bluuebunny/crossref_metadata_2025_split huggingface dataset:
A biallelic multiple nucleotide length polymorphism explains functional causality at 5p15.33 prostate cancer risk locus
Authors: Spisak Sandor , Tisza Viktoria , Nuzzo Pier Vitale , Seo Ji-Heui , Pataki Balint , Ribli Dezso , Sztupinszki Zsofia , Bell Connor , Rohanizadegan Mersedeh , Stillman David R. , Alaiwi Sarah Abou , Bartels Alan H. , Papp Marton , Shetty Anamay , Abbasi Forough , Lin Xianzhi , Lawrenson Kate , Gayther Simon A. , Pomerantz Mark , Baca Sylvan , Solymosi Norbert , Csabai Istvan , Szallasi Zoltan , Gusev Alexander , Freedman Matthew L. 
Published: August 2023

AbstractTo date, single-nucleotide polymorphisms (SNPs) have been the most intensively investigated class of polymorphisms in genome wide associations studies (GWAS), however, other classes such as insertion-deletion or multiple nucleotide length polymorphism (MNLPs) may also confer disease risk. Multiple reports have shown that the 5p15.33 prostate cancer risk region is a particularly strong expression quantitative trait locus (eQTL) for Iroquois Homeobox 4 (IRX4) transcripts. Here, we demonstrate using epigenome and genome editing that a biallelic (21 and 47 base pairs (bp)) MNLP is the causal variant regulating IRX4 transcript levels. In LNCaP prostate cancer cells (homozygous for the 21 bp short allele), a single copy knock-in of the 47 bp long allele potently alters the chromatin state, enabling de novo functional binding of the androgen receptor (AR) associated with increased chromatin accessibility, Histone 3 lysine 27 acetylation (H3K27ac), and ~3-fold upregulation of IRX4 expression. We further show that an MNLP is amongst the strongest candidate susceptibility variants at two additional prostate cancer risk loci. We estimated that at least 5% of prostate cancer risk loci could be explained by functional non-SNP causal variants, which may have broader implications for other cancers GWAS. More generally, our results underscore the importance of investigating other classes of inherited variation as causal mediators of human traits.
Single cell transcriptomic analyses implicate an immunosuppressive tumor microenvironment in pancreatic cancer liver metastasis
Authors: Zhang Shu , Fang Wen , Zhou Siqi , Zhu Dongming , Chen Ruidong , Gao Xin , Li Zhuojin , Fu Yao , Zhang Yixuan , Yang Fa , Zhao Jing , Wu Hao , Wang Pin , Shen Yonghua , Shen Shanshan , Xu Guifang , Wang Lei , Yan Chao , Zou Xiaoping , Chen Dijun , Lv Ying 
Published: August 2023

AbstractPancreatic ductal adenocarcinoma (PDAC) is a highly metastatic disease refractory to all targeted and immune therapies. However, our understanding of PDAC microenvironment especially the metastatic microenvironment is very limited partly due to the inaccessibility to metastatic tumor tissues. Here, we present the single-cell transcriptomic landscape of synchronously resected PDAC primary tumors and matched liver metastases. We perform comparative analysis on both cellular composition and functional phenotype between primary and metastatic tumors. Tumor cells exhibit distinct transcriptomic profile in liver metastasis with clearly defined evolutionary routes from cancer cells in primary tumor. We also identify specific subtypes of stromal and immune cells critical to the formation of the pro-tumor microenvironment in metastatic lesions, including RGS5+ cancer-associated fibroblasts, CCL18+ lipid-associated macrophages, S100A8+ neutrophils and FOXP3+ regulatory T cells. Cellular interactome analysis further reveals that the lack of tumor-immune cell interaction in metastatic tissues contributes to the formation of the immunosuppressive microenvironment. Our study provides a comprehensive characterization of the transcriptional landscape of PDAC liver metastasis.
Janus nanoparticles targeting extracellular polymeric substance achieve flexible elimination of drug-resistant biofilms
Authors: Liu Zhiwen , Guo Kangli , Yan Liemei , Zhang Kai , Wang Ying , Ding Xiaokang , Zhao Nana , Xu Fu-Jian 
Published: August 2023

AbstractSafe and efficient antibacterial materials are urgently needed to combat drug-resistant bacteria and biofilm-associated infections. The rational design of nanoparticles for flexible elimination of biofilms remains challenging. Herein, we propose the fabrication of Janus-structured nanoparticles targeting extracellular polymeric substance to achieve dispersion or near-infrared (NIR) light-activated photothermal elimination of drug-resistant biofilms, respectively. Asymmetrical Janus-structured dextran-bismuth selenide (Dex-BSe) nanoparticles are fabricated to exploit synergistic effects of both components. Interestingly, Janus Dex-BSe nanoparticles realize enhanced dispersal of biofilms over time. Alternatively, taking advantage of the preferential accumulation of nanoparticles at infection sites, the self-propelled active motion induced by the unique Janus structure enhances photothermal killing effect. The flexible application of Janus Dex-BSe nanoparticles for biofilm removal or NIR-triggered eradication in vivo is demonstrated by Staphylococcus aureus-infected mouse excisional wound model and abscess model, respectively. The developed Janus nanoplatform holds great promise for the efficient elimination of drug-resistant biofilms in diverse antibacterial scenarios.
Reef-building corals farm and feed on their photosynthetic symbionts
Authors: Wiedenmann Jörg , D’Angelo Cecilia , Mardones M. Loreto , Moore Shona , Benkwitt Cassandra E. , Graham Nicholas A. J. , Hambach Bastian , Wilson Paul A. , Vanstone James , Eyal Gal , Ben-Zvi Or , Loya Yossi , Genin Amatzia 
Published: August 2023

AbstractCoral reefs are highly diverse ecosystems that thrive in nutrient-poor waters, a phenomenon frequently referred to as the Darwin paradox1. The energy demand of coral animal hosts can often be fully met by the excess production of carbon-rich photosynthates by their algal symbionts2,3. However, the understanding of mechanisms that enable corals to acquire the vital nutrients nitrogen and phosphorus from their symbionts is incomplete4–9. Here we show, through a series of long-term experiments, that the uptake of dissolved inorganic nitrogen and phosphorus by the symbionts alone is sufficient to sustain rapid coral growth. Next, considering the nitrogen and phosphorus budgets of host and symbionts, we identify that these nutrients are gathered through symbiont ‘farming’ and are translocated to the host by digestion of excess symbiont cells. Finally, we use a large-scale natural experiment in which seabirds fertilize some reefs but not others, to show that the efficient utilization of dissolved inorganic nutrients by symbiotic corals established in our laboratory experiments has the potential to enhance coral growth in the wild at the ecosystem level. Feeding on symbionts enables coral animals to tap into an important nutrient pool and helps to explain the evolutionary and ecological success of symbiotic corals in nutrient-limited waters.
Generation of time-synchronized two-color X-ray free-electron laser pulses using phase shifters
Authors: Cho Myung-Hoon , Kang Teyoun , Yang Haeryong , Kim Gyujin , Kwon Seong-Hoon , Moon Kook-Jin , Nam Inhyuk , Min Chang-Ki , Heo Hoon , Kim Changbum , Kang Heung-Sik , Shim Chi Hyun 
Published: August 2023

AbstractTo optimize the intensity of X-ray free-electron lasers (XFELs), phase shifters, oriented in phase with the phases of the XFEL pulse and electron beam, are typically installed at undulator lines. Although a π-offset between the phases (i.e., an “out-of-phase” configuration) can suppress the XFEL intensity at resonant frequencies, it can also generate a side-band spectrum, which results in a two-color XFEL pulse; the dynamics of such a pulse can be described using the spontaneous radiation or low gain theory. This attributes of this two-color XFEL pulse can be amplified (log-scale amplification) through an undulator line with out-of-phase phase shifters. In this study, the features of two-color XFEL pulses were evaluated through theory, simulations and experiments performed at Pohang Accelerator Laboratory X-ray Free Electron Laser. The XFEL gain slope and energy separation between the two-color spectral peaks were consistent through theoretical expectation, and the results of simulation and experiment. The experimentally determined two-color XFEL pulse energy was 250 μJ at a photon energy of 12.38 keV with a separation of 60 eV.
Effects of 13C isotope-labeled allelochemicals on the growth of the invasive plant Alternanthera philoxeroides
Authors: Hua Zexun , Xie Qingsong , Li Yue , He Mengying , Wang Yan , Wu Hongmiao , Zhang Zhen 
Published: August 2023

AbstractThe secondary metabolites of indigenous plants have significant allelopathic inhibitory effects on the growth and development of invasive alien plants. Methyl palmitate (MP) and methyl linolenate (ML) were used as exogenous allelopathic substances. The research investigated the differences of inhibitory effects of MP and ML on the growth of seedlings of Alternantheraphiloxeroides, and calculated their morphological characteristics, biomass, physiological indicators and the response index (RI). The synthetical allelopathic index (SE) of 1 mmol/L MP was the smallest (− 0.26) and the allelopathic inhibition was the strongest; therefore, it was selected as a 13C-labeled allelochemical. The distribution of 1 mmol/L MP in different parts of A.philoxeroides and the correlation between the biomass ratios of roots, stems and leaves and the 13C content were studied by 13C stable isotope tracing experiments. Atom percent excess (APE) between roots, stems and leaves of A.philoxeroides treated with 1 mmol/L MP were significantly different in terms of magnitude, with leaves (0.17%) > roots (0.12%) > stems (0.07%). The root, stem and leaf biomass ratios of invasive weeds had great significant positive correlation with 13C content (p < 0.01, R2 between 0.96 and 0.99). This current research provides a new idea and method for the control of A.philoxeroides, but large-scale popularization remains to be studied.
Non cancer causes of death after gallbladder cancer diagnosis: a population-based analysis
Authors: Xia Yang , Lu Shuangshuang , Huo Chunyan , Fan Li , Lin Min , Huang Jin 
Published: August 2023

AbstractMortality from non cancer causes in patients with gallbladder cancer (GBC) still unclear. This study evaluated the causes and risk factors of non cancer death during different follow-up periods after GBC diagnosis. Non cancer causes of death for GBC patients diagnosed between 2000 and 2017 in Surveillance, Epidemiology and End Results database were analyzed and standardized mortality rates (SMR) for each non cancer death were calculated. Predictors for non cancer death were identified through multivariate competing risk analysis. A total 11,927 GBC patients were identified for further analysis, 9393 died during follow up. The largest proportion of non cancer deaths occurred > 3 years after diagnosis (39.4%). Most common non cancer cause were cardiovascular disease (43.3%), followed by other cause of death (34.4%) and infectious diseases (8.6%). Compared with US general population, GBC patients has higher risk of death from disease of heart (SMR, 1.58; 95%CI, 1.41–1.75), septicemia (SMR,3.21; 95%CI, 2.27–4.40), diabetes mellitus (SMR,1.97; 95%CI, 1.43–2.63), alone with other causes. Non cancer causes accounted for a significant proportion of deaths during the follow-up period after GBC diagnosis. The risk of non cancer death is higher in GBC patients than in the general population. Our study provides comprehensive assessment of death from non cancer cause in GBC patients, which has important implications for health management in GBC patients.
Association between physical demands, skin temperature and wellbeing status in elite football players
Authors: Majano Carlos , Garcia-Unanue Jorge , Fernández-Cuevas Ismael , Escamilla-Galindo Víctor , Alonso-Callejo Antonio , Sanchez-Sanchez Javier , Gallardo Leonor , Felipe Jose Luis 
Published: August 2023

AbstractThe demanding nature of elite football requires players to be closely monitored to ensure optimal performance and minimize injury risk. This study aimed to evaluate the relationship between physical demands, skin temperature, and well-being status in 30 elite football players over a 12-week competitive period. Thermography assessments, weekly Well-being questionnaires, and daily training and match load recordings were used to gather data. Results indicated that along the microcycles there was a decrease in high-intensity accelerations and decelerations distance completed, while maintaining other high-intensity actions. Furthermore, it was found that high-intensity movements contribute to the generation of thermal asymmetries in the thighs; the adductor thermal asymmetry showed a positive relationship with stress and muscle soreness, the knee thermal asymmetry had a positive relationship with fatigue and a negative relationship with rest and quality of rest, and finally the hamstrings muscles exhibited significant differences between the thermal asymmetry groups, with the high asymmetry completing less high intensity actions than the low asymmetry group. In conclusion, this study highlights the interconnections between physical demands, skin temperature, and well-being in elite football players and provides valuable insights for coaches and trainers in their efforts to optimize performance and health.
Chemical features and machine learning assisted predictions of protein-ligand short hydrogen bonds
Authors: Zhou Shengmin , Liu Yuanhao , Wang Sijian , Wang Lu 
Published: August 2023

AbstractThere are continuous efforts to elucidate the structure and biological functions of short hydrogen bonds (SHBs), whose donor and acceptor heteroatoms reside more than 0.3 Å closer than the sum of their van der Waals radii. In this work, we evaluate 1070 atomic-resolution protein structures and characterize the common chemical features of SHBs formed between the side chains of amino acids and small molecule ligands. We then develop a machine learning assisted prediction of protein-ligand SHBs (MAPSHB-Ligand) model and reveal that the types of amino acids and ligand functional groups as well as the sequence of neighboring residues are essential factors that determine the class of protein-ligand hydrogen bonds. The MAPSHB-Ligand model and its implementation on our web server enable the effective identification of protein-ligand SHBs in proteins, which will facilitate the design of biomolecules and ligands that exploit these close contacts for enhanced functions.
Plasma miR-195-5p predicts the severity of Covid-19 in hospitalized patients
Authors: Moatar Alexandra Ioana , Chis Aimee Rodica , Romanescu Mirabela , Ciordas Paula-Diana , Nitusca Diana , Marian Catalin , Oancea Cristian , Sirbu Ioan-Ovidiu 
Published: August 2023

AbstractPredicting the clinical course of Covid-19 is a challenging task, given the multi-systemic character of the disease and the paucity of minimally invasive biomarkers of disease severity. Here, we evaluated the early (first two days post-admission) level of circulating hsa-miR-195-5p (miR-195, a known responder to viral infections and SARS-CoV-2 interactor) in Covid-19 patients and assessed its potential as a biomarker of disease severity. We show that plasma miR-195 correlates with several clinical and paraclinical parameters, and is an excellent discriminator between the severe and mild forms of the disease. Our Gene Ontology analysis of miR-195 targets differentially expressed in Covid-19 indicates a strong impact on cardiac mitochondria homeostasis, suggesting a possible role in long Covid and chronic fatigue syndrome (CFS) syndromes.
Tropical leg lymphedema caused by podoconiosis is associated with increased colonisation by anaerobic bacteria
Authors: Neidhöfer Claudio , Nkwetta Derick Lekealem , Fuen Bangsi Rose , Yenban Njodzeka Flora , Mbiatong Nancielle , Nchanji Gordon Takop , Korir Patricia , Wetzig Nina , Sieber Martin , Thiele Ralf , Parcina Marijo , Klarmann-Schulz Ute , Hoerauf Achim , Wanji Samuel , Ritter Manuel 
Published: August 2023

AbstractThe non-filarial and non-communicable disease podoconiosis affects around 4 million people and is characterized by severe leg lymphedema accompanied with painful intermittent acute inflammatory episodes, called acute dermatolymphangioadenitis (ADLA) attacks. Risk factors have been associated with the disease but the mechanisms of pathophysiology remain uncertain. Lymphedema can lead to skin lesions, which can serve as entry points for bacteria that may cause ADLA attacks leading to progression of the lymphedema. However, the microbiome of the skin of affected legs from podoconiosis individuals remains unclear. Thus, we analysed the skin microbiome of podoconiosis legs using next generation sequencing. We revealed a positive correlation between increasing lymphedema severity and non-commensal anaerobic bacteria, especially Anaerococcus provencensis, as well as a negative correlation with the presence of Corynebacterium, a constituent of normal skin flora. Disease symptoms were generally linked to higher microbial diversity and richness, which deviated from the normal composition of the skin. These findings show an association of distinct bacterial taxa with lymphedema stages, highlighting the important role of bacteria for the pathogenesis of podoconiosis and might enable a selection of better treatment regimens to manage ADLA attacks and disease progression.
Diapirs of crystal-rich slurry explain granite emplacement temperature and duration
Authors: Copley Alex , Weller Owen , Bain Hero 
Published: August 2023

AbstractThe mechanism, temperature, and timescale of granite intrusion remain controversial, with wide-ranging implications for understanding continental growth, differentiation, rheology, and deformation dynamics. In this paper we present a method for determining intrusion emplacement temperature and timescale using the characteristics of the surrounding metamorphic aureole, and apply it to the Skiddaw granite in northern England. The estimated emplacement timescale (0.1–2 Myr) implies magma transport velocities of 1–100 mm/year. At the absent or low melt fractions relevant to our estimated emplacement temperature (580–650 $$^{\circ }$$

∘

C), such velocities are incompatible with pluton formation by successive injections through dykes. Instead, our results indicate the intrusion of a diapir of crystal-rich slurry, solidifying before emplacement, with a rheology governed by the solid crystals. The emplacement depth is likely to be governed by the depth-dependent rheology of the surrounding rocks, occurring close to the brittle-ductile transition. The wider implications of our results relate to (1) the appreciation that much of the chemical and textural characteristics of plutons may relate to pre-emplacement crystallisation at depth, passively transported to higher crustal levels, and (2) an explanation of the difficulty of seismically imaging active plutonism.
Combinations of lifestyle behaviors and cancer risk among Korean adults
Authors: Luu Ngoc Minh , Bui Thi Tra , Tran Thi Phuong Thao , Nguyen Thi Huyen Trang , Oh Jin-Kyoung 
Published: August 2023

AbstractCombinations of lifestyle behaviors may lead to different cancer risks. This study aimed to identify the latent classes based on lifestyle behavior trajectories and to investigate the association between these latent classes and cancer risk. Participants in the 2002–2003 National Health Insurance Service general health examination were included. Data on smoking, alcohol drinking, body mass index (BMI), and physical activity measured four times between 2002 and 2009 were analyzed. Incident cancer cases were tracked from 2010 to 2018. Patterns of alcohol drinking, smoking, BMI, and physical activity and latent classes based on trajectories of smoking, alcohol drinking, BMI, and physical activity were identified. Among 2,735,110 adults (1,787,486 men and 947,624 women), 111,218 (69,089 men and 42,129 women) developed incident cancer. Six latent classes of lifestyle behavior were identified, with Class 1 (healthy class) involving only 0.2% of men and 0.5% of women. The highest risk class in males tended to be steady light drinkers and steady moderate smokers, have steady low frequency of physical activity, and be obese. This class showed a 1.47 times higher (95% CI = 1.29–1.69) risk of all cancers than did the healthy class. Among women, there was only an association between the highest risk class (tendency to be non-drinkers, light smokers) and colorectal cancer (HR = 1.70, 95% CI = 1.02–2.83). Only a small percentage of participants maintained a long-term healthy lifestyle. Identifying classes of behavior combinations and their links to cancer development is therefore critical for cancer prevention.
A deep learning framework to scale linear facial measurements to actual size using horizontal visible iris diameter: a study on an Iranian population
Authors: Pirayesh Zeynab , Hassanzadeh-Samani Sahel , Farzan Arash , Rohban Mohammad Hossein , Ghorbanimehr Mohammad Soroush , Mohammad-Rahimi Hossein , Motamedian Saeed Reza 
Published: August 2023

AbstractDigital images allow for the objective evaluation of facial appearance and abnormalities as well as treatment outcomes and stability. With the advancement of technology, manual clinical measurements can be replaced with fully automatic photographic assessments. However, obtaining millimetric measurements on photographs does not provide clinicians with their actual value due to different image magnification ratios. A deep learning tool was developed to estimate linear measurements on images with unknown magnification using the iris diameter. A framework was designed to segment the eyes’ iris and calculate the horizontal visible iris diameter (HVID) in pixels. A constant value of 12.2 mm was assigned as the HVID value in all the photographs. A vertical and a horizontal distance were measured in pixels on photographs of 94 subjects and were estimated in millimeters by calculating the magnification ratio using HVID. Manual measurement of the distances was conducted on the subjects and the actual and estimated amounts were compared using Bland–Altman analysis. The obtained error was calculated as mean absolute percentage error (MAPE) of 2.9% and 4.3% in horizontal and vertical measurements. Our study shows that due to the consistent size and narrow range of HVID values, the iris diameter can be used as a reliable scale to calibrate the magnification of the images to obtain precise measurements in further research.