bluuebunny/crossref_metadata_2025_split huggingface dataset:
Integrative omics framework for characterization of coral reef ecosystems from the Tara Pacific expedition
Authors: Belser Caroline , Poulain Julie , Labadie Karine , Gavory Frederick , Alberti Adriana , Guy Julie , Carradec Quentin , Cruaud Corinne , Da Silva Corinne , Engelen Stefan , Mielle Paul , Perdereau Aude , Samson Gaelle , Gas Shahinaz ,   Genoscope Technical Team, Batisse Julie , Beluche Odette , Bertrand Laurie , Bohers Chloé , Bordelais Isabelle , Brun Elodie , Dubois Maria , Dumont Corinne , Zineb El Hajji , Estrada Barbara , Ettedgui Evelyne , Fernandez Patricia , Garidi Sonia , Guérin Thomas , Gorrichon Kevin , Hamon Chadia , Kientzel Lucille , Lebled Sandrine , Legrain Chloé , Lenoble Patricia , Lepretre Marine , Louesse Claudine , Magdelenat Ghislaine , Mahieu Eric , Martins Nathalie , Milani Claire , Orvain Céline , Oztas Sophie , Payen Emilie , Petit Emmanuelle , Rio Guillaume , Robert Dominique , Ronsin Muriel , Vacherie Benoit , Voolstra Christian R. , Galand Pierre E. , Flores J. Michel , Hume Benjamin C. C. , Perna Gabriela , Ziegler Maren , Ruscheweyh Hans-Joachim , Boissin Emilie , Romac Sarah , Bourdin Guillaume , Iwankow Guillaume , Moulin Clémentine , Paz García David A. , Agostini Sylvain , Banaigs Bernard , Boss Emmanuel , Bowler Chris , de Vargas Colomban , Douville Eric , Forcioli Didier , Furla Paola , Gilson Eric , Lombard Fabien , Pesant Stéphane , Reynaud Stéphanie , Sunagawa Shinichi , Thomas Olivier P. , Troublé Romain , Thurber Rebecca Vega , Zoccola Didier , Scarpelli Claude , Jacoby E’ Krame , Oliveira Pedro H. , Aury Jean-Marc , Allemand Denis , Planes Serge , Wincker Patrick 
Published: June 2023

AbstractCoral reef science is a fast-growing field propelled by the need to better understand coral health and resilience to devise strategies to slow reef loss resulting from environmental stresses. Key to coral resilience are the symbiotic interactions established within a complex holobiont, i.e. the multipartite assemblages comprising the coral host organism, endosymbiotic dinoflagellates, bacteria, archaea, fungi, and viruses. Tara Pacific is an ambitious project built upon the experience of previous Tara Oceans expeditions, and leveraging state-of-the-art sequencing technologies and analyses to dissect the biodiversity and biocomplexity of the coral holobiont screened across most archipelagos spread throughout the entire Pacific Ocean. Here we detail the Tara Pacific workflow for multi-omics data generation, from sample handling to nucleotide sequence data generation and deposition. This unique multidimensional framework also includes a large amount of concomitant metadata collected side-by-side that provide new assessments of coral reef biodiversity including micro-biodiversity and shape future investigations of coral reef dynamics and their fate in the Anthropocene.
PacBio Hi-Fi genome assembly of the Iberian dolphin freshwater mussel Unio delphinus Spengler, 1793
Authors: Gomes-dos-Santos André , Lopes-Lima Manuel , Machado M. André , Teixeira Amílcar , C. Castro L. Filipe , Froufe Elsa 
Published: June 2023

AbstractMussels of order Unionida are a group of strictly freshwater bivalves with nearly 1,000 described species widely dispersed across world freshwater ecosystems. They are highly threatened showing the highest record of extinction events within faunal taxa. Conservation is particularly concerning in species occurring in the Mediterranean biodiversity hotspot that are exposed to multiple anthropogenic threats, possibly acting in synergy. That is the case of the dolphin freshwater musselUnio delphinusSpengler, 1793, endemic to the western Iberian Peninsula with recently strong population declines. To date, only four genome assemblies are available for the order Unionida and only one European species. We present the first genome assembly ofUnio delphinus. We used the PacBio HiFi to generate a highly contiguous genome assembly. The assembly is 2.5 Gb long, possessing 1254 contigs with a contig N50 length of 10 Mbp. This is the most contiguous freshwater mussel genome assembly to date and is an essential resource for investigating the species’ biology and evolutionary history that ultimately will help to support conservation strategies.
Maternal and/or post-weaning supplementation with Bacillus altitudinis spores modulates the microbial composition of colostrum, digesta and faeces in pigs
Authors: Rattigan Ruth , Lawlor Peadar G. , Cormican Paul , Crespo-Piazuelo Daniel , Cullen James , Phelan John P. , Ranjitkar Samir , Crispie Fiona , Gardiner Gillian E. 
Published: June 2023

AbstractThis study examined the effects of maternal and/or post-weaning Bacillus altitudinis supplementation on the microbiota in sow colostrum and faeces, and offspring digesta and faeces. Sows (n = 12/group) were assigned to: (1) standard diet (CON), or (2) CON supplemented with probiotic B. altitudinis spores (PRO) from day (d)100 of gestation to weaning (d26 of lactation). At weaning, offspring were assigned to CON or PRO for 28d, resulting in: (1) CON/CON, (2) CON/PRO, (3) PRO/CON, and (4) PRO/PRO, after which all received CON. Samples were collected from sows and selected offspring (n = 10/group) for 16S rRNA gene sequencing. Rothia was more abundant in PRO sow colostrum. Sow faeces were not impacted but differences were identified in offspring faeces and digesta. Most were in the ileal digesta between PRO/CON and CON/CON on d8 post-weaning; i.e. Bacteroidota, Alloprevotella, Prevotella, Prevotellaceae, Turicibacter, Catenibacterium and Blautia were more abundant in PRO/CON, with Firmicutes and Blautia more abundant in PRO/PRO compared with CON/CON. Lactobacillus was more abundant in PRO/CON faeces on d118 post-weaning. This increased abundance of polysaccharide-fermenters (Prevotella, Alloprevotella, Prevotellaceae), butyrate-producers (Blautia) and Lactobacillus likely contributed to previously reported improvements in growth performance. Overall, maternal, rather than post-weaning, probiotic supplementation had the greatest impact on intestinal microbiota.
Optimizing gamma radiation shielding with cobalt-titania hybrid nanomaterials
Authors: Alhindawy Islam G. , Sayyed M. I. , Almuqrin Aljawhara H. , Mahmoud Karem A. 
Published: June 2023

AbstractCobalt-doped titania nanocomposites were fabricated to be utilized for radiation shielding aims. The chemical composition of the composites was measured using the energy-dispersive X-ray spectrometer. Moreover, the structure of the composites was evaluated using the X-ray diffractometer, and the morphology of the fabricated composites was presented using the scanning electron microscope. Furthermore, the γ-ray shielding properties were estimated using the Monte Carlo simulation between 0.059 and 2.506 MeV. The linear attenuation coefficient of the fabricated composites decreased by factors of 93% for all samples by raising the incident γ-energy between 0.059 and 2.506 MeV. Moreover, the partial replacement of the Ti4+ by Co3+ slightly enhanced the linear attenuation coefficient from 0.607 to 0.630 cm−1 when the Co3+ increased from 0 to 3.7 wt%. The improvement in the linear attenuation coefficient causes an enhancement in other radiation shielding properties.
Exosomes with overexpressed miR 147a suppress angiogenesis and infammatory injury in an experimental model of atopic dermatitis
Authors: Shi Chenlong , Pei Sujun , Ding Ying , Tao Congmin , Zhu Yuanzheng , Peng Ying , Li Wei , Yi Yangyan 
Published: June 2023

AbstractAtopic dermatitis is defined as an intensely systemic inflammation among skin diseases. Exosomes derived from adipose-derived stem cells may be a novel cell-free therapeutic strategy for atopic dermatitis treatment. This study aims to elucidate the possible underlying mechanism of adipose-derived stem cells-exosomes harboring microRNA-147a in atopic dermatitis pathogenesis. BALB/c mice treated withDermatophagoides farinaeextract/2,4-dinitrochlorobenzene were defined as a mouse model of atopic dermatitis, either with inflamed HaCaT cells and HUVECs exposed with TNF-α/IFN-γ stimulation were applied for a cell model of atopic dermatitis. The concentrations of IL-1β and TNF-α in the supernatants were examined by ELISA. Cell viability and migration were assessed by MTT and Transwell assay. The apoptosis was examined using flow cytometry and TUNEL staining. The tube formation assay was employed to analyzed angiogenesis. The molecular regulations among miR-147a, MEF2A, TSLP and VEGFA were confirmed using luciferase reporter assay, either with ChIP. microRNA-147a was markedly downregulated in the serum and skin samples of atopic dermatitis mice, of which overexpression remarkably promoted HaCaT cell proliferation, meanwhile inhibiting inflammatory response and cell apoptosis. microRNA-147a in adipose-derived stem cells was subsequently overexpressed, and exosomes (Exos-miR-147a mimics) were collected. Functionally, exos-microRNA-147a mimics attenuated TNF-α/IFN-γ-induced HaCaT cell inflammatory response and apoptosis, and suppressed HUVECs angiogenesis. Encouraging, molecular interaction experiments revealed that exosomal microRNA-147a suppressed TNF-α/IFN-γ-induced HUVECs angiogenesis by targeting VEGFA, and exosomal microRNA-147a repressed HaCaT cells inflammatory injury through the MEF2A-TSLP axis. Mechanistically, exosomal microRNA-147a repressed pathological angiogenesis and inflammatory injury during atopic dermatitis progression by targeting VEGFA and MEF2A-TSLP axis. microRNA-147a-overexpressing adipose-derived stem cells-derived exosomes suppressed pathological angiogenesis and inflammatory injury in atopic dermatitis by targeting VEGFA and MEF2A-TSLP axis.
Multiscale assessment of habitat selection and avoidance of sympatric carnivores by the endangered ocelot
Authors: Sergeyev Maksim , Cherry Michael J. , Tanner Evan P. , Lombardi Jason V. , Tewes Michael E. , Campbell Tyler A. 
Published: June 2023

AbstractHabitat selection by animals is a complex, dynamic process that can vary across spatial and temporal scales. Understanding habitat selection is a vital component of managing endangered species. Ocelots (Leopardus pardalis), a medium-sized endangered felid, overlap in their northern range with bobcats (Lynx rufus) and coyotes (Canis latrans), with all three species sharing similar space and resource use. As the potential for competition between these three carnivores is high, understanding differences in habitat use and the effect of these potential competitors on habitat selection of ocelots is essential to conservation. Our objective was to compare habitat selection between species and examine if ocelots avoided areas used by competitors at broad and fine scales. We captured and collared 8 ocelots, 13 bobcats, and 5 coyotes on the East Foundation’s El Sauz Ranch and the Yturria San Francisco Ranch in South Texas, USA from 2017 to 2021. We compared 2nd (position of home range) and 3rd (use within the home range) order selection across species and examined whether ocelots avoided areas categorized as high probability of use by bobcats and coyotes across both orders of selection. We found a preference for heterogeneous landscapes by bobcats and coyotes while ocelots were strongly tied to woody cover across both orders. At the 2nd order, ocelots selected areas with higher probability of use by bobcats and showed no response to higher probability of use by coyotes, suggesting ocelots did not avoid either species. However, at the 3rd order, ocelots avoided areas used by coyotes. Ocelots selected for areas of use by bobcats at the 2nd order and 3rd order. Results suggest that at the broader scale, placement of the home range is not affected by the presence of sympatric carnivores, however, at a finer scale, ocelots are avoiding coyotes but not bobcats. Our study emphasizes the importance of woody and herbaceous cover at the broad scale and dense vegetation at the finer scale to sustain ocelots. In addition, we show differing patterns of interspecific avoidance by ocelots across species and scales.
Machine learning for predicting survival of colorectal cancer patients
Authors: Buk Cardoso Lucas , Cunha Parro Vanderlei , Verzinhasse Peres Stela , Curado Maria Paula , Fernandes Gisele Aparecida , Wünsch Filho Victor , Natasha Toporcov Tatiana 
Published: June 2023

AbstractColorectal cancer is one of the most incident types of cancer in the world, with almost 2 million new cases annually. In Brazil, the scenery is the same, around 41 thousand new cases were estimated in the last 3 years. This increase in cases further intensifies the interest and importance of studies related to the topic, especially using new approaches. The use of machine learning algorithms for cancer studies has grown in recent years, and they can provide important information to medicine, in addition to making predictions based on the data. In this study, five different classifications were performed, considering patients’ survival. Data were extracted from Hospital Based Cancer Registries of São Paulo, which is coordinated by Fundação Oncocentro de São Paulo, containing patients with colorectal cancer from São Paulo state, Brazil, treated between 2000 and 2021. The machine learning models used provided us the predictions and the most important features for each one of the algorithms of the studies. Using part of the dataset to validate our models, the results of the predictors were around 77% of accuracy, with AUC close to 0.86, and the most important column was the clinical staging in all of them.
Seismic characteristics and AVO response for non-uniform Miocene reservoirs in offshore eastern Mediterranean region, Egypt
Authors: El-Ata Ahmed S. Abu , El-Gendy Nader H. , El-Nikhely Adly H. , Raslan Samir M. , El-Oribi Mahmoud S. , Barakat Moataz Kh. 
Published: June 2023

AbstractThe Eastern Mediterranean region, extending from the Offshore Nile Delta Cone of Egypt to the Levant Basin, is a confirmed hydrocarbon-rich territory with several giant gas discoveries. Numerous gas fields have been discovered in the Miocene reservoirs within the Nile Delta Cone, and the Levant Basin. The Miocene sedimentary sequences in this region are extremely heterogeneous, consisting mainly of turbiditic slope deposits, channels, and basin floor fans that were capped by evaporites formed during the Messinian Salinity Crisis. As a result, the seismic characteristics and interpreted properties of this heterogeneous section are ambiguous. The study area is located in the Offshore North Sinai Basin, where a thick Early Miocene section was deposited midway between the Nile Delta province, which includes the El-Fayrouz discovery, and the Levant Basin, which includes Tamar, Tanin, and several other discoveries. This study uses quantitative seismic interpretations methods, such as amplitude variations with offset and fluid replacement modeling, to assess the seismic acoustic impedance trend with depth. Also, determine the seismic amplitude response for the brine and gas sands reservoir of the Early and Late Miocene section to link the unexplored study area within the North Sinai Offshore Basin with the explored Nile Delta and Levant Basins. In addition to evaluate direct hydrocarbon indicator (DHI) of the dimming seismic amplitude that is compatible with the structure’s last closed contour of the Syrian Arc anticline of the Early Miocene reservoirs (EMT-1 prospect). Different vintages of 2D and 3D seismic data, six wells, and various published data were used in this study. The quantitative interpretation shows the pitfalls of the acoustic impedance trend and seismic response dependency on depth for gas and brine sand, which led to the drilling of the EMT-1 dry well. Also, the fluid replacement, P-wave velocity (Vp), and density (ρ) modeling confirmed that the seismic dimming amplitude was due to a seismic processing artifact, which was corrected by readjusting the overburden Messinian salt processing velocity model. This research concludes that the seismic quantitative interpretations are successfully used to assess the acoustic impedance versus depth and understand DHI pitfalls, as well as the processing workflow that could enhance the seismic image.
Prevalence, risk factors, and prognosis of central nervous system manifestations in antiphospholipid syndrome
Authors: Liu Meige , Li Gongming , Song Xiaodong , Fan Yangyi , Li Chun 
Published: June 2023

AbstractThe central nervous system (CNS) is considered as one of the most frequently affected organs in antiphospholipid syndrome (APS). This study investigated the prevalence of CNS manifestations in APS and associated risk factors and evaluated stroke recurrence. We carried out this retrospective study from 2009 to 2021 at Peking University People’s Hospital, which enrolled 342 APS patients, and 174 neurologic events were suffered by 119 patients (34.8%). Patients with and without CNS involvement were compared regarding demographics and laboratory parameters. The analysis showed that older age, livedo reticularis, and dyslipidaemia were significant related factors for CNS manifestations (P = 0.047, 0.038, and 0.030 respectively). The use of anticoagulants (P = 0.004), and/or hydroxychloroquine (P = 0.016) appeared to associated with a lower incidence of CNS manifestations. During a median follow-up of 4.1 years, 10 individuals developed new episodes of stroke in APS patients with previous ischemic strokes. Livedo reticularis, smoking and male gender may predict the risk of recurrent stroke (P = 0.020, 0.006, and 0.026 respectively). Collectively, our results indicated the protective and risk factors for CNS manifestations, as well as demonstrated that APS patients appeared at high risk of stroke recurrence despite current therapy.
A platform to reproducibly evaluate human colon permeability and damage
Authors: Marr Elizabeth E. , Mulhern Thomas J. , Welch Michaela , Keegan Philip , Caballero-Franco Celia , Johnson Bryce G. , Kasaian Marion , Azizgolshani Hesham , Petrie Timothy , Charest Joseph , Wiellette Elizabeth 
Published: June 2023

AbstractThe intestinal epithelium comprises diverse cell types and executes many specialized functions as the primary interface between luminal contents and internal organs. A key function provided by the epithelium is maintenance of a barrier that protects the individual from pathogens, irritating luminal contents, and the microbiota. Disruption of this barrier can lead to inflammatory disease within the intestinal mucosa, and, in more severe cases, to sepsis. Animal models to study intestinal permeability are costly and not entirely predictive of human biology. Here we present a model of human colon barrier function that integrates primary human colon stem cells into Draper’s PREDICT96 microfluidic organ-on-chip platform to yield a high-throughput system appropriate to predict damage and healing of the human colon epithelial barrier. We have demonstrated pharmacologically induced barrier damage measured by both a high throughput molecular permeability assay and transepithelial resistance. Using these assays, we developed an Inflammatory Bowel Disease-relevant model through cytokine induced damage that can support studies of disease mechanisms and putative therapeutics.
Combination of genetically diverse Pseudomonas phages enhances the cocktail efficiency against bacteria
Authors: Naknaen Ampapan , Samernate Thanadon , Wannasrichan Wichanan , Surachat Komwit , Nonejuie Poochit , Chaikeeratisak Vorrapon 
Published: June 2023

AbstractPhage treatment has been used as an alternative to antibiotics since the early 1900s. However, bacteria may acquire phage resistance quickly, limiting the use of phage treatment. The combination of genetically diverse phages displaying distinct replication machinery in phage cocktails has therefore become a novel strategy to improve therapeutic outcomes. Here, we isolated and studied lytic phages (SPA01 and SPA05) that infect a wide range of clinical Pseudomonas aeruginosa isolates. These relatively small myophages have around 93 kbp genomes with no undesirable genes, have a 30-min latent period, and reproduce a relatively high number of progenies, ranging from 218 to 240 PFU per infected cell. Even though both phages lyse their hosts within 4 h, phage-resistant bacteria emerge during the treatment. Considering SPA01-resistant bacteria cross-resist phage SPA05 and vice versa, combining SPA01 and SPA05 for a cocktail would be ineffective. According to the decreased adsorption rate of the phages in the resistant isolates, one of the anti-phage mechanisms may occur through modification of phage receptors on the target cells. All resistant isolates, however, are susceptible to nucleus-forming jumbophages (PhiKZ and PhiPA3), which are genetically distinct from phages SPA01 and SPA05, suggesting that the jumbophages recognize a different receptor during phage entry. The combination of these phages with the jumbophage PhiKZ outperforms other tested combinations in terms of bactericidal activity and effectively suppresses the emergence of phage resistance. This finding reveals the effectiveness of the diverse phage-composed cocktail for reducing bacterial growth and prolonging the evolution of phage resistance.
Association of citrullination with the progression of aortic stenosis
Authors: Kim Ah-Ram , Ji Eunhye , Lee Sahmin , Hong Seokchan , Kim Dae-Hee , Song Jong-Min , Kang Duk-Hyun , Song Jae-Kwan 
Published: June 2023

AbstractDespite its clinical importance, biomarkers of disease activity in aortic stenosis (AS) are lacking. We investigated the association between anti-cyclic citrullinated peptide (CCP) antibodies and AS. All 678 patients who underwent echocardiography and anti-CCP antibody testing were analysed. Anti-CCP antibody status was categorized as negative, low-positive, and high-positive. In addition, aortic valve (AV) tissues were obtained from the patients with and without AS to analyze the presence of citrullinated proteins. At baseline, 241 (35.5%) subjects with AV degeneration had a higher rate of anti-CCP antibody positivity (42.7% versus 34.6%, p = 0.035) than those without AV degeneration. Out of the 331 (48.8%) subjects who underwent echocardiographic follow-up, progression of AS was observed in 34 (10.3%) patients, with a higher incidence in the high-positive group compared to the low-positive or negative group (19.0% vs. 11.3% vs. 8.4%, respectively; p = 0.041). On multivariable analysis, high anti-CCP antibody positivity was independently associated with progression to AS (odds ratio: 2.312; 95% confidence interval: 1.006–5.310; p = 0.048). Furthermore, immunohistochemistry and Western blotting revealed increased citrullination in diseased AV compared to normal AV tissue. This study demonstrated that a high positive anti-CCP antibody result is associated with AV degeneration and may be an independent factor for AS progression.