bluuebunny/crossref_metadata_2025_split huggingface dataset:
Molecular characterization of colorectal cancer related peritoneal metastatic disease
Authors: Lenos Kristiaan J. , Bach Sander , Ferreira Moreno Leandro , ten Hoorn Sanne , Sluiter Nina R. , Bootsma Sanne , Vieira Braga Felipe A. , Nijman Lisanne E. , van den Bosch Tom , Miedema Daniel M. , van Dijk Erik , Ylstra Bauke , Kulicke Ruth , Davis Fred P. , Stransky Nicolas , Smolen Gromoslaw A. , Coebergh van den Braak Robert R. J. , IJzermans Jan N. M. , Martens John W. M. , Hallam Sally , Beggs Andrew D. , Kops Geert J. P. L. , Lansu Nico , Bastiaenen Vivian P. , Klaver Charlotte E. L. , Lecca Maria C. , El Makrini Khalid , Elbers Clara C. , Dings Mark P. G. , van Noesel Carel J. M. , Kranenburg Onno , Medema Jan Paul , Koster Jan , Koens Lianne , Punt Cornelis J. A. , Tanis Pieter J. , de Hingh Ignace H. , Bijlsma Maarten F. , Tuynman Jurriaan B. , Vermeulen Louis 
Published: August 2022

AbstractA significant proportion of colorectal cancer (CRC) patients develop peritoneal metastases (PM) in the course of their disease. PMs are associated with a poor quality of life, significant morbidity and dismal disease outcome. To improve care for this patient group, a better understanding of the molecular characteristics of CRC-PM is required. Here we present a comprehensive molecular characterization of a cohort of 52 patients. This reveals that CRC-PM represent a distinct CRC molecular subtype, CMS4, but can be further divided in three separate categories, each presenting with unique features. We uncover that the CMS4-associated structural protein Moesin plays a key role in peritoneal dissemination. Finally, we define specific evolutionary features of CRC-PM which indicate that polyclonal metastatic seeding underlies these lesions. Together our results suggest that CRC-PM should be perceived as a distinct disease entity.
Subversion of GBP-mediated host defense by E3 ligases acquired during Yersinia pestis evolution
Authors: Cao Shiyang , Jiao Yang , Jiang Wei , Wu Yarong , Qin Si , Ren Yifan , You Yang , Tan Yafang , Guo Xiao , Chen Hongyan , Zhang Yuan , Wu Gengshan , Wang Tong , Zhou Yazhou , Song Yajun , Cui Yujun , Shao Feng , Yang Ruifu , Du Zongmin 
Published: August 2022

AbstractPlague has caused three worldwide pandemics in history, including the Black Death in medieval ages. Yersinia pestis, the etiological agent of plague, has evolved a powerful arsenal to disrupt host immune defenses during evolution from enteropathogenic Y. pseudotuberculosis. Here, we find that two functionally redundant E3 ligase of Y. pestis, YspE1 and YspE2, can be delivered via type III secretion injectisome into host cytosol where they ubiquitinate multiple guanylate-binding proteins (GBPs) for proteasomal degradation. However, Y. pseudotuberculosis has no such capability due to lacking functional YspE1/2 homologs. YspE1/2-mediated GBP degradations significantly promote the survival of Y. pestis in macrophages and strongly inhibit inflammasome activation. By contrast, Gbpchr3−/−, chr5−/− macrophages exhibit much lowered inflammasome activation independent of YspE1/2, accompanied with an enhanced replication of Y. pestis. Accordingly, Gbpchr3−/−, chr5−/− mice are more susceptible to Y. pestis. We demonstrate that Y. pestis utilizes E3 ligases to subvert GBP-mediated host defense, which appears to be newly acquired by Y. pestis during evolution.
The ribosome stabilizes partially folded intermediates of a nascent multi-domain protein
Authors: Chan Sammy H. S. , Włodarski Tomasz , Streit Julian O. , Cassaignau Anaïs M. E. , Woodburn Lauren F. , Ahn Minkoo , Freiherr von Sass Georg Johannes , Waudby Christopher A. , Budisa Nediljko , Cabrita Lisa D. , Christodoulou John 
Published: August 2022

AbstractCo-translational folding is crucial to ensure the production of biologically active proteins. The ribosome can alter the folding pathways of nascent polypeptide chains, yet a structural understanding remains largely inaccessible experimentally. We have developed site-specific labelling of nascent chains to detect and measure, using 19F nuclear magnetic resonance (NMR) spectroscopy, multiple states accessed by an immunoglobulin-like domain within a tandem repeat protein during biosynthesis. By examining ribosomes arrested at different stages during translation of this common structural motif, we observe highly broadened NMR resonances attributable to two previously unidentified intermediates, which are stably populated across a wide folding transition. Using molecular dynamics simulations and corroborated by cryo-electron microscopy, we obtain models of these partially folded states, enabling experimental verification of a ribosome-binding site that contributes to their high stabilities. We thus demonstrate a mechanism by which the ribosome could thermodynamically regulate folding and other co-translational processes.
Antibiotic resistance genes in the gut microbiota of mothers and linked neonates with or without sepsis from low- and middle-income countries
Authors: Carvalho M. J. , Sands K. , Thomson K. , Portal E. , Mathias J. , Milton R. , Gillespie D. , Dyer C. , Akpulu C. , Boostrom I. , Hogan P. , Saif H. , Ferreira A. , Nieto M. , Hender T. , Hood K. , Andrews R. , Watkins W. J. , Hassan B. , Chan G. , Bekele D. , Solomon S. , Metaferia G. , Basu S. , Naha S. , Sinha A. , Chakravorty P. , Mukherjee S. , Iregbu K. , Modibbo F. , Uwaezuoke S. , Audu L. , Edwin C. P. , Yusuf A. H. , Adeleye A. , Mukkadas A. S. , Zahra R. , Shirazi H. , Muhammad A. , Ullah S. N. , Jan M. H. , Akif S. , Mazarati J. B. , Rucogoza A. , Gaju L. , Mehtar S. , Bulabula A. N. H. , Whitelaw A. , Roberts L. ,   BARNARDS Group, Walsh T. R. 
Published: August 2022

AbstractEarly development of the microbiome has been shown to affect general health and physical development of the infant and, although some studies have been undertaken in high-income countries, there are few studies from low- and middle-income countries. As part of the BARNARDS study, we examined the rectal microbiota of 2,931 neonates (term used up to 60 d) with clinical signs of sepsis and of 15,217 mothers screening for blaCTX-M-15, blaNDM, blaKPC and blaOXA-48-like genes, which were detected in 56.1%, 18.5%, 0% and 4.1% of neonates’ rectal swabs and 47.1%, 4.6%, 0% and 1.6% of mothers’ rectal swabs, respectively. Carbapenemase-positive bacteria were identified by MALDI-TOF MS and showed a high diversity of bacterial species (57 distinct species/genera) which exhibited resistance to most of the antibiotics tested. Escherichia coli, Klebsiella pneumoniae and Enterobacter cloacae/E. cloacae complex, the most commonly found isolates, were subjected to whole-genome sequencing analysis and revealed close relationships between isolates from different samples, suggesting transmission of bacteria between neonates, and between neonates and mothers. Associations between the carriage of antimicrobial resistance genes (ARGs) and healthcare/environmental factors were identified, and the presence of ARGs was a predictor of neonatal sepsis and adverse birth outcomes.
Functional ultrasound localization microscopy reveals brain-wide neurovascular activity on a microscopic scale
Authors: Renaudin Noémi , Demené Charlie , Dizeux Alexandre , Ialy-Radio Nathalie , Pezet Sophie , Tanter Mickael 
Published: August 2022

AbstractThe advent of neuroimaging has increased our understanding of brain function. While most brain-wide functional imaging modalities exploit neurovascular coupling to map brain activity at millimeter resolutions, the recording of functional responses at microscopic scale in mammals remains the privilege of invasive electrophysiological or optical approaches, but is mostly restricted to either the cortical surface or the vicinity of implanted sensors. Ultrasound localization microscopy (ULM) has achieved transcranial imaging of cerebrovascular flow, up to micrometre scales, by localizing intravenously injected microbubbles; however, the long acquisition time required to detect microbubbles within microscopic vessels has so far restricted ULM application mainly to microvasculature structural imaging. Here we show how ULM can be modified to quantify functional hyperemia dynamically during brain activation reaching a 6.5-µm spatial and 1-s temporal resolution in deep regions of the rat brain.
FIVES: A Fundus Image Dataset for Artificial Intelligence based Vessel Segmentation
Authors: Jin Kai , Huang Xingru , Zhou Jingxing , Li Yunxiang , Yan Yan , Sun Yibao , Zhang Qianni , Wang Yaqi , Ye Juan 
Published: August 2022

AbstractRetinal vasculature provides an opportunity for direct observation of vessel morphology, which is linked to multiple clinical conditions. However, objective and quantitative interpretation of the retinal vasculature relies on precise vessel segmentation, which is time consuming and labor intensive. Artificial intelligence (AI) has demonstrated great promise in retinal vessel segmentation. The development and evaluation of AI-based models require large numbers of annotated retinal images. However, the public datasets that are usable for this task are scarce. In this paper, we collected a color fundus image vessel segmentation (FIVES) dataset. The FIVES dataset consists of 800 high-resolution multi-disease color fundus photographs with pixelwise manual annotation. The annotation process was standardized through crowdsourcing among medical experts. The quality of each image was also evaluated. To the best of our knowledge, this is the largest retinal vessel segmentation dataset for which we believe this work will be beneficial to the further development of retinal vessel segmentation.
Active and avoidant coping profiles in children and their relationship with anxiety and depression during the COVID-19 pandemic
Authors: Zhang Qiaochu , Zhou Yanlin , Ho Samuel M. Y. 
Published: August 2022

AbstractActive and avoidant coping styles are important dispositional factors in the development of anxiety and depression symptoms. Children use both active and avoidant coping strategies together in daily life. No studies have investigated the relationship between active–avoidant coping profiles and internalizing symptoms in children. The present study aimed to investigate children’s active–avoidant coping profiles and assess the relationship that active–avoidant coping profiles have with anxiety and depression symptoms. A two-wave longitudinal study was conducted among 322 Chinese children in the People’s Republic of China during the COVID-19 pandemic. Participants completed the Children’s Coping Strategies Checklist-Revised 1 at Time 1 and the Revised Child Anxiety and Depression Scale at Time 1 and 6 months later (Time 2). Four active–avoidant coping profiles were revealed: low active copers, high active copers, balanced copers, and avoidant copers. Low and high active copers had lower levels of anxiety and depression symptoms than balanced copers and avoidant copers. Avoidant copers showed a larger decrease in depression symptoms than balanced copers and high active copers during the COVID-19 pandemic. It is important to improve children’s active–avoidant coping profiles to relieve anxiety and depression symptoms.
Simultaneous monitoring of eight human respiratory viruses including SARS-CoV-2 using liquid chromatography-tandem mass spectrometry
Authors: Hodgkins Christopher , Buckton Laura K. , Walker Gregory J. , Crossett Ben , Cordwell Stuart J. , Horvath Andrea R. , Rawlinson William D. 
Published: August 2022

AbstractDiagnosis of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) infection has primarily been achieved using reverse transcriptase polymerase chain reaction (RT-PCR) for acute infection, and serology for prior infection. Assay with RT-PCR provides data on presence or absence of viral RNA, with no information on virus replication competence, infectivity, or virus characterisation. Liquid chromatography-tandem mass spectrometry (LC–MS/MS) is typically not used in clinical virology, despite its potential to provide supplemental data about the presence of viral proteins and thus the potential for replication-competent, transmissible virus. Using the SARS-CoV-2 as a model virus, we developed a fast ‘bottom-up’ proteomics workflow for discovery of target virus peptides using ‘serum-free’ culture conditions, providing high coverage of viral proteins without the need for protein or peptide fractionation techniques. This workflow was then applied to Coronaviruses OC43 and 229E, Influenza A/H1N1 and H3N2, Influenza B, and Respiratory Syncytial Viruses A and B. Finally, we created an LC–MS/MS method for targeted detection of the eight-virus panel in clinical specimens, successfully detecting peptides from the SARS-CoV-2 ORF9B and nucleoprotein in RT-PCR positive samples. The method provides specific detection of respiratory viruses from clinical samples containing moderate viral loads and is an important further step to the use of LC–MS/MS in diagnosis of viral infection.
COVID-19’s impact on visitation behavior to US national parks from communities of color: evidence from mobile phone data
Authors: Alba Charles , Pan Bing , Yin Junjun , Rice William L. , Mitra Prasenjit , Lin Michael S. , Liang Yun 
Published: August 2022

AbstractThe widespread COVID-19 pandemic fundamentally changed many people’s ways of life. With the necessity of social distancing and lock downs across the United States, evidence shows more people engage in outdoor activities. With the utilization of location-based service (LBS) data, we seek to explore how visitation patterns to national parks changed among communities of color during the COVID-19 pandemic. Our results show that visitation rates to national parks located closer than 347 km to individuals have increased amidst the pandemic, but the converse was demonstrated amongst parks located further than 347 km from individuals. More importantly, COVID-19 has adversely impacted visitation figures amongst non-white and Native American communities, with visitation volumes declining if these communities are situated further from national parks. Our results show disproportionately low-representations amongst national park visitors from these communities of color. African American communities display a particularly concerning trend whereby their visitation to national parks is substantially lower amongst communities closer to national parks.
Designing of multi-objective optimal virtual power plant model for reliability enhancement in radial network: a case study of Indian power sector
Authors: Sharma Harpreet , Imanbayeva Akmaral 
Published: August 2022

AbstractOne of the major driving factors in the shifting of the present grid paradigm to an active grid network is the reliability and resiliency of the utility network. With hefty investment in the distribution network protection and maintenance, the reliability of the feeders is considerably enhanced; however, large numbers of outages are still occurring every year which caused major production loss to the manufacturing sector. In this paper, the role of the solar grid-based Virtual Power Plant (VPP) is evaluated in the state power utility for the reliability enhancement and cost minimization using a multi-objective model based on MILP optimization. A 90 bus industrial feeder having automatic reclosers, DER, and DSM is selected on which the MCS method is utilized for computing reliability indices using the utility reliability parameters. The value of reliability indices such as EENS is declined by 68% by utilizing the VPP scenario. These values of this reliability index are fed into the multi-objective model for cost minimization. After running the optimization, the results reveal that the operational and the annual energy cost are reduced by 61% and 55% respectively which advocates the VPP implementation in the utility network. Both modes of the Virtual Power Plant such as grid-connected and autonomous mode have been discussed in detail. Lastly, the results of the developed model with MILP are compared with the proprietary derivative algorithm, and it is found that the proposed MILP is more cost-effective. The overall results advocate the VPP implementation in the utility grid as the economical advantage is provided to both utility and the consumers in terms of reduction in EENS and energy charges respectively.
Effects of organic fertilizers on growth characteristics and fruit quality in Pear-jujube in the Loess Plateau
Authors: Ye Shenglan , Peng Biao , Liu Tiancheng 
Published: August 2022

AbstractThe ecological environment of the hilly and gully area of the Loess Plateau in northern Shaanxi is fragile and the soil fertility is low. As a result, the yield and quality of Pear-jujube which constitute one of the dominant economic forests in this region, have been severely restricted. At present, the scientific application of fertilizer is important for comprehensively improving the quality of fruit trees, and for devising the optimal management of fruit trees. In particular, the application of organic fertilizers plays an important role in improving soil and improving fruit quality. In this experiment, a field study was conducted to understand the effects of different organic fertilizer applications on physiological growth, photosynthetic characteristics, reproductive growth and nutritional quality of Pear-jujube in the Loess Plateau. The results showed that organic fertilizer significantly promoted the physiological growth of Pear-jujube. The Pear-jujube bearing branch and leaf area under the soybean cake fertilizer (SC) treatment were 20.17 cm and 1246 mm2/leaf, respectively, which are increased by 34% and 44.46% compared with the no fertilizer treatment, which was a control check (CK). The total chlorophyll content of fertilization treatment was significantly higher than that of CK (P < 0.05). The maximum of chlorophyll content was 10.90 mg/dm2 under the biogas fertilizer (BM). The content of LAI was in the order BM > conventional fertilizer (CF) > sheep manure (SM) > SC > CK. The changing trend of gap fraction was opposite to that of LAI, and the density of light was consistent with that of LAI. The density of light BM was the largest, reached 38.06 mol/(m2 d), which was 15.13% higher than that of CK. Organic fertilizer significantly improved the net photosynthetic rate (Pn) and water use efficiency (WUEp) of Pear-jujube. The WUEp of SC was up to 3.30%. Organic fertilizer significantly promoted the reproductive growth and improved the nutritional quality of Pear-jujube. The yield under the SC was 19,177 kg/hm2, increased by 138.5% compared with that of CK. The fruit water content (FWC), total soluble solids (TSS), solid-acid ratio (TSS/TA), Vc and total flavonoids content improved, and the maxima of FWC, TSS, TSS/TA, Vc and total flavonoids content under the SC treatment were 86.30%, 18.48%, 40.17, 46.18 mg/kg and 14.35 mg/kg, respectively, which were significantly different from those of CK (P < 0.05). Organic fertilization effectively promotes the growth, development, yield and fruit quality of Pear-jujube in the Loess Plateau and the effect of the soybean cake fertilizer is the most significant.
Vicarious ratings of self vs. other-directed social touch in women with and recovered from Anorexia Nervosa
Authors: Bellard Ashleigh , Trotter Paula , McGlone Francis , Cazzato Valentina 
Published: August 2022

AbstractAnorexia Nervosa (AN) is an eating pathology characterized by restricted eating, body image distortions and impaired socio-cognitive abilities. Altered responses to affective touch—a pleasant interoceptive stimulus hypothesised to involve activation of the C-Tactile (CT) system, may contribute to the aetiology and maintenance of this disorder. Here, we investigated whether third-party social touch vicarious ratings of different body sites at CT-optimal vs. non-CT optimal velocities differed in women with and recovered from AN (RAN) and healthy controls (HCs). Thirty-five HCs, 27 AN and 29 RAN provided pleasantness ratings for two different tasks designed to probe expectations of how touch is perceived by self (self-directed touch) vs. others (other-directed touch). Findings revealed that both clinical groups, compared to HCs, did not differ in their pleasantness ratings to touch for another but when evaluating touch for self, both clinical groups rated CT-optimal touch as less pleasant than HCs. These findings suggest that AN and RAN women demonstrate an atypical vicarious pleasantness response to affective touch involving self, but not others. Novel therapeutic approaches that help anorexics to better interpret or improve tolerance of affective tactile experiences involving the self may be an important addition to current standard treatments.
Nasopharyngeal microbiota profiling of pregnant women with SARS-CoV-2 infection
Authors: Crovetto Francesca , Selma-Royo Marta , Crispi Fàtima , Carbonetto Belén , Pascal Rosalia , Larroya Marta , Casas Irene , Tortajada Marta , Escudero Nuria , Muñoz-Almagro Carmen , Gomez-Roig Maria Dolores , González-Torres Pedro , Collado Maria Carmen , Gratacos Eduard 
Published: August 2022

AbstractWe aimed to analyze the nasopharyngeal microbiota profiles in pregnant women with and without SARS-CoV-2 infection, considered a vulnerable population during COVID-19 pandemic. Pregnant women were enrolled from a multicenter prospective population-based cohort during the first SARS-CoV-2 wave in Spain (March-June 2020 in Barcelona, Spain) in which the status of SARS-CoV-2 infection was determined by nasopharyngeal RT–PCR and antibodies in peripheral blood. Women were randomly selected for this cross-sectional study on microbiota. DNA was extracted from nasopharyngeal swab samples, and the V3-V4 region of the 16S rRNA of bacteria was amplified using region-specific primers. The differential abundance of taxa was tested, and alpha/beta diversity was evaluated. Among 76 women, 38 were classified as positive and 38 as negative for SARS-CoV-2 infection. All positive women were diagnosed by SARS-CoV-2 IgG and IgM/IgA antibodies, and 14 (37%) also had a positive RT–PCR. The overall composition of the nasopharyngeal microbiota differ in pregnant women with SARS-CoV-2 infection (positive SARS-CoV-2 antibodies), compared to those without the infection (negative SARS-CoV-2 antibodies) (p = 0.001), with a higher relative abundance of the Tenericutes and Bacteroidetes phyla and a higher abundance of the Prevotellaceae family. Infected women presented a different pattern of microbiota profiling due to beta diversity and higher richness (observed ASV < 0.001) and evenness (Shannon index < 0.001) at alpha diversity. These changes were also present in women after acute infection, as revealed by negative RT–PCR but positive SARS-CoV-2 antibodies, suggesting a potential association between SARS-CoV-2 infection and long-lasting shift in the nasopharyngeal microbiota. No significant differences were reported in mild vs. severe cases. This is the first study on nasopharyngeal microbiota during pregnancy. Pregnant women with SARS-CoV-2 infection had a different nasopharyngeal microbiota profile compared to negative cases.