bluuebunny/crossref_metadata_2025_split huggingface dataset:
Hydroponic potato production in wood fiber for food security
Authors: Kusnierek Krzysztof , Heltoft Pia , Møllerhagen Per Jarle , Woznicki Tomasz 
Published: June 2023

AbstractThe resilience of global food security is a critical concern. Facing limited access to land and potential disruption of the food markets, alternative, scalable, and efficient production systems are needed as a complementary buffer for maintenance of food production integrity. The purpose of this study was to introduce an alternative hydroponic potato growing system where potatoes are grown in bare wood fiber as a growing medium. A system utilizing drip irrigation and plastic bags as containers was tested for three different types of wood fiber, two cultivars and two fertigation strategies. Implementation of the system resulted in ~300% higher tuber production when compared to the local conventional farming. Mineral composition of the tubers obtained from hydroponic system was similar to the composition of tubers grown in the field and revealed potential for biofortification. In addition, a fertigation strategy where the two application points were separated across the root zone resulted in tubers with dry matter content comparable to the potatoes grown in soil. The recyclability, reusability, and simplicity of this solution may encourage its application for improving security of food production in selected areas of the world as well as its utilization in urban agriculture.
A systems biology approach to define mechanisms, phenotypes, and drivers in PanNETs with a personalized perspective
Authors: Werle Silke D. , Ikonomi Nensi , Lausser Ludwig , Kestler Annika M. T. U. , Weidner Felix M. , Schwab Julian D. , Maier Julia , Buchholz Malte , Gress Thomas M. , Kestler Angelika M. R. , Kestler Hans A. 
Published: June 2023

AbstractPancreatic neuroendocrine tumors (PanNETs) are a rare tumor entity with largely unpredictable progression and increasing incidence in developed countries. Molecular pathways involved in PanNETs development are still not elucidated, and specific biomarkers are missing. Moreover, the heterogeneity of PanNETs makes their treatment challenging and most approved targeted therapeutic options for PanNETs lack objective responses. Here, we applied a systems biology approach integrating dynamic modeling strategies, foreign classifier tailored approaches, and patient expression profiles to predict PanNETs progression as well as resistance mechanisms to clinically approved treatments such as the mammalian target of rapamycin complex 1 (mTORC1) inhibitors. We set up a model able to represent frequently reported PanNETs drivers in patient cohorts, such as Menin-1 (MEN1), Death domain associated protein (DAXX), Tuberous Sclerosis (TSC), as well as wild-type tumors. Model-based simulations suggested drivers of cancer progression as both first and second hits after MEN1 loss. In addition, we could predict the benefit of mTORC1 inhibitors on differentially mutated cohorts and hypothesize resistance mechanisms. Our approach sheds light on a more personalized prediction and treatment of PanNET mutant phenotypes.
POLCOVID: a multicenter multiclass chest X-ray database (Poland, 2020–2021)
Authors: Suwalska Aleksandra , Tobiasz Joanna , Prazuch Wojciech , Socha Marek , Foszner Pawel , Piotrowski Damian , Gruszczynska Katarzyna , Sliwinska Magdalena , Walecki Jerzy , Popiela Tadeusz , Przybylski Grzegorz , Nowak Mateusz , Fiedor Piotr , Pawlowska Malgorzata , Flisiak Robert , Simon Krzysztof , Zapolska Gabriela , Gizycka Barbara , Szurowska Edyta ,   for the POLCOVID Study Group, Oronowicz-Jaskowiak Agnieszka , Golebiewski Bogumil , Rataj Mateusz , Chmielarz Przemyslaw , Tur Adrianna , Drabik Grzegorz , Kozub Justyna , Kozanecka Anna , Hildebrandt Sebastian , Krutul-Walenciej Katarzyna , Jan Baron  , Jaroszewicz Jerzy , Wasilewski Piotr , Mazur Samuel , Klaude Krzysztof , Rataj Katarzyna , Golebiewski Bogumil , Rabiko Piotr , Rajewski Pawel , Blewaska Piotr , Sznajder Katarzyna , Plesniak Robert , Marczyk Michal , Cieszanowski Andrzej , Polanska Joanna 
Published: June 2023

AbstractThe outbreak of the SARS-CoV-2 pandemic has put healthcare systems worldwide to their limits, resulting in increased waiting time for diagnosis and required medical assistance. With chest radiographs (CXR) being one of the most common COVID-19 diagnosis methods, many artificial intelligence tools for image-based COVID-19 detection have been developed, often trained on a small number of images from COVID-19-positive patients. Thus, the need for high-quality and well-annotated CXR image databases increased. This paper introduces POLCOVID dataset, containing chest X-ray (CXR) images of patients with COVID-19 or other-type pneumonia, and healthy individuals gathered from 15 Polish hospitals. The original radiographs are accompanied by the preprocessed images limited to the lung area and the corresponding lung masks obtained with the segmentation model. Moreover, the manually created lung masks are provided for a part of POLCOVID dataset and the other four publicly available CXR image collections. POLCOVID dataset can help in pneumonia or COVID-19 diagnosis, while the set of matched images and lung masks may serve for the development of lung segmentation solutions.
The FORCIS database: A global census of planktonic Foraminifera from ocean waters
Authors: Chaabane Sonia , de Garidel-Thoron Thibault , Giraud Xavier , Schiebel Ralf , Beaugrand Gregory , Brummer Geert-Jan , Casajus Nicolas , Greco Mattia , Grigoratou Maria , Howa Hélène , Jonkers Lukas , Kucera Michal , Kuroyanagi Azumi , Meilland Julie , Monteiro Fanny , Mortyn Graham , Almogi-Labin Ahuva , Asahi Hirofumi , Avnaim-Katav Simona , Bassinot Franck , Davis Catherine V. , Field David B. , Hernández-Almeida Iván , Herut Barak , Hosie Graham , Howard Will , Jentzen Anna , Johns David G. , Keigwin Lloyd , Kitchener John , Kohfeld Karen E. , Lessa Douglas V. O. , Manno Clara , Marchant Margarita , Ofstad Siri , Ortiz Joseph D. , Post Alexandra , Rigual-Hernandez Andres , Rillo Marina C. , Robinson Karen , Sagawa Takuya , Sierro Francisco , Takahashi Kunio T. , Torfstein Adi , Venancio Igor , Yamasaki Makoto , Ziveri Patrizia 
Published: June 2023

AbstractPlanktonic Foraminifera are unique paleo-environmental indicators through their excellent fossil record in ocean sediments. Their distribution and diversity are affected by different environmental factors including anthropogenically forced ocean and climate change. Until now, historical changes in their distribution have not been fully assessed at the global scale. Here we present the FORCIS (Foraminifera Response to Climatic Stress) database on foraminiferal species diversity and distribution in the global ocean from 1910 until 2018 including published and unpublished data. The FORCIS database includes data collected using plankton tows, continuous plankton recorder, sediment traps and plankton pump, and contains ~22,000, ~157,000, ~9,000, ~400 subsamples, respectively (one single plankton aliquot collected within a depth range, time interval, size fraction range, at a single location) from each category. Our database provides a perspective of the distribution patterns of planktonic Foraminifera in the global ocean on large spatial (regional to basin scale, and at the vertical scale), and temporal (seasonal to interdecadal) scales over the past century.
Full-band, multi-angle, multi-scale, and temporal dynamic field spectral measurements in China
Authors: Wen Jianguang , Wu Xiaodan , Xiao Qing , Liu Qinhuo , Ma Mingguo , Zheng Xingming , Qu Yonghua , Jin Rui , You DongQin , Tang Yong , Lin Xingwen , Yu Wenpin , Gong Baochang , Yang Jian , Han Yuan 
Published: June 2023

AbstractField-measured spectra are critical for remote sensing physical modelling, retrieval of structural, biophysical, and biochemical parameters, and other practical applications. We present a library of field spectra, which includes (1) portable field spectroradiometer measurements of vegetation, soil, and snow in the full-wave band, (2) multi-angle spectra measurements of desert vegetation, chernozems, and snow with consideration of the anisotropic reflectance of land surface, (3) multi-scale spectra measurements of leaf and canopy of different vegetation cover surfaces, and (4) continuous reflectance spectra time-series data revealing vegetation growth dynamics of maize, rice, wheat, rape, grassland, and so on. To the best of our knowledge, this library is unique in simultaneously providing full-band, multi-angle, multi-scale spectral measurements of the main surface elements of China covering a large spatial extent over a 10-year period. Furthermore, the 101 by 101 satellite pixels of Landsat ETM/OLI and MODIS surface reflectance centered around the field site were extracted, providing a vital linkage between ground measurements and satellite observations. The code language used for this work is Matlab 2016a.
Impact of TAVR on coronary artery hemodynamics using clinical measurements and image‐based patient‐specific in silico modeling
Authors: Garber Louis , Khodaei Seyedvahid , Maftoon Nima , Keshavarz-Motamed Zahra 
Published: June 2023

AbstractIn recent years, transcatheter aortic valve replacement (TAVR) has become the leading method for treating aortic stenosis. While the procedure has improved dramatically in the past decade, there are still uncertainties about the impact of TAVR on coronary blood flow. Recent research has indicated that negative coronary events after TAVR may be partially driven by impaired coronary blood flow dynamics. Furthermore, the current technologies to rapidly obtain non-invasive coronary blood flow data are relatively limited. Herein, we present a lumped parameter computational model to simulate coronary blood flow in the main arteries as well as a series of cardiovascular hemodynamic metrics. The model was designed to only use a few inputs parameters from echocardiography, computed tomography and a sphygmomanometer. The novel computational model was then validated and applied to 19 patients undergoing TAVR to examine the impact of the procedure on coronary blood flow in the left anterior descending (LAD) artery, left circumflex (LCX) artery and right coronary artery (RCA) and various global hemodynamics metrics. Based on our findings, the changes in coronary blood flow after TAVR varied and were subject specific (37% had increased flow in all three coronary arteries, 32% had decreased flow in all coronary arteries, and 31% had both increased and decreased flow in different coronary arteries). Additionally, valvular pressure gradient, left ventricle (LV) workload and maximum LV pressure decreased by 61.5%, 4.5% and 13.0% respectively, while mean arterial pressure and cardiac output increased by 6.9% and 9.9% after TAVR. By applying this proof-of-concept computational model, a series of hemodynamic metrics were generated non-invasively which can help to better understand the individual relationships between TAVR and mean and peak coronary flow rates. In the future, tools such as these may play a vital role by providing clinicians with rapid insight into various cardiac and coronary metrics, rendering the planning for TAVR and other cardiovascular procedures more personalized.
Multicenter research priorities in pediatric CMR: results of a collaborative wiki survey
Authors: Beroukhim Rebecca S. , Merlocco Anthony , Gerardin Jennifer F. , Tham Edythe , Patel Jyoti K. , Siddiqui Saira , Goot Benjamin , Farooqi Kanwal , Soslow Jonathan , Grotenhuis Heynric , Hor Kan , Muthurangu Vivek , Raimondi Francesca 
Published: June 2023

AbstractMulticenter studies in pediatric cardiovascular magnetic resonance (CMR) improve statistical power and generalizability. However, a structured process for identifying important research topics has not been developed. We aimed to (1) develop a list of high priority knowledge gaps, and (2) pilot the use of a wiki survey to collect a large group of responses. Knowledge gaps were defined as areas that have been either unexplored or under-explored in the research literature. High priority goals were: (1) feasible and answerable from a multicenter research study, and (2) had potential for high impact on the field of pediatric CMR. Seed ideas were contributed by a working group and imported into a pairwise wiki survey format which allows for new ideas to be uploaded and voted upon (https://allourideas.org). Knowledge gaps were classified into 2 categories: ‘Clinical CMR Practice’ (16 ideas) and ‘Disease Specific Research’ (22 ideas). Over a 2-month period, 3,658 votes were cast by 96 users, and 2 new ideas were introduced. The 3 highest scoring sub-topics were myocardial disorders (9 ideas), translating new technology & techniques into clinical practice (7 ideas), and normal reference values (5 ideas). The highest priority gaps reflected strengths of CMR (e.g., myocardial tissue characterization; implementation of technologic advances into clinical practice), and deficiencies in pediatrics (e.g., data on normal reference values). The wiki survey format was effective and easy to implement, and could be used for future surveys.
Intelligent energy aware optimization protocol for vehicular adhoc networks
Authors: Elhoseny Mohamed , El-Hasnony Ibrahim M. , Tarek Zahraa 
Published: June 2023

AbstractVehicular adhoc network (VANET) plays a vital role in smart transportation. VANET includes a set of vehicles that communicate with one another via wireless links. The vehicular communication in VANET necessitates an intelligent clustering protocol to maximize energy efficiency. Since energy acts as an essential factor in the design of VANET, energy-aware clustering protocols depending upon metaheuristic optimization algorithms are required to be developed. This study introduces an intelligent energy-aware oppositional chaos game optimization-based clustering (IEAOCGO-C) protocol for VANET. The presented IEAOCGO-C technique aims to select cluster heads (CHs) in the network proficiently. The proposed IEAOCGO-C model constructs clusters based on oppositional-based learning (OBL) with the chaos game optimization (CGO) algorithm to improve efficiency. Besides, it computes a fitness function involving five parameters, namely throughput (THRPT), packet delivery ratio (PDR), network lifetime (NLT), end to end delay (ETED) and energy consumption (ECM). The experimental validation of the proposed model is accomplished, and the outcomes are studied in numerous aspects with existing models under several vehicles and measures. The simulation outcomes reported the enhanced performance of the proposed approach over the recent technologies. As a result, it has resulted in maximal NLT (4480), minimal ECM (65.6), maximal THRPT (81.6), maximal PDR (84.5), and minimal ETED (6.7) as average values over the other methods under all vehicle numbers.
Introgression of SUB1 aggravates the susceptibility of the popular rice cultivars Swarna and Savitri to stagnant flooding
Authors: Kuanar Sandhya Rani , Sarkar Ramani Kumar , Panigrahi Rashmi , Mohapatra Pravat Kumar 
Published: June 2023

AbstractIdentification of the Sub1 gene for tolerance to flash flooding and its introgression into high-yielding rice cultivars are major targets in rice breeding for flood-prone rice agro-ecosystems for ensuring yield stability. However, knowledge is scant on the response of the modified genotypes under stagnant flooding (SF) to meet the challenge of finding a superior allele that may confer greater resilience to the plant under a stress-prone environment. In pursuance, we have tested the response of Sub1-introgression in two popular rice varieties, Swarna and Savitri to SF by comparing the biochemical factors in the control of flag leaf senescence and its primary production mechanisms of the parental lines’ versus Sub1-introgressed lines. The activities of antioxidant enzymes like superoxide dismutase (SOD), catalase (CAT), glutathione peroxidase (GR), and ascorbate peroxidase (APX) increased while various parameters of primary production like total chlorophyll content, stomatal conductance (gs), normalized difference vegetation index (NDVI) and photosynthetic activity (Pn) decreased progressively with passage of time in the flag leaf of the cultivars during the post-anthesis period and SF-treatment increased the enzyme activity while depressing primary production further. Introgression of Sub1 had no influence on these activities under control conditions but widened the margin of effects under SF. It was concluded that the functional ability of flag leaf in mega rice cultivars like Swarna and Savitri decreased significantly by SF because of an ethylene-mediated promotion of senescence of the flag leaf. The enhancement of antioxidant enzyme activity by SF could not sustain the stability of primary production in the flag leaf. The introgression of the Sub1 gene made the cultivars more vulnerable to SF because the gene induced overexpression of ethylene.
Exploring the antimicrobial, antioxidant, anticancer, biocompatibility, and larvicidal activities of selenium nanoparticles fabricated by endophytic fungal strain Penicillium verhagenii
Authors: Nassar Abdel-Rahman A. , Eid Ahmed M. , Atta Hossam M. , El Naghy Wageih S. , Fouda Amr 
Published: June 2023

AbstractHerein, four endophytic fungal strains living in healthy roots of garlic were used to produce selenium nanoparticles (Se-NPs) via green synthesis. Penicillium verhagenii was found to be the most efficient Se-NPs producer with a ruby red color that showed maximum surface plasmon resonance at 270 nm. The as-formed Se-NPs were crystalline, spherical, and well-arranged without aggregation, and ranged from 25 to 75 nm in size with a zeta potential value of −32 mV, indicating high stability. Concentration-dependent biomedical activities of the P. verhagenii-based Se-NPs were observed, including promising antimicrobial activity against different pathogens (Escherichia coli, Pseudomonas aeruginosa, Bacillus subtilis, Staphylococcus aureus, Candida albicans, C. glabrata, C. tropicalis, and C. parapsilosis) with minimum inhibitory concentration (MIC) of 12.5–100 µg mL–1. The biosynthesized Se-NPs showed high antioxidant activity with DPPH-scavenging percentages of 86.8 ± 0.6% at a concentration of 1000 µg mL–1 and decreased to 19.3 ± 4.5% at 1.95 µg mL–1. Interestingly, the Se-NPs also showed anticancer activity against PC3 and MCF7 cell lines with IC50 of 225.7 ± 3.6 and 283.8 ± 7.5 µg mL–1, respectively while it is remaining biocompatible with normal WI38 and Vero cell lines. Additionally, the green synthesized Se-NPs were effective against instar larvae of a medical insect, Aedes albopictus with maximum mortality of 85.1 ± 3.1, 67.2 ± 1.2, 62.10 ± 1.4, and 51.0 ± 1.0% at a concentration of 50 µg mL–1 for I, II, III, and IV-instar larva, respectively. These data highlight the efficacy of endophytic fungal strains for cost-effective and eco-friendly Se-NPs synthesis with different applications.
Refining the evolutionary tree of the horse Y chromosome
Authors: Bozlak Elif , Radovic Lara , Remer Viktoria , Rigler Doris , Allen Lucy , Brem Gottfried , Stalder Gabrielle , Castaneda Caitlin , Cothran Gus , Raudsepp Terje , Okuda Yu , Moe Kyaw Kyaw , Moe Hla Hla , Kounnavongsa Bounthavone , Keonouchanh Soukanh , Van Nguyen Huu , Vu Van Hai , Shah Manoj Kumar , Nishibori Masahide , Kazymbet Polat , Bakhtin Meirat , Zhunushov Asankadyr , Paul Ripon Chandra , Dashnyam Bumbein , Nozawa Ken , Almarzook Saria , Brockmann Gudrun A. , Reissmann Monika , Antczak Douglas F. , Miller Donald C. , Sadeghi Raheleh , von Butler-Wemken Ines , Kostaras Nikos , Han Haige , Manglai Dugarjaviin , Abdurasulov Abdugani , Sukhbaatar Boldbaatar , Ropka-Molik Katarzyna , Stefaniuk-Szmukier Monika , Lopes Maria Susana , da Câmara Machado Artur , Kalashnikov Valery V. , Kalinkova Liliya , Zaitev Alexander M. , Novoa‐Bravo Miguel , Lindgren Gabriella , Brooks Samantha , Rosa Laura Patterson , Orlando Ludovic , Juras Rytis , Kunieda Tetsuo , Wallner Barbara 
Published: June 2023

AbstractThe Y chromosome carries information about the demography of paternal lineages, and thus, can prove invaluable for retracing both the evolutionary trajectory of wild animals and the breeding history of domesticates. In horses, the Y chromosome shows a limited, but highly informative, sequence diversity, supporting the increasing breeding influence of Oriental lineages during the last 1500 years. Here, we augment the primary horse Y-phylogeny, which is currently mainly based on modern horse breeds of economic interest, with haplotypes (HT) segregating in remote horse populations around the world. We analyze target enriched sequencing data of 5 Mb of the Y chromosome from 76 domestic males, together with 89 whole genome sequenced domestic males and five Przewalski’s horses from previous studies. The resulting phylogeny comprises 153 HTs defined by 2966 variants and offers unprecedented resolution into the history of horse paternal lineages. It reveals the presence of a remarkable number of previously unknown haplogroups in Mongolian horses and insular populations. Phylogenetic placement of HTs retrieved from 163 archaeological specimens further indicates that most of the present-day Y-chromosomal variation evolved after the domestication process that started around 4200 years ago in the Western Eurasian steppes. Our comprehensive phylogeny significantly reduces ascertainment bias and constitutes a robust evolutionary framework for analyzing horse population dynamics and diversity.
Increased plasma lipids in triple-negative breast cancer and impairment in HDL functionality in advanced stages of tumors
Authors: Sawada Maria Isabela Bloise Alves Caldas , de Fátima Mello Santana Monique , Reis Mozania , de Assis Sayonara Ivana Santos , Pereira Lucas Alves , Santos Danielle Ribeiro , Nunes Valéria Sutti , Correa-Giannella Maria Lucia Cardillo , Gebrim Luiz Henrique , Passarelli Marisa 
Published: June 2023

AbstractThe association between plasma lipids and breast cancer (BC) has been extensively explored although results are still conflicting especially regarding the relationship with high-density lipoprotein cholesterol (HDLc) levels. HDL mediates cholesterol and oxysterol removal from cells limiting sterols necessary for tumor growth, inflammation, and metastasis and this may not be reflected by measuring HDLc. We addressed recently diagnosed, treatment-naïve BC women (n = 163), classified according to molecular types of tumors and clinical stages of the disease, in comparison to control women (CTR; n = 150) regarding plasma lipids and lipoproteins, HDL functionality and composition in lipids, oxysterols, and apo A-I. HDL was isolated by plasma discontinuous density gradient ultracentrifugation. Lipids (total cholesterol, TC; triglycerides, TG; and phospholipids, PL) were determined by enzymatic assays, apo A-I by immunoturbidimetry, and oxysterols (27, 25, and 24-hydroxycholesterol), by gas chromatography coupled with mass spectrometry. HDL-mediated cell cholesterol removal was determined in macrophages previously overloaded with cholesterol and 14C-cholesterol. Lipid profile was similar between CTR and BC groups after adjustment per age. In the BC group, lower concentrations of TC (84%), TG (93%), PL (89%), and 27-hydroxicholesterol (61%) were observed in HDL, although the lipoprotein ability in removing cell cholesterol was similar to HDL from CRT. Triple-negative (TN) BC cases presented higher levels of TC, TG, apoB, and non-HDLc when compared to other molecular types. Impaired HDL functionality was observed in more advanced BC cases (stages III and IV), as cholesterol efflux was around 28% lower as compared to stages I and II. The altered lipid profile in TN cases may contribute to channeling lipids to tumor development in a hystotype with a more aggressive clinical history. Moreover, findings reinforce the dissociation between plasma levels of HDLc and HDL functionality in determining BC outcomes.