Digital Commons Network^™

Do I Sound Anxious? Emotional Arousal Is Linked To Changes In Vocalisations In Domestic Chicks (Gallus Gallus Dom.), Sarah A. Collins, Katherine Herborn, Kenneth J. Sufka, Lucy Asher, Ben Brilot

School of Biological and Marine Sciences

A major goal in animal welfare science is the development of methods that quantify or ‘read-out’ current affective states in freely behaving animals. In mammalian models, changes in acoustic parameters within vocalisations have been linked to differences in emotional arousal, although there are very few studies showing changes in vocalisations that act as indicators of valence (positive or negative affect). Currently, there are very few studies on vocal indicators of emotion in birds. To determine the link between acoustic parameters within vocalisations and emotion in domestic chicks (Gallus gallus dom.), we used a well-validated paradigm that purports to elicit two …

Integration Of Attractive And Defensive Phytochemicals Is Unlikely To Constrain Chemical Diversification In A Perennial Herb, Hanna Eriksdotter Thosteman, Katherine Eisen, Hampus Petrén, Sotiria Boutsi, Loretta Pace, John M. Halley, Consuelo M. De Moraes, Mark C. Mescher, James Buckley, Magne Friberg

School of Biological and Marine Sciences

Diversification of plant chemical phenotypes is typically associated with spatially and temporally variable plant–insect interactions. Floral scent is often assumed to be the target of pollinator-mediated selection, whereas foliar compounds are considered targets of antagonist-mediated selection. However, floral and vegetative phytochemicals can be biosynthetically linked and may thus evolve as integrated phenotypes. Utilizing a common garden of 28 populations of the perennial herb Arabis alpina (Brassicaceae), we investigated integration within and among floral scent compounds and foliar defense compounds (both volatile compounds and tissue-bound glucosinolates). Within floral scent volatiles, foliar volatile compounds, and glucosinolates, phytochemicals were often positively correlated, and …

The Embryonic Thermal Environment Has Positive But Weak Effects On Thermal Tolerance Later In Life In The Aquatic Invertebrate Gammarus Chevreuxi, Honor Haskett, Luke Gill, John I. Spicer, Manuela Truebano

School of Biological and Marine Sciences

Recent evidence suggests that the adult phenotype is influenced by temperatures experienced in early life. However, our understanding of the extent to which the embryonic environment can modulate thermal tolerance later in life is limited, owing to the paucity of studies with appropriate experimental designs to test for this form of developmental plasticity. We investigated whether the thermal environment experienced during embryonic development affects thermal limits in later life. Embryos of the estuarine amphipod Gammarus chevreuxi were incubated until hatching to 15 °C, 20 °C and 25 °C, then reared under a common temperature. Using thermal ramping assays, we determined …

Invasive Macroalgae In Native Seagrass Beds: Vectors Of Spread And Impacts, Louise Firth, Andy Foggo, Thomas Watts, Antony Knights, Stacey Deamicis

School of Biological and Marine Sciences

Background and AimsWorldwide, invasive species are spreading through marine systems at an unprecedented rate with both positive and negative consequences for ecosystems and the biological functioning of organisms. Human activities from shipping to habitat damage and modification are known vectors of spread, although biological interactions including epibiosis are increasingly recognized as potentially important to introduction into susceptible habitats.MethodsWe assessed a novel mechanism of spread – limpets as transporters of an invasive alga, Sargassum muticum, into beds of the seagrass Zostera marina – and the physiological impact of its invasion. The association of S. muticum with three limpet species and other …

From Riverbank To The Sea: An Initial Assessment Of Plastic Pollution Along The Ciliwung River, Indonesia, Muhammad Reza Cordova, Max R. Kelly, Muhammad Hafizt, Singgih Prasetyo Adi Wibowo, Yaya Ihya Ulumuddin, Triyoni Purbonegoro, Deny Yogaswara, Muhammad Taufik Kaisupy, Riyana Subandi, Sofia Yuniar Sani, Richard C. Thompson, Susan Jobling

School of Biological and Marine Sciences

This study presents the first comprehensive analysis of anthropogenic debris on the riverbanks of the Ciliwung River, covering upstream to downstream areas. The mean of debris found in each measurement was 32.79 ± 15.38 items/m² with a weight of 106.00 ± 50.23 g/m². Plastic debris accounted for over 50 % of all litter items identified and represents 55 % by weight, signifying a significantly high prevalence compared to global studies examining litter along riverbanks. The majority of the plastics found originated from Single-use applications and were predominantly made from Styrofoam. This investigation demonstrated the importance of actions …

Victim Of Changes? Marine Macroalgae In A Changing World, Mick E. Hanley, Louise B. Firth, Andy Foggo

School of Biological and Marine Sciences

Background Marine macroalgae (‘seaweeds’) are a diverse and globally distributed group of photosynthetic organisms that together generate considerable primary productivity, provide an array of different habitats for other organisms, and contribute many important ecosystem functions and services. As a result of continued anthropogenic stress on marine systems, many macroalgal species and habitats face an uncertain future, risking their vital contribution to global productivity and ecosystem service provision. Scope After briefly considering the remarkable taxonomy and ecological distribution of marine macroalgae, we review how the threats posed by a combination of anthropogenically induced stressors affect seaweed species and communities. From there …

Insights From Early Career Researcher Representatives At The Sustainability Research & Innovation Congress 2022 Asia Spotlight Event, Cho Kwong Charlie Lam

School of Geography, Earth and Environmental Sciences

The Sustainability Research & Innovation Congress 2022 Asia Spotlight Event (SRI-ASE 2022) was held virtually from June 21-24, 2022 and co-organized by Future Earth Global Secretariat Hubs in Asia based in Japan, Taipei, China, and South Asia, during the main sessions of the SRI 2022. SRI-ASE 2022 included over 70 speakers and more than 300 participants from within and outside the Asia region. The aim of the event was to provide space to reflect on inspiring research and discussions related to the themes: New Horizons, Different Ways of Knowing, Nexus Issues, and Cross-cutting Science and Innovation in Asia. This report …

Aquatic Connectivity: Challenges And Solutions In A Changing Climate, Paul A. Franklin, Tea Bašić, Phil I. Davison, Katie Dunkley, Jonathan Ellis, Mayuresh Gangal, Alexia M. González-Ferreras, Catherine Gutmann Roberts, Georgina Hunt, Domino Joyce, C. Antonia Klöcker, Rachel Mawer, Timo Rittweg, Velizara Stoilova, Lee Frank Gordon Gutowsky

School of Geography, Earth and Environmental Sciences

The challenge of managing aquatic connectivity in a changing climate is exacerbated in the presence of additional anthropogenic stressors, social factors, and economic drivers. Here we discuss these issues in the context of structural and functional connectivity for aquatic biodiversity, specifically fish, in both the freshwater and marine realms. We posit that adaptive management strategies that consider shifting baselines and the socio-ecological implications of climate change will be required to achieve management objectives. The role of renewable energy expansion, particularly hydropower, is critically examined for its impact on connectivity. We advocate for strategic spatial planning that incorporates nature-positive solutions, ensuring …

Practical Actions To Strengthen Capacity For Deep-Water Research In Africa, Kirsty A Mcquaid, Kerry Howell, Agnes W.N. Muthumbi, Olusola Adeoye, Isa Elegbede, Luther Adams, Blessing Charuka, Ana Hilário, Hendrina Kadila, Sophia Laarissa, Randa Mejri, Sidi Mohamed, Damaris Mutia, Angela Nyangwe, Angus Paterson, Sinothando Shibe, Kerry Sink, Sheena Talma, Urias Taylor, Arthur Tuda

School of Biological and Marine Sciences

While Africa's deep marine biodiversity offers economic prospects it also supports crucial ecosystem services and sustainable development is dependent on knowledge of these systems. Building understanding of deep-water ecosystems is key, but there are substantial discrepancies in countries' abilities to achieve this. Coinciding with the 2024 Ocean Decade Conference, the Challenger 150 African Network of Deep-water Researchers is pleased to release a report on “Practical Actions to Strengthen Capacity for Deep-water Research in Africa”. Through a series of online workshops, the ANDR brought together 98 individuals from 19 African nations to discuss challenges for deep-water research in Africa, identify solutions …

Amplifying Pcr Productivity And Environmental Sustainability Through Shortened Cycling Protocols, Matthew Pedlar, Matthew J. Emery, Philip J. Warburton

School of Biological and Marine Sciences

Since its inception in the 1980s, advancements in PCR technology using improved thermal cyclers, engineered DNA polymerases and commercial master mixes, have led to increased PCR productivity. Despite these advancements, PCR cycling protocols have largely remained unchanged over the same period. This study aimed to systemically evaluate the effect of reduced PCR cycling parameters on amplicon production. The 1466bp fragment from the 16S rRNA gene present in low-, medium- and high-CG bacteria was amplified using three commercially available PCR master mixes. The shortest cycling parameters required to successfully amplify the 16S fragment from all bacteria and master mixes comprised 30-cycles …

Shifting The Focus From Species To Individuals In Invasion Biology: Individual Differences In Jumping Behaviour, Aaron Jessop, Miguel Barbosa, Michael Morrissey

School of Biological and Marine Sciences

Dispersal is critical to population persistence, colonization and connectivity which are all critical components of invasive success. While individual propensity to disperse varies within populations, the underlying mechanisms promoting individual dispersal remain unclear. Collectively, dispersal is influenced by the environment and individual phenotype. Here we investigated individual dispersal propensity in the Trinidadian guppy, Poecilia reticulata, and related individual variation in dispersal behaviour to phenotype and social/environmental conditions. Namely, we addressed the effect of sex ratio (social/environmental factor) on the tendency for individuals to disperse across physical barriers via jumping behaviour. Jumping is vital for the dispersal of many aquatic species …

Electrochemical Based Quantification Of Bacterial Growth In Media Using Square Wave Voltammetry And Low Cost Screen Printed Electrodes, Simon Peter Whelan, Shirin Naserikarimvand, Zari Tehrani, Martin Peacock, Owen Guy, David Gethin

School of Geography, Earth and Environmental Sciences

A novel method for determining the yield of bacterial growth using square wave voltammetry and screen printed electrodes is described here. This procedure was shown to be a reliable and accurate way to quickly determine the level of bacterial growth within culturing media and these results suggest that the combination of such sensors and the application of square wave voltammetry is suitable for applications such as within a bioreactor where the rapid determination of bacterial growth may be necessary.

Blood From A Stone: Do The Trace Metals Of Sperm Whale Coproliths Reveal A Contribution From Squid Haemolymph?, Steven J. Rowland, Robert Clough, Paul A. Sutton, George H. Rowland

School of Geography, Earth and Environmental Sciences

Background: Ambergris is a coprolith produced by some sperm whales (∼1 %). It has been hypothesised that the metals in ambergris derive from the haemolymph of squid in the whale diet (mainly copper). However, few data exist. We report analysis of 10 trace metals in each of 50 ambergris samples by inductively coupled plasma-mass spectrometry. Main Findings: Acid digests of the samples contained ∼5 to >6880 µg g⁻¹ air-dried weight total metals; mainly of iron (present in ∼90 % of samples, 38), copper (∼95 % of samples, 40), zinc (93 % of samples, 39) and cadmium (∼95 % of …

Guidelines For Protecting And Promoting Decapod Crustacean Welfare In Research, Mark Briffa

School of Biological and Marine Sciences

The decapod order contains ~15,000 species, including crabs, lobsters, crayfish, prawns, and shrimps. The idea that these animals might experience pain was long dismissed because they were thought to respond to noxious stimuli and tissue damage purely by nociceptive reflex—a position questioned by Sherwin (2001). Later experimental studies demonstrated that their responses were complex, long-lasting, and largely consistent with criteria for pain that had been produced initially for vertebrates (Elwood 2019). While the nature and extent of potential sentience in decapods remains an active area of research, these animals were recently recognized as sentient for the purposes of UK law, …

Aquaculture In Zambia: The Current Status, Challenges, Opportunities And Adaptable Lessons Learnt From China, Lin Zhang, Sahya Maulu, Fenglei Hua, Majory K.H. Chama, Pao Xu

School of Biological and Marine Sciences

As a land-locked country in Southern Africa, Zambia is rich in natural resources suitable for fish production. However, aquaculture is still in its infancy with enormous potential as most of Zambia’s fish now comes from capture fisheries. The aim of this study was to review the recent progress, status, challenges, and opportunities in Zambia’s aquaculture industry while drawing some lessons from China’s aquaculture experience, focusing on policy instruments, external support, quality seeds, and the investment environment for possible adaptation. To achieve this, we reviewed the existing literature about aquaculture in Zambia. This paper starts by reviewing the overall fishery sector’s …

The Application Of Protease In Aquaculture: Prospects For Enhancing The Aquafeed Industry, Shiyou Chen, Sahya Maulu, Jie Wang, Xiaoze Xie, Xiaofang Liang, Hao Wang, Junjun Wang, Min Xue

School of Biological and Marine Sciences

Low-fishmeal and protein-saving diets are two prominent nutritional strategies utilized to address challenges related to the scarcity and sustainability of protein sources in aquaculture. However, these diets have been associated with adverse effects on the growth performance, feed utilization, and disease resistance of aquatic animals. To mitigate these challenges, exogenous protease has been applied to enhance the quality of diets with lower protein contents or fishmeal alternatives, thereby improving the bioavailability of nutritional ingredients. Additionally, protease preparations were also used to enzymatically hydrolyze fishmeal alternatives, thus enhancing their nutritional utilization. The present review aims to consolidate recent research progress on …

Labembryocam: An Opensource Phenotyping System For Developing Aquatic Animals, Ziad Ibbini, Maria Bruning, Sakina Allili, Luke A. Holmes, Ellen Tully, Jamie Mccoy, Benjamin Larsen, Tony Wilson, Guy Ludford, Jack Barrett-Kelly, John I. Spicer, Oliver Tills

School of Biological and Marine Sciences

Phenomics is the acquisition of high-dimensional data on an individual-wide scale and is proving transformational in areas of biological research related to human health including medicine and the crop sciences. However, more broadly, a lack of accessible transferrable technologies and research approaches is significantly hindering the uptake of phenomics, in contrast to molecular-omics for which transferrable technologies have been a significant enabler. Aquatic embryos are natural models for phenomics, due to their small size, taxonomic diversity, ecological relevance, and high levels of temporal, spatial and functional change. Here, we present LabEmbryoCam, an autonomous phenotyping platform for timelapse imaging of developing …

Sediment Sorting Within A Relatively Wave-Exposed And Sandy Subtidal Seagrass (Zostera Marina) Meadow, Gerd Masselink, Tom Brown, Tim Scott, Liane Brodie

School of Biological and Marine Sciences

Seagrasses impact on sedimentary intertidal and subtidal ecosystems by affecting local hydrodynamics, geomorphology and sediment properties. Their influence on hydrodynamics is to reduce flow velocities in their canopies, and this leads to increased net sedimentation rates and reduction of the grain size. Most investigations of the seagrass-hydrodynamics-sediment feedback system has been carried out over silt and fine-sand beds under tide-dominated conditions, mostly in the intertidal zone. Here, we use sedimentological data from a relatively wave-exposed and subtidal seagrass (Zostera marina) meadow in the Isles of Scilly with a fine-to-medium sand bed and show that the sand within the seagrass meadow …

Critical Data For Critical Care: A Primer On Leveraging Electronic Health Record Data For Research From Society Of Critical Care Medicine's Panel On Data Sharing And Harmonization, Donna Lee Armaignac

All Publications

A growing body of critical care research draws on real-world data from electronic health records (EHRs). The bedside clinician has myriad data sources to aid in clinical decision-making, but the lack of data sharing and harmonization standards leaves much of this data out of reach for multi-institution critical care research. The Society of Critical Care Medicine (SCCM) Discovery Data Science Campaign convened a panel of critical care and data science experts to explore and document unique advantages and opportunities for leveraging EHR data in critical care research. This article reviews and illustrates six organizing topics (data domains and common data …

Incorporating Variable Rbe In Impt Optimization For Ependymoma, Hadis Moazami Goudarzi, Gino Lim, David Grosshans, Radhe Mohan, Wenhua Cao

Faculty, Staff and Student Publications

PURPOSE: To study the dosimetric impact of incorporating variable relative biological effectiveness (RBE) of protons in optimizing intensity-modulated proton therapy (IMPT) treatment plans and to compare it with conventional constant RBE optimization and linear energy transfer (LET)-based optimization.

METHODS: This study included 10 pediatric ependymoma patients with challenging anatomical features for treatment planning. Four plans were generated for each patient according to different optimization strategies: (1) constant RBE optimization (ConstRBEopt) considering standard-of-care dose requirements; (2) LET optimization (LETopt) using a composite cost function simultaneously optimizing dose-averaged LET (LET

RESULTS: We found that the LETopt plans consistently achieved increased LET in …

Placental Co-Transcriptional Activator Vestigial-Like 1 (Vgll1) Drives Tumorigenesis Via Increasing Transcription Of Proliferation And Invasion Genes, Heather M Sonnemann, Barbara Pazdrak, Barbara Nassif, Yimo Sun, Lama Elzohary, Amjad H Talukder, Arjun S Katailiha, Krishna Bhat, Gregory Lizée

Faculty, Staff and Student Publications

Introduction: Vestigial-like 1 (VGLL1) is a co-transcriptional activator that binds to TEA domain-containing transcription factors (TEADs). Its expression is upregulated in a variety of aggressive cancer types, including pancreatic and basal-like breast cancer, and increased transcription of VGLL1 is strongly correlated with poor prognosis and decreased overall patient survival. In normal tissues, VGLL1 is most highly expressed within placental trophoblast cells, which share the common attributes of rapid cellular proliferation and invasion with tumor cells. The impact of VGLL1 in cancer has not been fully elucidated and no VGLL1-targeted therapy currently exists.

Methods: The aim of this study was to …

Crosstalk Between Breast Cancer-Derived Micrornas And Brain Microenvironmental Cells In Breast Cancer Brain Metastasis, Munazza S Khan, Grace L Wong, Chuling Zhuang, Mariana K Najjar, Hui-Wen Lo

Faculty, Staff and Student Publications

Breast cancer is the most frequent malignancy in women, constituting 15.2% of all new cancers diagnosed in the United States. Distant breast cancer metastasis accounts for the majority of breast cancer-related deaths; brain metastasis is the third most common site for metastatic breast cancer but is associated with worst prognosis of approximately eight months of survival. Current treatment options for breast cancer brain metastasis (BCBM) are limited and ineffective. To help identify new and effective therapies for BCBM, it is important to investigate the mechanisms by which breast cancer cells metastasize to the brain and thrive in the brain microenvironment. …

Does Varicocele Repair Improve Conventional Semen Parameters? A Meta-Analytic Study Of Before-After Data, Rossella Cannarella, Rupin Shah, Taha Abo-Almagd Abdel-Meguid Hamoda, Florence Boitrelle, Ramadan Saleh, Murat Gul, Amarnath Rambhatla, Parviz Kavoussi, Tuncay Toprak, Ahmed M Harraz, Edmund Ko, Gökhan Çeker, Damayanthi Durairajanayagam, Noora Alkahidi, Shinnosuke Kuroda, Andrea Crafa, Ralf Henkel, Gianmaria Salvio, Berk Hazir, Mahsa Darbandi, Marion Bendayan, Sara Darbandi, Marco Falcone, Nicolas Garrido, Raghavender Kosgi, Raneen Sawaid Kaiyal, Keshab Karna, Nguyen Ho Vinh Phuoc, Ponco Birowo, Giovanni M Colpi, Jean De La Rosette, Germar-Michael Pinggera, Quang Nguyen, Armand Zini, Wael Zohdy, Rajender Singh, Pallavi Saini, Sidney Glina, Haocheng Lin, Taymour Mostafa, Cesar Rojas-Cruz, Mohamed Arafa, Aldo E Calogero, Fotios Dimitriadis, Priyank Kothari, Vilvapathy Senguttuvan Karthikeyan, Keisuke Okada, Koji Chiba, Ates Kadıoglu, Baris Altay, Tahsin Turunc, Birute Zilaitiene, Fatih Gokalp, Aram Adamyan, Darren Katz, Eric Chung, Tiago Cesar Mierzwa, Daniel Suslik Zylbersztejn, Gustavo Marquesine Paul, Nikolaos Sofikitis, Ioannis Sokolakis, Vineet Malhotra, Sakti Ronggowardhana Brodjonegoro, Ricky Adriansjah, Akira Tsujimura, Toshiyasu Amano, Giancarlo Balercia, Imad Ziouziou, Isaac Ardianson Deswanto, Marlon Martinez, Hyun Jun Park, Mustafa Emre Bakırcıoglu, Erman Ceyhan, Kaan Aydos, Jonathan Ramsay, Suks Minhas, Manaf Al Hashimi, Ramy Abou Ghayda, Nicholas Tadros, Puneet Sindhwani, Christopher C K Ho, Rinaldo Indra Rachman, Marcelo Rodriguez Pena, Ahmad Motawi, Arun Karthik Ponnusamy, Satish Dipankar, Azwar Amir, Saleh Binsaleh, Ege Can Serefoglu, Ravi Banthia, Kareim Khalafalla, Ari Basukarno, Nguyen Hoai Bac, Karun Singla, Rafael F Ambar, Konstantinos Makarounis, Shivam Priyadarshi, Gede Wirya Kusuma Duarsa, Widi Atmoko, Sunil Jindal, Eko Arianto, Hamed Akhavizadegan, Haitham El Bardisi, Ohad Shoshany, Gian Maria Busetto, Mohamad Moussa, Mounir Jamali, Mohamed S Al-Marhoon, Mikhail Ruzaev, Hasan M A Farsi, Shingai Mutambirwa, Dong Sup Lee, Deniz Kulaksiz, Yu-Sheng Cheng, Abderrazak Bouzouita, Selcuk Sarikaya, Hussein Kandil, Georgios Tsampoukas, Ala'a Farkouh, Kasonde Bowa, Missy Savira, Nasser Mogharabian, Tan V Le, Maruto Harjanggi, Dang Tuan Anh, Tran Quang Tien Long, Mohammad Ayodhia Soebadi, Lukman Hakim, Marko Tanic, Umut Cagin Ari, Firuza R Parikh, Gokhan Calik, Vinod Kv, Gyem Dorji, Andri Rezano, Osvaldo Rajmil, Dung Mai Ba Tien, Yiming Yuan, Juan Francisco Lizarraga-Salas, Balantine Eze, Kay Seong Ngoo, Joe Lee, Umut Arslan, Ashok Agarwal, Global Andrology Forum

Faculty, Staff and Student Publications

Purpose: The purpose of this meta-analysis is to study the impact of varicocele repair in the largest cohort of infertile males with clinical varicocele by including all available studies, with no language restrictions, comparing intra-person conventional semen parameters before and after the repair of varicoceles.

Materials and methods: The meta-analysis was performed according to PRISMA-P and MOOSE guidelines. A systematic search was performed in Scopus, PubMed, Cochrane, and Embase databases. Eligible studies were selected according to the PICOS model (Population: infertile male patients with clinical varicocele; Intervention: varicocele repair; Comparison: intra-person before-after varicocele repair; Outcome: conventional semen parameters; Study type: …

Technical Aspects And Clinical Limitations Of Sperm Dna Fragmentation Testing In Male Infertility: A Global Survey, Current Guidelines, And Expert Recommendations, Ashok Agarwal, Ala'a Farkouh, Ramadan Saleh, Taha Abo-Almagd Abdel-Meguid Hamoda, Gianmaria Salvio, Florence Boitrelle, Ahmed M Harraz, Ramy Abou Ghayda, Parviz Kavoussi, Murat Gül, Tuncay Toprak, Giorgio Ivan Russo, Damayanthi Durairajanayagam, Amarnath Rambhatla, Ponco Birowo, Rossella Cannarella, Nguyen Ho Vinh Phuoc, Armand Zini, Mohamed Arafa, Christine Wyns, Kelton Tremellen, Selçuk Sarıkaya, Sheena Lewis, Donald P Evenson, Edmund Ko, Aldo E Calogero, Fahmi Bahar, Marlon Martínez, Rafael F Ambar, Giovanni M Colpi, Mustafa Emre Bakircioglu, Ralf Henkel, Hussein Kandil, Ege Can Serefoglu, Abdullah Alfakhri, Akira Tsujimura, Alireza Kheradmand, Angelo Marino, Aram Adamyan, Birute Zilaitiene, Cevahir Ozer, Edoardo Pescatori, Paraskevi Vogiatzi, Gian Maria Busetto, Giancarlo Balercia, Haitham Elbardisi, Hamed Akhavizadegan, Hesamoddin Sajadi, Hisanori Taniguchi, Hyun Jun Park, Israel Maldonado Rosas, Mohamed Al-Marhoon, Mohammad Ali Sadighi Gilani, Naif Alhathal, Nguyen Quang, Germar-Michael Pinggera, Priyank Kothari, Sava Micic, Sheryl Homa, Tran Quang Tien Long, Wael Zohdy, Widi Atmoko, Wael Ibrahim, Marjan Sabbaghian, Saad Mohammed Abumelha, Eric Chung, Muhammet Rasit Ugur, Mehmet Serkan Ozkent, Osama Selim, Mahsa Darbandi, Shinichiro Fukuhara, Mounir Jamali, Jean De La Rosette, Shinnosuke Kuroda, Ryan P Smith, Aykut Baser, Arif Kalkanli, Nicholas N Tadros, Kaan Aydos, Tiago Cesar Mierzwa, Kareim Khalafalla, Vineet Malhotra, Mohamad Moussa, Federica Finocchi, Rinaldo Indra Rachman, Carlo Giulioni, Tomer Avidor-Reiss, Oguzhan Kahraman, Gökhan Çeker, Cătălina Zenoaga-Barbăroșie, Trenton L Barrett, Mehmet Yilmaz, Ates Kadioglu, Sunil Jindal, Huda Omran, Kadir Bocu, Vilvapathy Senguttuvan Karthikeyan, Giorgio Franco, Jesús Fernando Solorzano, Ranjit B Vishwakarma, Eko Arianto, Nicolas Garrido, Divyanu Jain, Nazim Gherabi, Ioannis Sokolakis, Ayad Palani, Gokhan Calik, Deniz Kulaksiz, Vaida Simanaviciene, Mara Simopoulou, Nur Dokuzeylül Güngör, Gideon Blecher, Marco Falcone, Davor Jezek, Mirko Preto, Edouard Amar, Tan V Le, Sun Tae Ahn, Andri Rezano, Keerti Singh, Lucia Rocco, Missy Savira, Osvaldo Rajmil, Sara Darbandi, Emrullah Sogutdelen, Luca Boeri, Guadalupe Hernández, Lukman Hakim, Yoshiharu Morimoto, Andrian Japari, Nikolaos Sofikitis, Baris Altay, Asli Metin Mahmutoglu, Manaf Al Hashimi, Imad Ziouziou, Christina Anagnostopoulou, Haocheng Lin, Rupin Shah

Faculty, Staff and Student Publications

Purpose: Sperm DNA fragmentation (SDF) is a functional sperm abnormality that can impact reproductive potential, for which four assays have been described in the recently published sixth edition of the WHO laboratory manual for the examination and processing of human semen. The purpose of this study was to examine the global practices related to the use of SDF assays and investigate the barriers and limitations that clinicians face in incorporating these tests into their practice.

Materials and methods: Clinicians managing male infertility were invited to complete an online survey on practices related to SDF diagnostic and treatment approaches. Their responses …

Pet Image Denoising Based On Denoising Diffusion Probabilistic Model, Kuang Gong, Keith Johnson, Georges El Fakhri, Quanzheng Li, Tinsu Pan

Faculty, Staff and Student Publications

Purpose: Due to various physical degradation factors and limited counts received, PET image quality needs further improvements. The denoising diffusion probabilistic model (DDPM) was a distribution learning-based model, which tried to transform a normal distribution into a specific data distribution based on iterative refinements. In this work, we proposed and evaluated different DDPM-based methods for PET image denoising.

Methods: Under the DDPM framework, one way to perform PET image denoising was to provide the PET image and/or the prior image as the input. Another way was to supply the prior image as the network input with the PET image included …

Transcriptomics Analysis Reveals Potential Mechanisms Underlying Mitochondrial Dysfunction And T Cell Exhaustion In Astronauts’ Blood Cells In Space, Maria Moreno-Villanueva, Luis E Jimenez-Chavez, Stephanie Krieger, Liang-Hao Ding, Ye Zhang, Adriana Babiak-Vazquez, Mark Berres, Sandra Splinter, Kristen E Pauken, Brian C Schaefer, Brian E Crucian, Honglu Wu

Faculty, Staff and Student Publications

Introduction: The impact of spaceflight on the immune system and mitochondria has been investigated for decades. However, the molecular mechanisms underlying spaceflight-induced immune dysregulations are still unclear.

Methods: In this study, blood from eleven crewmembers was collected before and during International Space Station (ISS) missions. Transcriptomic analysis was performed in isolated peripheral blood mononuclear cells (PBMCs) using RNA-sequencing. Differentially expresses genes (DEG) in space were determined by comparing of the inflight to the preflight samples. Pathways and statistical analyses of these DEG were performed using the Ingenuity Pathway Analysis (IPA) tool.

Results: In comparison to pre-flight, a total of 2030 …

Cryptosporidium Infection Of Human Small Intestinal Epithelial Cells Induces Type Iii Interferon And Impairs Infectivity Of Rotavirus, Valentin Greigert, Iti Saraav, Juhee Son, Yinxing Zhu, Denise Dayao, Avan Antia, Saul Tzipori, William H Witola, Thaddeus S Stappenbeck, Siyuan Ding, L David Sibley

2020-Current year OA Pubs

Cryptosporidiosis is a major cause of severe diarrheal disease in infants from resource poor settings. The majority of infections are caused by the human-specific pathogen

Hyperbaric Oxygen Augments Susceptibility To C. Difficile Infection By Impairing Gut Microbiota Ability To Stimulate The Hif-1Α-Il-22 Axis In Ilc3, José L Fachi, Laís P Pral, Helder C Assis, Sarah Oliveira, Vinícius R Rodovalho, Jefferson A C Dos Santos, Mariane F Fernandes, Valquíria A Matheus, Renata Sesti-Costa, Paulo J Basso, Marina Flóro E Silva, Niels O S Câmara, Selma Giorgio, Marco Colonna, Marco A R Vinolo

2020-Current year OA Pubs

Hyperbaric oxygen (HBO) therapy is a well-established method for improving tissue oxygenation and is typically used for the treatment of various inflammatory conditions, including infectious diseases. However, its effect on the intestinal mucosa, a microenvironment known to be physiologically hypoxic, remains unclear. Here, we demonstrated that daily treatment with hyperbaric oxygen affects gut microbiome composition, worsening antibiotic-induced dysbiosis. Accordingly, HBO-treated mice were more susceptible to

The Type Ii Raf Inhibitor Tovorafenib In Relapsed/Refractory Pediatric Low-Grade Glioma: The Phase 2 Firefly-1 Trial, Lindsay B Kilburn, Mohamed S Abdelbaki, Et Al.

2020-Current year OA Pubs

BRAF genomic alterations are the most common oncogenic drivers in pediatric low-grade glioma (pLGG). Arm 1 (n = 77) of the ongoing phase 2 FIREFLY-1 (PNOC026) trial investigated the efficacy of the oral, selective, central nervous system-penetrant, type II RAF inhibitor tovorafenib (420 mg m

Increased Hif-2Α Activity In The Nucleus Pulposus Causes Intervertebral Disc Degeneration In The Aging Mouse Spine, Shira N Johnston, Maria Tsingas, Rahatul Ain, Ruteja A Barve, Makarand V Risbud

2020-Current year OA Pubs

Hypoxia-inducible factors (HIFs) are essential to the homeostasis of hypoxic tissues. Although HIF-2α, is expressed in nucleus pulposus (NP) cells, consequences of elevated HIF-2 activity on disc health remains unknown. We expressed HIF-2α with proline to alanine substitutions (P405A; P531A) in the Oxygen-dependent degradation domain (HIF-2αdPA) in the NP tissue using an inducible, nucleus pulposus-specific K19