumulation of Rab7 on late endosome and lysosome (LEL) membranes, combined with …

Cross-Cultural Preferences For Women’S Waist To Hip Ratio And Men’S Shoulder To Hip Ratio: Data From Iran, Norway, Poland, And Russia, Farid Pazhoohi, Reza Afhami, Razieh Chegeni, Dmitrii Dubrov, Katarzyna Gałasińska, Ray Garza, Nasim Ghahraman Moharrampour, Dmitry Grigoryev, Marta Kowal, Ståle Pallesen, Gerit Pfuhl

School of Psychology

Objectives: Body size and shape are sexually dimorphic in humans, with men being characterized with larger upper bodies, while women typically having broader pelvises. Such sexually dimorphic traits, quantified as shoulder to hip ratio (SHR) in men and waist to hip ratio (WHR) in women, serve as cues of an individual’s genetic fitness, reproductive potential, health, and resource holding power, and, thereby, functioning as attractiveness cues to the opposite sex. Methods: In the current study, we investigated men’s and women’s preference for the opposite sex body shape (WHR in women and SHR in men) in samples from Iran, Norway, Poland, …

The Coming Wave By Mustafa Suleyman: A Review, Puspa Damai

Critical Humanities

A Review of Mustafa Suleyman's The Coming Wave: Technology, Power, and the 21^st Century’s Greatest Dilemma (NY: Crown, 2023).

How Fears Of Ai In The Classroom Reflect Anxieties About Choosing Sophistry Over True Knowledge In The American Education System, David Arellano Smith

Critical Humanities

The rise of ChatGPT has educators across the United States of America worried about scholastic integrity like never before. This paper argues, however, that underneath this initial concern lies an even greater one, that the education system in the United States so closely resembles the style of teaching used by the sophists in Ancient Greece that it has ultimately failed to cultivate critical thinking skills in America’s youth, so much so that ChatGPT has become a far greater issue than it ever needed to be. The practice of ‘teaching to the test’ and the commodification of education, which is akin …

Cognitive Reappraisal Is Associated With Lower Dysphoria Symptoms During The Covid-19 Pandemic, Nadia Armstrong, Diane Moon, Holly Bowen

SMU Journal of Undergraduate Research

The COVID-19 pandemic has created unprecedented mental health concerns generally, but particularly for young adults navigating an already fluctuating and uncertain period of their lives. While there are many factors related to mental health, it is well-documented that emotion regulation– the ability to modulate an emotion or set of emotions– and risk perception appear to be relevant to the development, maintenance, and treatment of psychopathology. The current study aimed to assess the relationship between emotion regulation processes, COVID-19 risk perception, and dysphoria symptoms during the early months of the pandemic. Between April - May 2020, 243 undergraduate participants completed the …

Acute Ingestion Of Dark Chocolate Fails To Affect Running Economy In Recreational Female Runners, Bianca J. De Lucia, Beau Kjerulf Greer, Christopher B. Taber

Topics in Exercise Science and Kinesiology

Topics in Exercise Science and Kinesiology Volume 5: Issue 1, Article 1, 2024. Ingestion of dark chocolate (DC), a dietary source high in flavanols, may increase nitric oxide bioavailability. Elevating blood nitric oxide concentrations may augment metabolic efficiency by reducing the amount of oxygen or energy needed to perform a given task. Utilizing a crossover design, the purpose of this study was to investigate the effect of acute ingestion of DC on running economy (RE). Nineteen recreationally trained females (age: 20±1 years) volunteered for this investigation, with 16 completing all procedures (n = 16). Two-hours before RE assessment, participants consumed …

The Cetacean Sanctuary: A Sea Of Unknowns, Jason N. Bruck

Faculty Publications

Housing cetaceans in netted sea pens is not new and is common for many accredited managed- care facilities. Hence, the distinction between sanctuary and sea pen is more about the philosophies of those who run these sanctuary facilities, the effects of these philosophies on the animals’ welfare, and how proponents of these sanctuaries fund the care of these animals. Here, I consider what plans exist for cetacean sanctuaries and discuss the caveats and challenges associated with this form of activist-managed captivity. One goal for stakeholders should be to disregard the emotional connotations of the word “sanctuary” …

Gender In Children's Literature And Kindergartener's Responses To Gender In Interactive Read-Alouds, Vahide Yigit-Gencten, Mehmet Gultekin, Rabia Ozen Uyar, Filiz Aydemir

Curriculum and Instruction Faculty Publications and Presentations

The underrepresentation of women and the perpetuation of gender stereotypes in children's literature has long been a concern. This study examined the portrayal of women in children's picture books and the potential of interactive read-alouds to promote gender equity in early childhood education, with the aim of shedding light on gender inequality. This study used critical discourse analysis, theoretically informed by Rosenblatt's transactional theory and gender schema theory, to analyse 19 books and interactive read-aloud sessions between preservice teachers and children in six preschools. The results showed that books on women's inequality are discussed in three categories: the absence of …

Ecological Assessment Of Drainage Water Input On The Water Quality Of A Coastal Estuary, Mediterranean Coast Of Egypt, Fatma A. Zaghloul, Hoda A. E. Hemaida, Hayat M. Faragallah, Ahmed A. Radwan

Blue Economy

El Mex Bay, located west of Alexandria City, is identified as a hot spot of pollution along the Mediterranean coast of Egypt. It is a large, shallow, and turbid water body of socioeconomic importance. However, El Mex Bay receives a large amount of untreated industrial wastewater, as well as agricultural runoff from different land-based sources.

A comprehensive environmental study was carried out seasonally during 2020-2021. To evaluate the effect of this discharged wastewater on the water quality of El Mex Bay.

The physicochemical parameters were measured at both the surface and near-bottom water at nine stations.

Principal component analysis indicated …

Mypathway Human Epidermal Growth Factor Receptor 2 Basket Study: Pertuzumab + Trastuzumab Treatment Of A Tissue-Agnostic Cohort Of Patients With Human Epidermal Growth Factor Receptor 2-Altered Advanced Solid Tumors, Christopher J Sweeney, Ron Bose, Et Al.

2020-Current year OA Pubs

No abstract provided.

Snare-Ing The Reason For Post-Cardiac Surgery Critical Illness-Related Corticosteroid Insufficiency, Nicholas Diehl, Nataliya Kibiryeva, Jenny Marshall, Sarah Tsai, Juan S. Farias, Jaime Silva-Gburek, Lori A. Erickson

Manuscripts, Articles, Book Chapters and Other Papers

Critical illness-related corticosteroid insufficiency (CIRCI) can cause hemodynamic instability in neonates after congenital heart surgery with manifestations that increase morbidity and potential mortality. We retrospectively reviewed neonates who underwent cardiac surgery between August 2018 and July 2020 at a freestanding children’s hospital, had next-generation sequencing performed, and had their cortisol levels drawn as standard clinical care after cardiac surgery. The groups were defined as CIRCI (with a cortisol level ≤ 4.5 mcg/dL) and non-CIRCI (level > 4.5 mcg/dL). The CIRCI group (n = 8) had a 100% incidence of heterozygous gene mutation on STX1A with splicing or loss of function, and …

Alumna Provides Support For Accountancy School, Andy Belt

University of Mississippi News

OXFORD, Miss. – The University of Mississippi's Patterson School of Accountancy plans to name two study spaces in its new home in honor of alumna Jackie Bailey's family, showing appreciation for their $100,000 gift to the school's new building fund.

Obstacle Avoidance Motion In Mobile Robotics, Yunchao Tang, Shaojun Qi, Lixue Zhu, Xianrong Zhuo, Yunqi Zhang, Fan Meng

Journal of System Simulation

Abstract: The advancement of artificial intelligence technology has significantly enhanced the utilization of mobile robots in various fields such as industry, aerospace, and agriculture. The autonomous obstacle avoidance capability of these robots is crucial to the safety and efficiency of their operations in diverse settings. Path planning, a key technology in obstacle avoidance, plays an essential role in the overall performance of these systems. This paper presents a comprehensive review of path planning technology for mobile robots, categorizing the algorithms into global planning and local obstacle avoidance according to their operational requirements. Specific focus is given to the global planning …

Research On Campus Epidemic Evolution Based On Multi-Scale Modeling And Simulation In Microscopic & Microscopic View, Mingwei Hu, Wenjie Yang

Journal of System Simulation

Abstract: High density of population leads to high possibility of cross-infection. It is necessary to focus on campus epidemic prevention and control. Basing on existing studies in macroscopic or microscopic view, this paper proposed a multi-scale means to analyze a short-term evolution of Corona virus disease 2019 (COVID-19) on campus and estimated the efficiency of prevention strategies. Macroscopic model was based on the susceptible-exposed-infections-recovered(SEIR) model, which exported the time curve of the number of asymptomatic patients and symptomatic patients. Microscopic model combined discrete event simulation modeling and agent-based modeling to simulate the behavior of campus students and the state evolution …

Sense Of Belonging Of Underrepresented Students: Role Of Faculty Inclusiveness And Online Versus Campus Learning, Elisavet Chaoua Intoumpor

Walden Dissertations and Doctoral Studies

No abstract provided.

Impacts Of Farrowing Pen Design, Season, And Sow Parity On Litter Performance And Piglet Mortality, Verônica Madeira Pacheco, Tami M. Brown-Bandl, Gary A. Rohrer, Rafael Vieira De Sousa, Luciane Silva Martello

Department of Agricultural and Biological Systems Engineering: Faculty Publications

Piglet mortality during lactation is a significant concern in swine production, influenced by complex interactions involving sow, piglet, environmental, and management factors. While crushing by the sow may be the ultimate cause of piglet mortality, there are many factors influencing the outcome, including parity, thermal stress, and animal housing systems. New farrowing systems are continuously being developed; however, it is difficult for producers to make decisions without any scientific basis. This study aimed to assess the impact of different farrowing pen layouts on piglet performance, considering parity and season. A total of 546 sows and 9123 piglets were monitored across …

Major Stressful Life Events And The Risk Of Pancreatic, Head And Neck Cancers: A Case-Control Study, Arthi Sridhar, Vishaldeep Kaur Sekhon, Chandler Nguyen, Kamelah Abushalha, Amirali Tahanan, Mohammad Hossein Rahbar, Syed Hasan Jafri

Faculty, Staff and Student Publications

BACKGROUND: Major stressful life events have been shown to be associated with an increased risk of lung cancer, breast cancer and the development of various chronic illnesses. The stress response generated by our body results in a variety of physiological and metabolic changes which can affect the immune system and have been shown to be associated with tumor progression. In this study, we aim to determine if major stressful life events are associated with the incidence of head and neck or pancreatic cancer (HNPC).

METHODS: This is a matched case-control study. Cases (CAs) were HNPC patients diagnosed within the previous …

Assessment Of Drug Adherence And Adverse Effects Of Disease-Modifying Antirheumatic Drugs (Dmards) In Patients Of Rheumatoid Arthritis Attending A Tertiary Care Hospital In India, Tejal C. Patel, Prasad R. Pandit, Zankrut R. Doshi, Vikram A. Londhe

Pharmacology and Clinical Pharmacy Research

Adherence to drug treatment is one of the key factors in treating chronic diseases like rheumatoid arthritis (RA) to maintain remission and prevent functional disability. Poor medication adherence is directly associated with a worse prognosis and an increase in healthcare utilization, adding to a financial burden. Hence, the present study was proposed to assess drug adherence in diagnosed patients of RA attending a tertiary care hospital. The study was initiated after obtaining institutional ethics committee permission, and written informed consent was requested from all the eligible patients before their enrolment. This cross-sectional questionnaire based study was conducted on RA patients …

Chronic Pain Interventions: Considering Hypnotherapy As A Viable Treatment Option, Madelyn Isom

Student Works

Chronic pain is a widespread and debilitating condition, demanding advancements in current interventions. Conventional medical paradigms have traditionally treated the mind and body separately, but advancement has advocated shifts toward more integrated mind-body approaches to address holistic health. Despite prevailing skepticism and friction within patient-doctor relationships surrounding hypnosis, there is substantial support for its use as a pain management tool (Declercq, 2023; Thompson et al., 2019). This analysis explores the potential of hypnosis as a viable treatment for chronic pain, highlighting its merits and addressing current research limitations. Noteworthy findings underscore hypnosis’ distinctive influence on the physical body through mental …

Exploration Of Programmed Cell Death-Associated Characteristics And Immune Infiltration In Neonatal Sepsis: New Insights From Bioinformatics Analysis And Machine Learning, Yun Hang, Huanxia Qu, Juanzhi Yang, Zhang Li, Shiqi Ma, Chenlu Tang, Chuyan Wu, Yunlei Bao, Feng Jiang, Jin Shu

Faculty, Staff and Student Publications

BACKGROUND: Neonatal sepsis, a perilous medical situation, is typified by the malfunction of organs and serves as the primary reason for neonatal mortality. Nevertheless, the mechanisms underlying newborn sepsis remain ambiguous. Programmed cell death (PCD) has a connection with numerous infectious illnesses and holds a significant function in newborn sepsis, potentially serving as a marker for diagnosing the condition.

METHODS: From the GEO public repository, we selected two groups, which we referred to as the training and validation sets, for our analysis of neonatal sepsis. We obtained PCD-related genes from 12 different patterns, including databases and published literature. We first …

Current Status And Applications Of Microbial Chassis Strains For Chinese Biomanufacturing Industry, Guoqiang Chen, Fuqing Wu, Shuang Zheng, Jun Ding, Junting Sheng

Bulletin of Chinese Academy of Sciences (Chinese Version)

Biomanufacturing is an important component of new quality productive forces, representing the commanding height of the new round of technological revolution and serving as a new engine for industrial transformation following information technology. It demonstrates vast application prospects in fields such as renewable energy, advanced materials, biomedicine, green food, and environmental protection. Biomanufacturing utilizes chassis microorganisms similar as “microchip” to produce various bioproducts via processes including chassis design and construction, large-scale cell cultivation, and product purifications. Most chassis microorganisms in biomanufacturing were not domestically identified. This study summarizes the types of common chassis microorganisms both domestically and internationally, as well …

Recent Progress And Perspectives On Development Of Gene Editing Tools, Zixian Liu, Chengping Li, Gogo Jun-Jie Liu

Bulletin of Chinese Academy of Sciences (Chinese Version)

The gene editing field has witnessed remarkable advancements in recent years, leading to the establishment and refinement of multidimensional gene editing platforms. These innovations have enabled precise targeted gene knockout, repair, and insertion. These tools have stimulated significant progress in fundamental research, therapeutics, agriculture, environment protection, and industrial applications. In this review, we provide a comprehensive overview of the milestones in gene editing tool development and offer perspectives on potential future directions for this rapidly evolving field.

Digitalized Design Of Cell Factory Enables Green Biomanufacturing, Fanze Meng, Rui Cao, Bing Hu, Lei Qin, Chun Li

Bulletin of Chinese Academy of Sciences (Chinese Version)

Green manufacturing is a modern manufacturing mode in the consideration of both environmental impact and efficiency of resource utilization, it represents a significant component of the “new productive force”. Centered on cell factories, green biomanufacturing leverages renewable resources to efficiently produce products that conform to the concepts of low-carbon, green, and sustainable development. The design of high-performance cell factories is pivotal for achieving efficient green biomanufacturing. Nevertheless, traditional cell factory design processes are complex, time-consuming, and labor-intensive. With advancements in artificial intelligence, digital-assisted cell factory design has emerged as a solution to save time and reduce costs. By integrating technologies …

Research Progress In High-Throughput Phenotype Testing Technology And Equipment For Engineering Cells Based On Microfluidics, Shuang Li, Xiaojie Guo, Haibo Chen, Sisi Chen, Xin Da, Zhenghui Li, Qinxiu Liu, Yi Wang, Xinhui Xing, Chong Zhang

Bulletin of Chinese Academy of Sciences (Chinese Version)

Engineering cells are a core component of green bio-manufacturing. The efficient testing and acquisition of engineering cells with the desired phenotype is a critical factor in the successful implementation of bio-manufacturing. In recent years, based on microfluidics technologies, non-culture type single-cell phenotype high-throughput test equipment and culture type phenotype high-throughput test equipment for the growth and metabolism of single cell in a bioreactor have been developed such as microdroplet and microchamber, realizing high-throughput, automated, miniaturized, and integrated testing of the phenotypes of engineering cells and providing a powerful tool for the breeding of engineering cells. This review systematically compiles the …

Bioprocess Engineering And Intelligent Biomanufacturing, Guan Wang, Yingping Zhuang

Bulletin of Chinese Academy of Sciences (Chinese Version)

In the era of rapid development of synthetic biology, biomanufacturing, as a bridge between life sciences and engineering technologies, is gradually demonstrating its extraordinary potential to reshape industrial landscapes. However, challenges such as production efficiency, cost control, and process monitoring still hinder the smooth transition from laboratory innovations to industrial-scale implementation. Intelligent biomanufacturing has emerged as a new form of productive force, offering innovative solutions to these problems. This study reviews the latest advances in bioprocess engineering and intelligent biomanufacturing, focusing on three key technological systems: intelligent sensing, intelligent analysis, and intelligent control. Intelligent sensing technology acts as the “eyes” …

Strengthen Research On Environmental Control Technologies And Management Policies For Emerging Contaminants In China, Ying Ma, Xiang Li, Yongming Luo

Bulletin of Chinese Academy of Sciences (Chinese Version)

The prevention and management of emerging contaminants (ECs) have become critical measures in China’s battle against environmental pollution. This study focuses on the environmental control technologies and policy governance related to emerging contaminants (ECs), analyzing their environmental pathways and challenges to public health, and highlighting advancements and limitations in current physical, chemical, and biological control technologies. Based on a comprehensive analysis of international policies and regulations on ECs control, the study identifies existing challenges and shortcomings in domestic management. Recommendations are proposed to enhance research on environmental control technologies and policies for ECs in China, aiming to provide insights for …

Computing System For Simulation Intelligence, Guangming Tan, Weile Jia, Zhan Wang, Guojun Yuan, En Shao, Ninghui Sun

Bulletin of Chinese Academy of Sciences (Chinese Version)

This study refers computer simulation in scientific research to as scientific simulation. Based on its narrow and broad definitions, this study divides scientific simulation into three stages: numerical computation, simulation intelligence, and science brain. Now, scientific simulation is entering the era of simulation intelligence, i. e., driven by scientific big data and artificial intelligence technology, scientific simulation is shifting from traditional numerical simulation to simulation integrated with artificial intelligence. In order to understand what the right computing system for simulation intelligence is, the design guidelines, basic methods, and key technical problems are discussed.

Large Model-Driven, Human-Computer Collaborative Robotic Ai-Chemist Cloud Facility, Yuanyuan Chong, Shuo Feng, Song Wang, Jun Jiang

Bulletin of Chinese Academy of Sciences (Chinese Version)

At present, chemical science is facing unprecedented opportunities and challenges due to the technological changes brought by artificial intelligence. In order to promote the paradigm shift in chemical research, this study proposes the construction plan of the robotic AI-chemist cloud facility. This system realizes a new paradigm of scientific research by collecting multi-channel data to build a database, developing large scientific models enhanced by chemical knowledge, constructing clusters of robotic facilities, and building an intelligent management decision system, which will dramatically improve the efficiency of scientific research and solve scientific problems in terminal applications. This infrastructure is expected to change …