bluuebunny/crossref_metadata_2025_split huggingface dataset:
The default network dominates neural responses to evolving movie stories
Authors: Yang Enning , Milisav Filip , Kopal Jakub , Holmes Avram J. , Mitsis Georgios D. , Misic Bratislav , Finn Emily S. , Bzdok Danilo 
Published: July 2023

AbstractNeuroscientific studies exploring real-world dynamic perception often overlook the influence of continuous changes in narrative content. In our research, we utilize machine learning tools for natural language processing to examine the relationship between movie narratives and neural responses. By analyzing over 50,000 brain images of participants watching Forrest Gump from the studyforrest dataset, we find distinct brain states that capture unique semantic aspects of the unfolding story. The default network, associated with semantic information integration, is the most engaged during movie watching. Furthermore, we identify two mechanisms that underlie how the default network liaises with the amygdala and hippocampus. Our findings demonstrate effective approaches to understanding neural processes in everyday situations and their relation to conscious awareness.
Engineering broad-spectrum inhibitors of inflammatory chemokines from subclass A3 tick evasins
Authors: Devkota Shankar Raj , Aryal Pramod , Pokhrel Rina , Jiao Wanting , Perry Andrew , Panjikar Santosh , Payne Richard J. , Wilce Matthew C. J. , Bhusal Ram Prasad , Stone Martin J. 
Published: July 2023

AbstractChemokines are key regulators of leukocyte trafficking and attractive targets for anti-inflammatory therapy. Evasins are chemokine-binding proteins from tick saliva, whose application as anti-inflammatory therapeutics will require manipulation of their chemokine target selectivity. Here we describe subclass A3 evasins, which are unique to the tick genus Amblyomma and distinguished from “classical” class A1 evasins by an additional disulfide bond near the chemokine recognition interface. The A3 evasin EVA-AAM1001 (EVA-A) bound to CC chemokines and inhibited their receptor activation. Unlike A1 evasins, EVA-A was not highly dependent on N- and C-terminal regions to differentiate chemokine targets. Structures of chemokine-bound EVA-A revealed a deep hydrophobic pocket, unique to A3 evasins, that interacts with the residue immediately following the CC motif of the chemokine. Mutations to this pocket altered the chemokine selectivity of EVA-A. Thus, class A3 evasins provide a suitable platform for engineering proteins with applications in research, diagnosis or anti-inflammatory therapy.
Genetic strategies for sex-biased persistence of gut microbes across human life
Authors: Tarracchini Chiara , Alessandri Giulia , Fontana Federico , Rizzo Sonia Mirjam , Lugli Gabriele Andrea , Bianchi Massimiliano Giovanni , Mancabelli Leonardo , Longhi Giulia , Argentini Chiara , Vergna Laura Maria , Anzalone Rosaria , Viappiani Alice , Turroni Francesca , Taurino Giuseppe , Chiu Martina , Arboleya Silvia , Gueimonde Miguel , Bussolati Ovidio , van Sinderen Douwe , Milani Christian , Ventura Marco 
Published: July 2023

AbstractAlthough compositional variation in the gut microbiome during human development has been extensively investigated, strain-resolved dynamic changes remain to be fully uncovered. In the current study, shotgun metagenomic sequencing data of 12,415 fecal microbiomes from healthy individuals are employed for strain-level tracking of gut microbiota members to elucidate its evolving biodiversity across the human life span. This detailed longitudinal meta-analysis reveals host sex-related persistence of strains belonging to common, maternally-inherited species, such as Bifidobacterium bifidum and Bifidobacterium longum subsp. longum. Comparative genome analyses, coupled with experiments including intimate interaction between microbes and human intestinal cells, show that specific bacterial glycosyl hydrolases related to host-glycan metabolism may contribute to more efficient colonization in females compared to males. These findings point to an intriguing ancient sex-specific host-microbe coevolution driving the selective persistence in women of key microbial taxa that may be vertically passed on to the next generation.
Tumor-agnostic ctDNA levels by mFAST-SeqS in first-line HR-positive, HER2 negative metastatic breast cancer patients as a biomarker for survival
Authors: Verschoor Noortje , de Weerd Vanja , Van Mai N. , Kraan Jaco , Smid Marcel , Heijns Joan B. , Drooger Jan C. , Zuetenhorst Johanna M. , van der Padt-Pruijsten Annemieke , Jager Agnes , Sleijfer Stefan , Martens John W. M. , Wilting Saskia M. 
Published: July 2023

AbstractThis prospective cohort study reports aneuploidy score by mFast-SeqS as a strong prognostic marker in MBC patients. mFAST-SeqS is an affordable and easily implementable method for the assessment of total ctDNA levels and, as such, provides an alternative prognostic tool. One mixed cohort (cohort A, n = 45) starting any type of treatment in any line of therapy and one larger cohort (cohort B, n = 129) consisting of patients starting aromatase inhibitors (AI) as first-line therapy were used. mFAST-SeqS was performed using plasma of blood in which CTCs (CellSearch) were enumerated. The resulting aneuploidy score was correlated with categorized CTC count and associated with outcome. The aneuploidy score was significantly correlated with CTC count, but discordance was observed in 31.6% when applying cut-offs of 5. In both cohorts, aneuploidy score was a significant prognostic marker for both PFS and OS. In the Cox regression models, the HR for aneuploidy score for PFS was 2.52 (95% CI: 1.56–4.07), and the HR for OS was 2.37 (95% CI: 1.36–4.14). Results presented here warrant further investigations into the clinical utility of this marker in MBC patients.
Quantum advantages for transportation tasks - projectiles, rockets and quantum backflow
Authors: Trillo David , Le Thinh P. , Navascués Miguel 
Published: July 2023

AbstractConsider a scenario where a quantum particle is initially prepared in some bounded region of space and left to propagate freely. After some time, we verify if the particle has reached some distant target region. We find that there exist ‘ultrafast’ (‘ultraslow’) quantum states, whose probability of arrival is greater (smaller) than that of any classical particle prepared in the same region with the same momentum distribution. For both projectiles and rockets, we prove that the quantum advantage, quantified by the difference between the quantum and optimal classical arrival probabilities, is limited by the Bracken-Melloy constant cbm, originally introduced to study the phenomenon of quantum backflow. In this regard, we substantiate the 29-year-old conjecture that cbm ≈ 0.038 by proving the bounds 0.0315 ≤ cbm ≤ 0.072. Finally, we show that, in a modified projectile scenario where the initial position distribution of the particle is also fixed, the quantum advantage can reach 0.1262.
A geopositioned and evidence-graded pan-species compendium of Mayaro virus occurrence
Authors: Celone Michael , Potter Alexander M. , Han Barbara A. , Beeman Sean P. , Okech Bernard , Forshey Brett , Dunford James , Rutherford George , Mita-Mendoza Neida K. , Estallo Elizabet Lilia , Khouri Ricardo , de Siqueira Isadora Cristina , Petersen Kyle , Maves Ryan C. , Anyamba Assaf , Pollett Simon 
Published: July 2023

AbstractMayaro Virus (MAYV) is an emerging health threat in the Americas that can cause febrile illness as well as debilitating arthralgia or arthritis. To better understand the geographic distribution of MAYV risk, we developed a georeferenced database of MAYV occurrence based on peer-reviewed literature and unpublished reports. Here we present this compendium, which includes both point and polygon locations linked to occurrence data documented from its discovery in 1954 until 2022. We describe all methods used to develop the database including data collection, georeferencing, management and quality-control. We also describe a customized grading system used to assess the quality of each study included in our review. The result is a comprehensive, evidence-graded database of confirmed MAYV occurrence in humans, non-human animals, and arthropods to-date, containing 262 geo-positioned occurrences in total. This database - which can be updated over time - may be useful for local spill-over risk assessment, epidemiological modelling to understand key transmission dynamics and drivers of MAYV spread, as well as identification of major surveillance gaps.
Ecological correlation between short term exposure to particulate matter and hospitalization for mental disorders in Shijiazhuang, China
Authors: Wang Lan , Gao Xian , Wang Ran , Song Mei , Liu Xiaoli , Wang Xueyi , An Cuixia 
Published: July 2023

AbstractThe associations between particulate matter (PM) and overall and specific mental disorders (MDs) are investigated using data from two general hospitals in Shijiazhuang, China, from January 2014 to December 2019. A longitudinal time series study, as one type of ecological study, is conducted using a generalized additive model to examine the relationship between short-term exposure to PM2.5, PM10, and daily hospital admissions for MDs, and further stratification by subtypes, age, and gender. A total of 10,709 cases of hospital admissions for MDs have been identified. The significant short-time effects of PM2.5 on overall MDs at lag01 and PM10 at lag05 are observed, respectively. For specific mental disorders, there are substantial associations of PM pollution with mood disorders and organic mental disorders. PM2.5 has the greatest cumulative effect on daily admissions of mood disorders and organic mental disorders in lag01, and PM 10 has the greatest cumulative effect in lag05. Moreover, the effect modification by sex or age is statistically significant, with males and the elderly (≥ 45 years) having a stronger effect. Short-term exposure to PM2.5 and PM10can be associated with an increased risk of daily hospital admissions for MDs.
Learning models for classifying Raman spectra of genomic DNA from tumor subtypes
Authors: Lancia Giacomo , Durastanti Claudio , Spitoni Cristian , De Benedictis Ilaria , Sciortino Antonio , Cirillo Emilio N. M. , Ledda Mario , Lisi Antonella , Convertino Annalisa , Mussi Valentina 
Published: July 2023

AbstractAn early and accurate detection of different subtypes of tumors is crucial for an effective guidance to personalized therapy and in predicting the ability of tumor to metastasize. Here we exploit the Surface Enhanced Raman Scattering (SERS) platform, based on disordered silver coated silicon nanowires (Ag/SiNWs), to efficiently discriminate genomic DNA of different subtypes of melanoma and colon tumors. The diagnostic information is obtained by performing label free Raman maps of the dried drops of DNA solutions onto the Ag/NWs mat and leveraging the classification ability of learning models to reveal the specific and distinct physico-chemical interaction of tumor DNA molecules with the Ag/NW, here supposed to be partly caused by a different DNA methylation degree.
Mitogenomes revealed the history of bison colonization of Northern Plains after the Last Glacial Maximum
Authors: Ovchinnikov Igor V. , McCann Blake 
Published: July 2023

AbstractAmerican bison demonstrated differential patterns of extinction, survival, and expansion since the terminal Pleistocene. We determined population dynamics of the Northern Great Plains bison using 40 mitochondrial genomes from radiocarbon dated remains with the age ranging from 12,226 to 167 calibrated years before present. Population dynamics correlated with environmental and anthropogenic factors and was characterized by three primary periods: terminal Pleistocene population growth starting 14,000 years ago, mid Holocene demographic stability between 6700 and 2700 years ago, and late Holocene population decline in the last 2700 years. Most diversification of mtDNA haplotypes occurred in the early Holocene when bison colonized new territories opened by retreating ice sheets. Holocene mtDNA lineages were not found in modern bison and lacked association with archaeological sites and morphological forms.
Molecular dissection and testing of PRSS37 function through LC–MS/MS and the generation of a PRSS37 humanized mouse model
Authors: Sutton Courtney , Nozawa Kaori , Kent Katarzyna , Saltzman Alexander , Leng Mei , Nagarajan Sureshbabu , Malovannaya Anna , Ikawa Masahito , Garcia Thomas X. , Matzuk Martin M. 
Published: July 2023

AbstractThe quest for a non-hormonal male contraceptive pill for men still exists. Serine protease 37 (PRSS37) is a sperm-specific protein that when ablated in mice renders them sterile. In this study we sought to examine the molecular sequelae of PRSS37 loss to better understand its molecular function, and to determine whether human PRSS37 could rescue the sterility phenotype of knockout (KO) mice, allowing for a more appropriate model for drug molecule testing. To this end, we used CRISPR-EZ to create mice lacking the entire coding region of Prss37, used pronuclear injection to create transgenic mice expressing human PRSS37, intercrossed these lines to generate humanized mice, and performed LC–MS/MS of KO and control tissues to identify proteomic perturbances that could attribute a molecular function to PRSS37. We found that our newly generated Prss37 KO mouse line is sterile, our human transgene rescues the sterility phenotype of KO mice, and our proteomics data not only yields novel insight into the proteome as it evolves along the male reproductive tract, but also demonstrates the proteins significantly influenced by PRSS37 loss. In summary, we report vast biological insight including insight into PRSS37 function and the generation of a novel tool for contraceptive evaluation.
Monolayer organic thin films as particle-contamination–resistant coatings
Authors: Jia Ruobin , Hoffman Brittany N. , Kozlov Alexei V. , Demos Stavros G. , Shestopalov Alexander A. 
Published: July 2023

AbstractThree organic monolayers coatings were developed and tested for their effectiveness to increase cleaning efficiency of attached microscale particles by air flows. The experiments were performed using silica substrates coated with these organic thin films and subsequently exposed to stainless-steel and silica microparticles as a model of contamination. Laser-induced–damage tests confirmed that the coatings do not affect the laser-induced–damage threshold values. The particle exposure results suggest that although the accumulation of particles is not significantly affected under the experimental conditions used in this work, the coated substrates exhibit significantly improved cleaning efficiency with a gas flow. A size-distribution analysis was conducted to study the adsorption and cleaning efficiency of particles of different sizes. It was observed that larger size (> 5-μm) particles can be removed from coated substrates with almost 100% efficiency. It was also determined that the coatings improve the cleaning efficiency of the smaller particles (≤ 5 μm) by 17% to 30% for the stainless steel metal and 19% to 38% for the silica particles.
Time series causal relationships discovery through feature importance and ensemble models
Authors: Castro Manuel , Mendes Júnior Pedro Ribeiro , Soriano-Vargas Aurea , de Oliveira Werneck Rafael , Moreira Gonçalves Maiara , Lusquino Filho Leopoldo , Moura Renato , Zampieri Marcelo , Linares Oscar , Ferreira Vitor , Ferreira Alexandre , Davólio Alessandra , Schiozer Denis , Rocha Anderson 
Published: July 2023

AbstractInferring causal relationships from observational data is a key challenge in understanding the interpretability of Machine Learning models. Given the ever-increasing amount of observational data available in many areas, Machine Learning algorithms used for forecasting have become more complex, leading to a less understandable path of how a decision is made by the model. To address this issue, we propose leveraging ensemble models, e.g., Random Forest, to assess which input features the trained model prioritizes when making a forecast and, in this way, establish causal relationships between the variables. The advantage of these algorithms lies in their ability to providefeature importance, which allows us to build the causal network. We present our methodology to estimate causality in time series from oil field production. As it is difficult to extract causal relations from a real field, we also included a synthetic oil production dataset and a weather dataset, which is also synthetic, to provide the ground truth. We aim to performcausal discovery, i.e., establish the existing connections between the variables in each dataset. Through an iterative process of improving the forecasting of a target’s value, we evaluate whether the forecasting improves by adding information from a new potential driver; if so, we state that the driver causally affects the target. On the oil field-related datasets, our causal analysis results agree with the interwell connections already confirmed by tracer information; whenever the tracer data are available, we used it as our ground truth. This consistency between both estimated and confirmed connections provides us the confidence about the effectiveness of our proposed methodology. To our knowledge, this is the first time causal analysis using solely production data is employed to discover interwell connections in an oil field dataset.
Immunogenicity of poxvirus-based vaccines against Nipah virus
Authors: Medina-Magües Emily S. , Lopera-Madrid Jaime , Lo Michael K. , Spiropoulou Christina F. , Montgomery Joel M. , Medina-Magües Lex G. , Salas-Quinchucua Cristhian , Jiménez-Mora Angela P. , Osorio Jorge E. 
Published: July 2023

AbstractNipah virus (NiV), an emerging zoonotic pathogen in Southeast Asia, is transmitted from Pteropus species of fruit bats to a wide range of species, including humans, pigs, horses, dogs, and cats. NiV has killed millions of animals and caused highly fatal human outbreaks since no vaccine is commercially available. This study characterized the immunogenicity and safety of poxvirus-based Nipah vaccines that can be used in humans and species responsible for NiV transmission. Mice were vaccinated with modified vaccinia Ankara (MVA) and raccoon pox (RCN) viral vectors expressing the NiV fusion (F) and glycoprotein (G) proteins subcutaneously (SC) and intranasally (IN). Importantly, both vaccines did not induce significant weight loss or clinical signs of disease while generating high circulating neutralizing antibodies and lung-specific IgG and IgA responses. The MVA vaccine saw high phenotypic expression of effector and tissue resident memory CD8ɑ+ T cells in lungs and splenocytes along with the expression of central memory CD8ɑ+ T cells in lungs. The RCN vaccine generated effector memory (SC) and tissue resident (IN) CD8ɑ+ T cells in splenocytes and tissue resident (IN) CD8ɑ+ T cells in lung cells. These findings support MVA-FG and RCN-FG viral vectors as promising vaccine candidates to protect humans, domestic animals, and wildlife from fatal disease outcomes and to reduce the global threat of NiV.
Alterations in cortical morphometry of the contralesional hemisphere in children, adolescents, and young adults with perinatal stroke
Authors: Shinde Karan , Craig Brandon T. , Hassett Jordan , Dlamini Nomazulu , Brooks Brian L. , Kirton Adam , Carlson Helen L. 
Published: July 2023

AbstractPerinatal stroke causes most hemiparetic cerebral palsy and cognitive dysfunction may co-occur. Compensatory developmental changes in the intact contralesional hemisphere may mediate residual function and represent targets for neuromodulation. We used morphometry to explore cortical thickness, grey matter volume, gyrification, and sulcal depth of the contralesional hemisphere in children, adolescents, and young adults after perinatal stroke and explored associations with motor, attention, and executive function. Participants aged 6–20 years (N = 109, 63% male) with unilateral perinatal stroke underwent T1-weighted imaging. Participants had arterial ischemic stroke (AIS; n = 36), periventricular venous infarction (PVI; n = 37) or were controls (n = 36). Morphometry was performed using the Computational Anatomy Toolbox (CAT12). Group differences and associations with motor and executive function (in a smaller subsample) were assessed. Group comparisons revealed areas of lower cortical thickness in contralesional hemispheres in both AIS and PVI and greater gyrification in AIS compared to controls. Areas of greater grey matter volume and sulcal depth were also seen for AIS. The PVI group showed lower grey matter volume in cingulate cortex and less volume in precuneus relative to controls. No associations were found between morphometry metrics, motor, attention, and executive function. Cortical structure of the intact contralesional hemisphere is altered after perinatal stroke. Alterations in contralesional cortical morphometry shown in perinatal stroke may be associated with different mechanisms of damage or timing of early injury. Further investigations with larger samples are required to more thoroughly explore associations with motor and cognitive function.
Thermophilisation of communities differs between land plant lineages, land use types and elevation
Authors: Kiebacher Thomas , Meier Markus , Kipfer Tabea , Roth Tobias 
Published: July 2023

AbstractBryophytes provide key ecosystem services at the global scale such as carbon storage and primary production in resource limited habitats, but compared to vascular plants knowledge on how these organisms face recent climate warming is fragmentary. This is particularly critical because bryophytes differ fundamentally from vascular plants in their ecophysiological and biological characteristics, so that community alterations most likely have different dynamics. In a comparative approach, we analysed thermophilisation of bryophyte and vascular plant communities in 1146 permanent plots distributed along an elevational gradient of nearly 3.000 m in Switzerland (Central Europe) that were visited in 5-years intervals between 2001 and 2021. We estimated thermophilisation from changes in unweighted mean temperature indicator values of species, compared it to expected thermophilisation rates given the shift of isotherms and addressed differences between the two lineages, major land use types (managed grasslands, forests, unmanaged open areas), life strategy types (long- and short-lived species) and in elevation. Thermophilisation of bryophyte communities was on average 2.1 times higher than of vascular plant communities and at high elevations it approximated the expected rate given the shift of isotherms. Thermophilisation of both, bryophyte and vascular plant communities was not driven by a loss of cryophilic species but by an increase in thermophilic and mesophilic species, indicating an in-filling process. Furthermore, our data show that thermophilisation is higher in managed grasslands than in forests. We suggest that the higher responsiveness of bryophytes compared to vascular plants depends on their poikilohydry and dispersal capacity and that lower thermophilisation of forests communities is related to the buffering effect of microclimatic conditions in the interior of forests. Our study emphasises the heterogeneity of climate warming effects on plants because response dynamics differ between taxonomic groups as well as between land use types and along elevational gradients.