bluuebunny/crossref_metadata_2025_split huggingface dataset:
The carbon footprint of young-beef cattle finishing systems in the Eastern Plains of the Orinoco River Basin of Colombia
Authors: Ramírez-Restrepo Carlos A. , Vera-Infanzón Raul R. , Rao Idupulapati M. 
Published: February 2023

IntroductionPrevious research has shown increased productivity amongst sown grass pastures compared to native savanna pastures by year-round grazing for fattening of adult and young Brahman (Bos indicus)-bred cattle in the well-drained native savanna ecosystem of the Colombian Orinoquía. But there is limited information on the carbon footprint (CF) of commercial young-Brahman heifers and steers reared throughout life on well-managed Brachiaria decumbens Stapf pastures.MethodsThe present study characterized growth, lifetime enteric methane (CH4) emissions, carcass carbon dioxide equivalent (CO2-eq) CH4 efficiency intensities (i.e., emissions per kg of product), and estimated the overall CF of young cattle grazing B. decumbens pastures subject to a range of daily liveweight gains (DLWGs; 0.428 – 0.516 kg) and fattening framework (405 – 574 kg). Weaning data from seven consecutive calving seasons in a commercial Brahman breeding herd continuously grazed on B. decumbens were integrated with a Microsoft Excel® dynamic greenhouse gas emission (GHGE) simulation of stockers-yearlings, and seven fattening, and processing scenarios.ResultsThe model predicted that heifers subject to low and high DLWGs (0.428 vs 0.516 kg) and steers (0.516 kg) may be successfully fattened without supplementation assuming that animals had access to a well-managed grass pasture. Depending on the fattening strategy, kg CO2-eq CH4/kg edible protein values ranged from 66.843 to 87.488 ± 0.497 for heifers and from 69.689 to 91.291 ± 0.446 for steers.DiscussionAssuming that forage on offer is at least 1,500-2,000 kg of dry matter/ha during the rainy season, all the simulated systems showed potential for C neutrality and net-zero C emission when considering GHGEs from the soil, pasture, and animal components vs the estimated soil C capture over seven seasons. However, under a more optimistic scenario, these beef systems could accomplish substantial net gains of soil C, over the period for which field data are available. Overall, this study projects the positive impact of the design of plausible fattening strategies on grasslands for improving cattle productivity and reducing emission intensities with concomitant increases in technical efficiency.
Angiotensin receptor-neprilysin inhibitor improves coronary collateral perfusion
Authors: Li Kangbo , Kratzmann Victoria , Dai Mengjun , Gatzke Nora , Rocic Petra , Bramlage Peter , Grisk Olaf , Lubomirov Lubomir T. , Hoffmeister Meike , Lauxmann Martin A. , Ritter Oliver , Buschmann Eva , Bader Michael , Persson Anja Bondke , Buschmann Ivo , Hillmeister Philipp 
Published: February 2023

BackgroundWe investigated the pleiotropic effects of an angiotensin receptor-neprilysin inhibitor (ARNi) on collateral-dependent myocardial perfusion in a rat model of coronary arteriogenesis, and performed comprehensive analyses to uncover the underlying molecular mechanisms.MethodsA rat model of coronary arteriogenesis was established by implanting an inflatable occluder on the left anterior descending coronary artery followed by a 7-day repetitive occlusion procedure (ROP). Coronary collateral perfusion was measured by using a myocardial particle infusion technique. The putative ARNi-induced pro-arteriogenic effects were further investigated and compared with an angiotensin-converting enzyme inhibitor (ACEi). Expression of the membrane receptors and key enzymes in the natriuretic peptide system (NPS), renin-angiotensin-aldosterone system (RAAS) and kallikrein-kinin system (KKS) were analyzed by quantitative polymerase chain reaction (qPCR) and immunoblot assay, respectively. Protein levels of pro-arteriogenic cytokines were measured by enzyme-linked immunosorbent assay, and mitochondrial DNA copy number was assessed by qPCR due to their roles in arteriogenesis. Furthermore, murine heart endothelial cells (MHEC5-T) were treated with a neprilysin inhibitor (NEPi) alone, or in combination with bradykinin receptor antagonists. MHEC5-T proliferation was analyzed by colorimetric assay.ResultsThe in vivo study showed that ARNis markedly improved coronary collateral perfusion, regulated the gene expression of KKS, and increased the concentrations of relevant pro-arteriogenic cytokines. The in vitro study demonstrated that NEPis significantly promoted MHEC5-T proliferation, which was diminished by bradykinin receptor antagonists.ConclusionARNis improve coronary collateral perfusion and exert pro-arteriogenic effects via the bradykinin receptor signaling pathway.
Adjusting in a pandemic: Experiences of incoming international students
Authors: Tseu Anne , Ganesh Kirthana , Wirtz Derrick 
Published: February 2023

IntroductionOver 4 million students travel outside their home countries to pursue tertiary education in the world, with over 600,000 students traveling to Canada alone. Adjustment to new cultures has often been shown to be stressful. The COVID-19 pandemic has been a significant global event that has affected all aspects of life in different ways. Although there is research showing the negative impact of the COVID-19 pandemic on international students globally, the study of the experiences of incoming cohorts of international students, particularly during the process of planning, traveling, and arriving at the host country, is still evolving.MethodsGiven that international students are sometimes at higher risk for mental health concerns, this qualitative study sought to explore the experiences of six incoming international graduate students, ages 18 to 32, through a semi-structured interview, as they moved from their home country to Canada. It explored their cultural adjustment in the context of the COVID-19 pandemic using a thematic analysis, through a descriptive phenomenological paradigm.ResultsSix themes emerged: choosing graduate programs; influence of pandemic on admission acceptance, moving to Canada, university experiences, adjustment; and adjustment as a student. Overall, international students appear to experience a “double dose” of stressors - the typical stressors of student hood, COVID-19 related challenges, as well as their unique manifestations in the context of being an international student.DiscussionLimitations and implications of the study are discussed.
Development of a Syrian hamster anti-PD-L1 monoclonal antibody enables oncolytic adenoviral immunotherapy modelling in an immunocompetent virus replication permissive setting
Authors: Clubb James H. A. , Kudling Tatiana V. , Girych Mykhailo , Haybout Lyna , Pakola Santeri , Hamdan Firas , Cervera-Carrascon Víctor , Hemmes Annabrita , Grönberg-Vähä-Koskela Susanna , Santos João Manuel , Quixabeira Dafne C. A. , Basnet Saru , Heiniö Camilla , Arias Victor , Jirovec Elise , Kaptan Shreyas , Havunen Riikka , Sorsa Suvi , Erikat Abdullah , Schwartz Joel , Anttila Marjukka , Aro Katri , Viitala Tapani , Vattulainen Ilpo , Cerullo Vincenzo , Kanerva Anna , Hemminki Akseli 
Published: February 2023

IntroductionImmune checkpoint inhibitors (ICIs) have revolutionized the treatment of cancer, but preclinical testing of hypotheses such as combination therapies has been complicated, in part due to species incompatibility issues. For example, one of few known permissive animal models for oncolytic adenoviruses is the Syrian hamster, for which an ICI, mainly an anti-PD-L1 monoclonal antibody (mAb) was not previously available. In this study, we developed an anti-Syrian hamster PD-L1 mAb to enable the evaluation of safety and efficacy, when combining anti-PD-L1 with an oncolytic adenovirus encoding tumour necrosis factor alpha (TNFα) and interleukin-2 (IL-2) (Ad5/3-E2F-D24-hTNFα-IRES-hIL-2 or TILT-123).MethodsRecombinant Syrian hamster PD-L1 was expressed and mice immunized for mAb formation using hybridoma technology. Clonal selection through binding and functional studies in vitro, in silico and in vivo identified anti-PD-L1 clone 11B12-1 as the primary mAb candidate for immunotherapy modelling. The oncolytic virus (OV) and ICI combination approach was then evaluated using 11B12-1 and TILT-123 in a Syrian hamster model of pancreatic ductal adenocarcinoma (PDAC).ResultsSupernatants from hybridoma parent subclone 11B12B4 provided the highest positive PD-L1 signal, on Syrian hamster PBMCs and three cancer cell lines (HT100, HapT1 and HCPC1). In vitro co-cultures revealed superior immune modulated profiles of cell line matched HT100 tumour infiltrating lymphocytes when using subclones of 7G2, 11B12 and 12F1. Epitope binning and epitope prediction using AlphaFold2 and ColabFold revealed two distinct functional epitopes for clone 11B12-1 and 12F1-1. Treatment of Syrian hamsters bearing HapT1 tumours, with 11B12-1 induced significantly better (p&lt;0.05) tumour growth control than isotype control by day 12. 12F1-1 did not induce significant tumour growth control. The combination of 11B12-1 with oncolytic adenovirus TILT-123 improved tumour growth control further, when compared to monotherapy (p&lt;0.05) by day 26.ConclusionsNovel Syrian hamster anti-PD-L1 clone 11B12-1 induces tumour growth control in a hamster model of PDAC. Combining 11B12-1 with oncolytic adenovirus TILT-123 improves tumour growth control further and demonstrates good safety and toxicity profiles.
Construction and comprehensive analysis of a novel prognostic signature associated with pyroptosis molecular subtypes in patients with pancreatic adenocarcinoma
Authors: Huang Qian , Peng Xingyu , Li Qingqing , Zhu Jinfeng , Xue Ju , Jiang Hua 
Published: February 2023

BackgroundTreatment of cancer with pyroptosis is an emerging strategy. Molecular subtypes based on pyroptosis-related genes(PRGs) seem to be considered more conducive to individualized therapy. It is meaningful to construct a pyroptosis molecular subtypes-related prognostic signature (PMSRPS) to predict the overall survival (OS) of patients with pancreatic adenocarcinoma(PAAD) and guide treatment.MethodsBased on the transcriptome data of 23 PRGs, consensus clustering was applied to divide the TCGA and GSE102238 combined cohort into three PRGclusters. Prognosis-related differentially expressed genes(DEGs) among PRGclusters were subjected to LASSO Cox regression analysis to determine a PMSRPS. External cohort and in vitro experiments were conducted to verify this PMSRPS. The CIBERSORT algorithm, the ESTIMATE algorithm and the Immunophenoscore (IPS) were used to analyze the infiltrating abundance of immune cells, the tumor microenvironment (TME), and the response to immunotherapy, respectively. Wilcoxon analysis was used to compare tumor mutational burden (TMB) and RNA stemness scores (RNAss) between groups. RT-qPCR and in vitro functional experiments were used for evaluating the expression and function of SFTA2.ResultsBased on three PRGclusters, 828 DEGs were obtained and a PMSRPS was subsequently constructed. In internal and external validation, patients in the high-risk group had significantly lower OS than those in the low-risk group and PMSRPS was confirmed to be an independent prognostic risk factor for patients with PAAD with good predictive performance. Immune cell infiltration abundance and TME scores indicate patients in the high-risk group have typical immunosuppressive microenvironment characteristics. Analysis of IPS suggests patients in the high-risk group responded better to novel immune checkpoint inhibitors (ICIs) than PD1/CTLA4. The high-risk group had higher TMB and RNAss. In addition, 10 potential small-molecule compounds were screened out. Finally, we found that the mRNA expression of SFTA2 gene with the highest risk coefficient in PMSRPS was significantly higher in PAAD than in paracancerous tissues, and knockdown of it significantly delayed the progression of PAAD.ConclusionsPMSRPS can well predict the prognosis, TME and immunotherapy response of patients with PAAD, identify potential drugs, and provide treatment guidance based on individual needs.
Distinct responses of abundant and rare foraminifera to environmental variables in the Antarctic region revealed by DNA metabarcoding
Authors: Li Qingxia , Lei Yanli , Li Haotian , Li Tiegang 
Published: February 2023

The Antarctic region plays a key role in regulating the Earth’s climate and contains a unique record of environmental change. Foraminifera, a group of shell-bearing protists, are widely used as paleoenvironmental proxies. However, core-based reconstructions of Antarctic paleoenvironments are often hindered by the lack of foraminiferal fossil record. Foraminiferal ancient DNA provides new avenues for understanding environmental change, but the correlation between molecular ecological features of foraminifera and environmental conditions remains poorly understood. Here, we obtained surface sediment samples from the Southern Ocean at water depths ranging from 50 to 4399 m and measured eight environmental variables. We generated a DNA metabarcoding dataset of foraminifera and presented the first assessment of relationships between foraminiferal molecular diversity and environmental variables in the Antarctic region. The results showed that the alpha diversity of whole community and abundant subcommunity was positively correlated with water depth and negatively correlated with temperature, chlorophyll a and pheophytin a, while the alpha diversity of rare subcommunity had no linear correlation with the above environmental variables. Both rare and abundant foraminiferal subcommunities exhibited distance-decay relationships, but only the beta diversity of rare subcommunity showed a significant positive correlation with water depth. This study reveals contrasting biogeographical patterns of abundant and rare foraminifera and their different correlations with Antarctic environmental variables, holding promise to provide more proxies for reconstructing past environments using foraminiferal ancient DNA and more information for predicting the impact of future environmental changes on polar biodiversity.
Machine learning approach for automated beach waste prediction and management system: A case study of Mumbai
Authors: Apte Sayali Deepak , Sandbhor Sayali , Kulkarni Rushikesh , Khanum Humera 
Published: February 2023

Asia’s coastlines are choking in waste. The region is now home to many of the world’s most polluted beaches. The populous Indian Cities are growing economically but in an unsustainable manner. With Mumbai counted among topmost polluted beaches in the world, it is the need of the hour to take necessary steps for effective waste management by systematic data analysis for deriving useful information from waste generation patterns. The major objective of the study is pattern recognition and beach waste quantum prediction based on 5 years data, with a frequency of daily waste collection. The size of the training data set is 1,661 days and the validation data set is 335 days. The influence of population trend, waste generation during festivals, special days, weekends, and seasonal variations form the basis for the analysis. Using machine learning algorithms, the study identifies and investigates data patterns for the case study of Dadar-Mahim beach. Data frequency and weights are correlated with occurrence of events, festivals, weekends, and seasons. Exploratory Data Analysis (EDA) is employed for data preprocessing and wrangling, followed by a Random Forest algorithm-based model for the prediction of waste generated at Dadar-Mahim beach. The major challenges in data prediction are limited data availability and variation in the dates of festivals and holidays as well as lack of waste segregation information. Despite the above-mentioned challenges, the observations indicate the model’s average accuracy for making predictions of around 60%. The Graphic User Interface (GUI) developed based on the model provides a user-friendly application for predicting the total daily generation of beach waste with reasonable precision. On the basis of the model’s outcome and applicability, a schematic approach for efficient beach waste management is proposed. The recommendations would serve as guidelines for Urban Local Bodies (ULBs) to automate the collection, transport, and disposal of beach waste.
Adverse perinatal outcomes associated with antiretroviral therapy in women living with HIV: A systematic review and meta-analysis
Authors: Portwood Clara , Sexton Harriet , Kumarendran Mary , Brandon Zoe , Kirtley Shona , Hemelaar Joris 
Published: February 2023

BackgroundMaternal HIV infection is associated with an increased risk of adverse perinatal outcomes. The World Health Organization (WHO) recommends immediate initiation of lifelong antiretroviral therapy (ART) for all people living with HIV, including pregnant women living with HIV (WLHIV). We aimed to assess the risk of adverse perinatal outcomes in WLHIV receiving ART compared to ART-naïve WLHIV and HIV-negative women.Materials and methodsWe conducted a systematic literature review by searching PubMed, CINAHL, Global Health, and EMBASE for studies published between Jan 1, 1980, and April 20, 2020. Two investigators independently selected relevant studies and extracted data from studies reporting on the association of pregnant WLHIV receiving ART with adverse perinatal outcomes. Perinatal outcomes examined were preterm birth (PTB), very PTB, spontaneous PTB (sPTB), low birth weight (LBW), very LBW (VLBW), term LBW, preterm LBW, small for gestational age (SGA), very SGA (VSGA), stillbirth, and neonatal death. Random-effects meta-analyses examined the risk of adverse perinatal outcomes in WLHIV receiving ART compared to ART-naïve WLHIV and HIV-negative women. Subgroup and sensitivity analyses were performed based on country income status and study quality, and adjustment for confounding factors assessed.ResultsOf 94,594 studies identified, 73 cohort studies, including 424,277 pregnant women, met the inclusion criteria. We found that WLHIV receiving ART are associated with a significantly decreased risk of PTB (relative risk 0.79, 95% CI 0.67–0.93), sPTB (0.46, 0.32–0.66), LBW (0.86, 0.79–0.93), and VLBW (0.62, 0.39–0.97) compared to ART-naïve WLHIV. However, WLHIV receiving ART are associated with a significantly increased risk of PTB (1.42, 1.28–1.57), sPTB (2.20, 1.32–3.67), LBW (1.58, 1.36–1.84), term LBW (1.88, 1.23–2.85), SGA (1.69, 1.32–2.17), and VSGA (1.22, 1.10–1.34) compared to HIV-negative women.ConclusionART reduces the risk of adverse perinatal outcomes in pregnant WLHIV, but the risk remains higher than in HIV-negative women. Our findings support the WHO recommendation of immediate initiation of lifelong ART for all people living with HIV, including pregnant WLHIV.Systematic review registrationhttps://www.crd.york.ac.uk/prospero/, identifier CRD42021248987.
The mammalian target of rapamycin contributes to synovial fibroblast pathogenicity in rheumatoid arthritis
Authors: Barker Brianne E. , Hanlon Megan M. , Marzaioli Viviana , Smith Conor M. , Cunningham Clare C. , Fletcher Jean M. , Veale Douglas J. , Fearon Ursula , Canavan Mary 
Published: February 2023

ObjectivesThe mammalian target of Rapamycin (mTOR) is a metabolic master regulator of both innate and adaptive immunity; however, its exact role in stromal cell biology is unknown. In this study we explored the role of the mTOR pathway on Rheumatoid Arthritis synovial fibroblast (RASF) metabolism and activation and determined if crosstalk with the Hippo-YAP pathway mediates their effects.MethodsPrimary RA synovial fibroblasts (RASF) were cultured with TNFα alone or in combination with the mTOR inhibitor Rapamycin or YAP inhibitor Verteporfin. Chemokine production, matrix metalloproteinase (MMP) production, and adhesion marker expression were quantified by real-time PCR, ELISA, and/or Flow Cytometry. Invasion assays were performed using Transwell invasion chambers, while wound repair assays were used to assess RASF migration. Cellular bioenergetics was assessed using the Seahorse XFe96 Analyzer. Key metabolic genes (GLUT-1, HK2, G6PD) were measured using real-time PCR. Reanalysis of RNA-Seq analysis was performed on RA (n = 151) and healthy control (HC) (n = 28) synovial tissue biopsies to detect differential gene and pathway expression. The expression of YAP was measured by Western Blot.ResultsTranscriptomic analysis of healthy donor and RA synovial tissue revealed dysregulated expression of several key components of the mTOR pathway in RA. Moreover, the expression of phospho-ribosomal protein S6 (pS6), the major downstream target of mTOR is specifically increased in RA synovial fibroblasts compared to healthy tissue. In the presence of TNFα, RASF display heightened phosphorylation of S6 and are responsive to mTOR inhibition via Rapamycin. Rapamycin effectively alters RASF cellular bioenergetics by inhibiting glycolysis and the expression of rate limiting glycolytic enzymes. Furthermore, we demonstrate a key role for mTOR signaling in uniquely mediating RASF migratory and invasive mechanisms, which are significantly abrogated in the presence of Rapamycin. Finally, we report a significant upregulation in several genes involved in the Hippo-YAP pathway in RA synovial tissue, which are predicted to converge with the mTOR pathway. We demonstrate crosstalk between the mTOR and YAP pathways in mediating RASF invasive mechanism whereby Rapamycin significantly abrogates YAP expression and YAP inhibition significantly inhibits RASF invasiveness.ConclusionmTOR drives pathogenic mechanisms in RASF an effect which is in part mediated via crosstalk with the Hippo-YAP pathway.
Fast myocardial perfusion SPECT denoising using an attention-guided generative adversarial network
Authors: Sun Jingzhang , Yang Bang-Hung , Li Chien-Ying , Du Yu , Liu Yi-Hwa , Wu Tung-Hsin , Mok Greta S. P. 
Published: February 2023

PurposeDeep learning-based denoising is promising for myocardial perfusion (MP) SPECT. However, conventional convolutional neural network (CNN)-based methods use fixed-sized convolutional kernels to convolute one region within the receptive field at a time, which would be ineffective for learning the feature dependencies across large regions. The attention mechanism (Att) is able to learn the relationships between the local receptive field and other voxels in the image. In this study, we propose a 3D attention-guided generative adversarial network (AttGAN) for denoising fast MP-SPECT images.MethodsFifty patients who underwent 1184 MBq 99mTc-sestamibi stress SPECT/CT scan were retrospectively recruited. Sixty projections were acquired over 180° and the acquisition time was 10 s/view for the full time (FT) mode. Fast MP-SPECT projection images (1 s to 7 s) were generated from the FT list mode data. We further incorporated binary patient defect information (0 = without defect, 1 = with defect) into AttGAN (AttGAN-def). AttGAN, AttGAN-def, cGAN, and Unet were implemented using Tensorflow with the Adam optimizer running up to 400 epochs. FT and fast MP-SPECT projection pairs of 35 patients were used for training the networks for each acquisition time, while 5 and 10 patients were applied for validation and testing. Five-fold cross-validation was performed and data for all 50 patients were tested. Voxel-based error indices, joint histogram, linear regression, and perfusion defect size (PDS) were analyzed.ResultsAll quantitative indices of AttGAN-based networks are superior to cGAN and Unet on all acquisition time images. AttGAN-def further improves AttGAN performance. The mean absolute error of PDS by AttcGAN-def was 1.60 on acquisition time of 1 s/prj, as compared to 2.36, 2.76, and 3.02 by AttGAN, cGAN, and Unet.ConclusionDenoising based on AttGAN is superior to conventional CNN-based networks for MP-SPECT.