bluuebunny/crossref_metadata_2025_split huggingface dataset:
spinDrop: a droplet microfluidic platform to maximise single-cell sequencing information content
Authors: De Jonghe Joachim , Kaminski Tomasz S. , Morse David B. , Tabaka Marcin , Ellermann Anna L. , Kohler Timo N. , Amadei Gianluca , Handford Charlotte , Findlay Gregory M. , Zernicka-Goetz Magdalena , Teichmann Sarah A. , Hollfelder Florian 
Published: January 2023

AbstractDroplet microfluidic methods have massively increased the throughput of single-cell sequencing campaigns. The benefit of scale-up is, however, accompanied by increased background noise when processing challenging samples and the overall RNA capture efficiency is lower. These drawbacks stem from the lack of strategies to enrich for high-quality material or specific cell types at the moment of cell encapsulation and the absence of implementable multi-step enzymatic processes that increase capture. Here we alleviate both bottlenecks using fluorescence-activated droplet sorting to enrich for droplets that contain single viable cells, intact nuclei, fixed cells or target cell types and use reagent addition to droplets by picoinjection to perform multi-step lysis and reverse transcription. Our methodology increases gene detection rates fivefold, while reducing background noise by up to half. We harness these unique properties to deliver a high-quality molecular atlas of mouse brain development, despite starting with highly damaged input material, and provide an atlas of nascent RNA transcription during mouse organogenesis. Our method is broadly applicable to other droplet-based workflows to deliver sensitive and accurate single-cell profiling at a reduced cost.
Mass cytometry identifies characteristic immune cell subsets in bronchoalveolar lavage fluid from interstitial lung diseases
Authors: Hata Kentaro , Yanagihara Toyoshi , Matsubara Keisuke , Kunimura Kazufumi , Suzuki Kunihiro , Tsubouchi Kazuya , Eto Daisuke , Ando Hiroyuki , Uehara Maki , Ikegame Satoshi , Baba Yoshihiro , Fukui Yoshinori , Okamoto Isamu 
Published: January 2023

AbstractImmune cells have been implicated in interstitial lung diseases (ILDs), although their phenotypes and effector mechanisms remain poorly understood. To better understand these cells, we conducted an exploratory mass cytometry analysis of immune cell subsets in bronchoalveolar lavage fluid (BALF) from patients with idiopathic pulmonary fibrosis (IPF), connective-tissue disease (CTD)-related ILD, and sarcoidosis, using two panels including 64 markers. Among myeloid cells, we observed the expansion of CD14+CD36hiCD84himonocyte populations in IPF. These CD14+CD36hiCD84hisubsets were also increased in ILDs with a progressive phenotype, particularly in a case of acute exacerbation (AEx) of IPF. Analysis of B cells revealed the presence of cells at various stages of differentiation in BALF, with a higher percentage of IgG memory B cells in CTD-ILDs and a trend toward more FCRL5+B cells. These FCRL5+B cells were also present in the patient with AEx-IPF and sarcoidosis with advanced lung lesions. Among T cells, we found increased levels of IL-2R+TIGIT+LAG3+CD4+T cells in IPF, increased levels of CXCR3+CD226+CD4+T cells in sarcoidosis, and increased levels of PD1+TIGIT+CD57+CD8+T cells in CTD-ILDs. Together, these findings underscore the diverse immunopathogenesis of ILDs.
Evaluation of the morphological and biological functions of vascularized microphysiological systems with supervised machine learning
Authors: Tronolone James J. , Mathur Tanmay , Chaftari Christopher P. , Jain Abhishek 
Published: January 2023

AbstractVascularized microphysiological systems and organoids are contemporary preclinical experimental platforms representing human tissue or organ function in health and disease. While vascularization is emerging as a necessary physiological organ-level feature required in most such systems, there is no standard tool or morphological metric to measure the performance or biological function of vascularized networks within these models. Further, the commonly reported morphological metrics may not correlate to the network’s biological function – oxygen transport. Here, a large library of vascular network images was analyzed by the measure of each sample’s morphology and oxygen transport potential. The oxygen transport quantification is computationally expensive and user-dependent, so machine learning techniques were examined to generate regression models relating morphology to function. Principal component and factor analyses were applied to reduce dimensionality of the multivariate dataset, followed by multiple linear regression and tree-based regression analyses. These examinations reveal that while several morphological data relate poorly to the biological function, some machine learning models possess a relatively improved, but still moderate predictive potential. Overall, random forest regression model correlates to the biological function of vascular networks with relatively higher accuracy than other regression models.
SSI: A Statistical Sensitivity Index for Chemical Reaction Networks in cancer
Authors: Biddau Giorgia , Caviglia Giacomo , Piana Michele , Sommariva Sara 
Published: January 2023

SummaryAt the cellular level, cancer is triggered by mutations of the proteins involved in signalling networks made of hundreds of reacting species. The corresponding mathematical model consists of a large system of non-linear Ordinary Differential Equations for the unknown proteins concentrations depending on a consistently large number of kinetic parameters and initial concentrations. For this model, the present paper considers the problem of assessing the impact of each parameter and initial concentration on the system’s output. More specifically, we introduced a statistical sensitivity index whose values can be easily computed by means of principal component analysis, and which leads to the partition of the parameters’ and initial concentrations’ sets into sensible and non-sensible families. This approach allows the identification of those kinetic parameters and initial concentrations that mostly impact the mutation-driven modification of the proteomic profile at equilibrium, and of those pathways in the network that are mostly affected by the presence of mutations in the cancer cell.
Identification of a novel path for cerebrospinal fluid (CSF) drainage of the human brain
Authors: Pessa Joel E. , Hoxworth Ronald M. 
Published: January 2023

ABSTRACTHow cerebrospinal fluid (CSF) drains from the human brain is of paramount importance to cerebral health and physiology. Obstructed CSF drainage may result in increased intracranial pressure and a predictable cascade of events including an enlarged subarachnoid space, dilated cerebral ventricles and ultimately cell death. The current and accepted model of CSF drainage in humans suggests CSF drains from the subarachnoid space into the sagittal sinus vein. Here we identify a new structure in the sagittal sinus of the human brain by anatomic cadaver dissection. TheCSF canalicular systemis the terminal CSF drainage of the human brain. It consists of paired channels on either side of the sagittal sinus vein that communicate directly with subarachnoid cerebrospinal fluid via virchow robin (perivascular) spaces. Fluorescent injection confirms that these channels are patent and that flow is independent of the venous system. Computer assisted tomography identified flow from the sagittal sinus to the cranial base. We verify our previous identification of CSF channels in the neck that travel from the cranial base to the subclavian vein. This information suggests a novel path for CSF drainage of the human brain and nerves that may represent the primary route for CSF recirculation. These findings have implications for basic anatomy, surgery, and neuroscience, and highlight the continued importance of gross anatomy to medical research and discovery.
Immunogenicity and seroefficacy of pneumococcal conjugate vaccines – a systematic review and network meta-analysis
Authors: Feng Shuo , McLellan Julie , Pidduck Nicola , Roberts Nia , Higgins Julian PT , Choi Yoon , Izu Alane , Jit Mark , Madhi Shabir A , Mulholland Kim , Pollard Andrew J , Temple Beth , Voysey Merryn 
Published: January 2023

AbstractBackgroundVaccination of infants with pneumococcal conjugate vaccines (PCV) is recommended by the World Health Organisation. Evidence is mixed regarding the differences in immunogenicity and efficacy of the different pneumococcal vaccines.MethodsIn this systematic-review and network meta-analysis, we searched the Cochrane Library, Embase, Global Health, Medline,clinicaltrials.govand trialsearch.who.int up to July 2022 (Protocol PROSPERO ID CRD42019124580). Studies were eligible if they presented data comparing the immunogenicity of either PCV7, PCV10 or PCV13 in head- to-head randomised trials for young children, and provided at least one time point after the primary vaccination series and/or one-month after a booster dose. Individual participant level data were requested from publication authors and/or the relevant vaccine manufacturer; aggregate data were extracted if individual data were unavailable. Outcomes included the geometric mean ratio (GMR) of serotype-specific IgG and relative risk (RR) of seroinfection. Seroinfection is defined as a rise in antibody between the primary vaccination series and the booster dose, as evidence of subclinical infection. We also estimated the relationship between the GMR one month after priming and the RR of seroinfection by the time of the booster dose.FindingsIn total 45 studies were eligible from 38 countries across six continents. 27 and 12 studies with data available were included in immunogenicity and seroefficacy analyses respectively. GMRs comparing PCV13 vs PCV10 favoured PCV13 for serotypes 4, 9V, and 23F at 1 month after primary vaccination series, with 1.14- to 1.54-fold significantly higher IgG responses with PCV13. Risk of seroinfection prior to the time of booster dose was lower for PCV13 for serotype 4, 6B, 9V, 18C and 23F than for PCV10. Two-fold higher antibody after primary vaccination was associated with 54% decrease in risk of seroinfection (RR 0.46, 95%CI 0.23-0.96).ConclusionSerotype-specific differences were found in immunogenicity and seroefficacy between PCV10 and PCV13. Higher immunogenicity of PCVs are associated with lower risk of subsequent infection. These findings could be further used to compare PCVs and optimise vaccination strategy.FundingThis study is funded by the NIHR Health Technology Assessment programme (17/148/03).
Global biogeography of the smallest plankton across ocean depths
Authors: Junger Pedro C. , Sarmento Hugo , Giner Caterina. R. , Mestre Mireia , Sebastián Marta , Morán Xosé Anxelu G. , Arístegui Javier , Agustí Susana , Duarte Carlos M. , Acinas Silvia G. , Massana Ramon , Gasol Josep M. , Logares Ramiro 
Published: January 2023

AbstractTiny ocean plankton (picoplankton) are fundamental for the functioning of the biosphere, but the ecological mechanisms shaping their biogeography are partially understood. Comprehending whether these microorganisms are structured by niche vs. neutral processes is highly relevant in the context of global change. The ecological drivers structuring picoplankton communities differ between prokaryotes and minute eukaryotes (picoeukaryotes) in the global surface ocean: while prokaryotic communities are shaped by a balanced combination ofdispersal, selection, anddrift, picoeukaryotic communities are mainly shaped bydispersal limitation. Yet, whether or not the relative importance of these processes in structuring picoplankton varies as we dive into the deep ocean was unknown. Here we investigate the mechanisms structuring picoplanktonic communities inhabiting different ocean depths. We analyzed 451 samples from the tropical and subtropical global ocean and the Mediterranean Sea covering the epi- (0-200m), meso- (200- 1,000m), and bathypelagic (1,000-4,000m) depth zones. We found that selection decreased with depth possibly due to lower habitat heterogeneity. In turn, dispersal limitation increased with depth, possibly due to dispersal barriers such as water masses and bottom topography. Picoplankton β-diversity positively correlated with environmental heterogeneity and water mass variability in both the open-ocean and the Mediterranean Sea. However, this relationship tended to be weaker for picoeukaryotes than for prokaryotes. Community patterns were generally more pronounced in the Mediterranean Sea, probably because of its substantial cross-basin environmental heterogeneity and deep-water isolation. Altogether, we found that different combinations of ecological mechanisms shape the biogeography of the smallest members of the ocean microbiome across ocean depths.
Seedling performance in a dioecious tree species is similar near female and male conspecific adults despite differences in colonization by arbuscular mycorrhizal fungi
Authors: Eck Jenalle L. , Delavaux Camille S. , Wilson Dara M. , Queenborough Simon A. , Comita Liza S. 
Published: January 2023

AbstractPlant-soil feedbacks are a key driver of species diversity and composition in plant communities worldwide; however, the factors that may cause feedbacks to vary within species are rarely examined. In dioecious species, the strength of feedbacks may differ near female plants that produce seed versus near male plants (which do not) because repeated inputs of seeds and high seedling densities near females may cause accumulation of host-specific soil microbes that influence seedling performance. To test whether conspecific seedling performance is reduced near seed-producing female trees relative to male or heterospecific trees, we conducted shadehouse and field experiments with a dioecious tropical tree species,Virola surinamensis(Myristicaceae), on Barro Colorado Island, Panama. The shadehouse experiment isolated the effect of soil microbial communities on seedling growth and allowed us to quantify colonization by mutualistic arbuscular mycorrhizal (AM) fungi, while the field experiment allowed us to assess seedling survival and growth in the presence of nearby conspecific adults and seedlings. In both experiments, seedling performance was similar between seedlings grown in the soil microbial communities and field environments underneath female conspecific, male conspecific, and heterospecific trees. However, contrary to expectation, seedling colonization by AM fungi was higher in male conspecific soil microbial communities than in female or heterospecific soil microbial communities at the end of the shadehouse experiment. Together, our experiments show that while differences among female and male plants in dioecious species may influence the association of conspecific seedlings with AM fungi in their soils, this variation does not necessarily translate directly to differences in seedling performance, at least over the time frame of our experiments. Studies of additional dioecious species are needed to help determine differences in soil microbial communities beneath male and female plants and to assess the role of seed input versus adult root systems in driving plant-soil feedbacks.
Cortical beta power reflects a neural implementation of decision boundary collapse in speeded decisions
Authors: Kirschner Hans , Fischer Adrian G. , Danielmeier Claudia , Klein Tilmann A. , Ullsperger Markus 
Published: January 2023

AbstractA prominent account of decision-making assumes that information is accumulated until a fixed response threshold is crossed. However, many decisions require weighting of information appropriately against time. Collapsing response thresholds are a mathematically optimal solution to this decision problem. However, our understanding of the neurocomputational mechanisms that underly dynamic response thresholds remains very incomplete. To investigate this issue, we used a multistage drift diffusion model (DDM) and also analysed EEG beta power lateralization (BPL). The latter served as a neural proxy for decision signals. We analysed a large dataset (n=863) from a speeded flanker task and data from an independent confirmation sample (n=119). We show that a DDM with collapsing decision thresholds, a process where the decision boundary reduces over time, captured participants’ time-dependent decision policy better than a model with fixed thresholds. Previous research suggests that BPL over motor cortices reflects features of a decision signal and that its peak may serve as a neural proxy for the decision threshold. Our findings offer compelling evidence for the existence of collapsing decision thresholds in decision-making processes.
A highly divergent mitochondrial genome in extant Cape buffalo from Addo Elephant National Park, South Africa
Authors: de Jager Deon , Möller Marlo , Hoal Eileen , van Helden Paul , Glanzmann Brigitte , Harper Cindy , Bloomer Paulette 
Published: January 2023

AbstractThe reduced cost of next-generation sequencing (NGS) has allowed researchers to generate nuclear and mitochondrial genome data to gain deeper insights into the phylogeography, evolutionary history, and biology of non-model species. While the Cape buffalo (Syncerus caffer caffer) has been well-studied across its range with traditional genetic markers over the last 25 years, researchers are building on this knowledge by generating whole genome, population-level data sets to improve understanding of the genetic composition and evolutionary history of the species. Using publicly available NGS data, we assembled 40 Cape buffalo mitochondrial genomes (mitogenomes) from four protected areas in South Africa, expanding the geographical range and almost doubling the number of mitogenomes available for this species. Coverage of the mitogenomes ranged from 154-1,036X. Haplotype and nucleotide diversity for Kruger National Park (n = 15) and Mokala National Park (n = 5) were similar to diversity levels in southern and eastern Africa. Hluhluwe-iMfolozi Park (n = 15) had low levels of genetic diversity, with only four haplotypes detected, reflecting its past bottleneck. Addo Elephant National Park (n = 5) had the highest nucleotide diversity of all populations across Africa, which was unexpected, as it is known from previous studies to have low nuclear diversity. This diversity was driven by a highly divergent mitogenome from one sample, which was subsequently identified in another sample via Sanger sequencing of the cytochromebgene. Using a fossil-calibrated phylogenetic analysis, we estimated that this lineage diverged from all other Cape buffalo lineages approximately 2.51 million years ago. We discuss several potential sources of this mitogenome but propose that it most likely originated through introgressive hybridisation with an extinct buffalo species, eitherS. acoelotusorS. antiquus. We conclude by discussing the conservation consequences of this finding for the Addo Elephant National Park population, proposing careful genetic management to prevent inbreeding depression while maintaining this highly unique diversity.
Grey fuzzy prediction model of soil organic matter content using hyper-spectral data
Authors: Yu Jintao , Li Xican , Cao Shuang , Liu Fajun 
Published: January 2023

PurposeIn order to overcome the uncertainty and improve the accuracy of spectral estimation, this paper aims to establish a grey fuzzy prediction model of soil organic matter content by using grey theory and fuzzy theory.Design/methodology/approachBased on the data of 121 soil samples from Zhangqiu district and Jiyang district of Jinan City, Shandong Province, firstly, the soil spectral data are transformed by spectral transformation methods, and the spectral estimation factors are selected according to the principle of maximum correlation. Then, the generalized greyness of interval grey number is used to modify the estimation factors of modeling samples and test samples to improve the correlation. Finally, the hyper-spectral prediction model of soil organic matter is established by using the fuzzy recognition theory, and the model is optimized by adjusting the fuzzy classification number, and the estimation accuracy of the model is evaluated using the mean relative error and the determination coefficient.FindingsThe results show that the generalized greyness of interval grey number can effectively improve the correlation between soil organic matter content and estimation factors, and the accuracy of the proposed model and test samples are significantly improved, where the determination coefficient R2 = 0.9213 and the mean relative error (MRE) = 6.3630% of 20 test samples. The research shows that the grey fuzzy prediction model proposed in this paper is feasible and effective, and provides a new way for hyper-spectral estimation of soil organic matter content.Practical implicationsThe research shows that the grey fuzzy prediction model proposed in this paper can not only effectively deal with the three types of uncertainties in spectral estimation, but also realize the correction of estimation factors, which is helpful to improve the accuracy of modeling estimation. The research result enriches the theory and method of soil spectral estimation, and it also provides a new idea to deal with the three kinds of uncertainty in the prediction problem by using the three kinds of uncertainty theory.Originality/valueThe paper succeeds in realizing both the grey fuzzy prediction model for hyper-spectral estimating soil organic matter content and effectively dealing with the randomness, fuzziness and grey uncertainty in spectral estimation.
The role of social media engagement and emotional intelligence in successful employment
Authors: Ashaye Olusoyi Richard , Mahmoud Ali B. , Munna Afzal Sayed , Ali Nurhanisah 
Published: January 2023

PurposeThis paper focusses on demonstrating the role of social media engagement and considering emotional intelligence (hereafter EI) as a critical concept to successful employment, mainly when individuals fail to reach the desired employment despite “meeting” the role requirements.Design/methodology/approachThe authors adopted a qualitative approach through semi-structured in-depth interviews of some randomly selected university students in the UK, young adults aged 19–32. The participants were selected based on different demographics to provide a broader and less biased representation of young adults in the UK.FindingsThis research suggests that recruitment organisations should introduce the latest requirements and trends of employers to ensure that the expectations of employers and potential candidates are aligned to improve the employment rate in young adults.Originality/valueThis research extends the literature regarding EI in social media engagement and successful employment. It also brings new perspectives on successful employment in young adults by demonstrating the role of social media engagement and EI traits leading to a conceptual framework exploring successful employment based on the role of social media engagement and EI.