bluuebunny/crossref_metadata_2025_split huggingface dataset:
Quantitative T1-relaxation corrected metabolite mapping of 12 metabolites in the human brain at 9.4 T
Authors: Wright Andrew Martin , Murali-Manohar Saipavitra , Henning Anke 
Published: December 2021

AbstractMagnetic resonance spectroscopic imaging (MRSI) is a non-invasive imaging modality that enables observation of metabolites. Applications of MRSI for neuroimaging applications has shown promise for monitoring and detecting various diseases. This study builds off previously developed techniques of short TR, 1H FID MRSI by correcting for T1-weighting of the metabolites and utilizing an internal water reference to produce quantitative (mmol kg−1) metabolite maps. This work reports and shows quantitative metabolite maps for 12 metabolites for a single slice. Voxel-specific T1-corrections for water are common in MRSI studies; however, most studies use either averaged T1-relaxation times to correct for T1-weighting of metabolites or omit this correction step entirely. This work employs the use of voxel-specific T1-corrections for metabolites in addition to water. Utilizing averaged T1-relaxation times for metabolites can bias metabolite maps for metabolites that have strong differences between T1-relaxation for GM and WM (i.e. Glu). This work systematically compares quantitative metabolite maps to single voxel quantitative results and qualitatively compares metabolite maps to previous works.HighlightsQuantitative metabolite maps of 12 metabolites human brains acquired at 9.4 T.Voxel-specific T1-weighting corrections for water and metabolites.Comparisons of T1-weighted and T1-corrected metabolite maps.
Chaperoning of the histone octamer by the acidic domain of DNA repair factor APLF
Authors: Corbeski Ivan , Guo Xiaohu , Eckhardt Bruna V. , Fasci Domenico , Wiegant Wouter , Graewert Melissa A. , Vreeken Kees , Wienk Hans , Svergun Dmitri I. , Heck Albert J.R. , van Attikum Haico , Boelens Rolf , Sixma Titia K. , Mattiroli Francesca , van Ingen Hugo 
Published: December 2021

Nucleosome assembly requires the coordinated deposition of histone complexes H3-H4 and H2A-H2B to form a histone octamer on DNA. In the current paradigm, specific histone chaperones guide the deposition of first H3-H4 and then H2A-H2B(1–5). Here, we show that the acidic domain of DNA repair factor APLF (APLFAD) can assemble the histone octamer in a single step, and deposit it on DNA to form nucleosomes. The crystal structure of the APLFAD–histone octamer complex shows that APLFAD tethers the histones in their nucleosomal conformation. Mutations of key aromatic anchor residues in APLFAD affect chaperone activity in vitro and in cells. Together, we propose that chaperoning of the histone octamer is a mechanism for histone chaperone function at sites where chromatin is temporarily disrupted.one sentence summaryHistone chaperone APLF assembles histones H2A-H2B/H3-H4 into histone octamers to deposit them onto DNA and form nucleosomes.
Hemocyte Differentiation to the Megacyte Lineage Enhances Mosquito Immunity Against Plasmodium
Authors: Barletta Ferreira Ana Beatriz , Saha Banhisikha , Trisnadi Nathanie , Talyuli Octavio , Raddi Gianmarco , Barillas-Mury Carolina 
Published: December 2021

AbstractSilencing Cactus, a suppressor of Toll signaling, in Anopheles gambiae, eliminates Plasmodium ookinetes by enhancing local release of hemocyte-derived microvesicles that promote activation of the mosquito complement-like system. We report that Cactus silencing dramatically increases the proportion of megacytes, a new effector hemocyte subpopulation of large granulocytes, from 5 to 79% of circulating granulocytes. Transcriptomic and morphological analysis, as well as cell counts, in situ hybridization and expression of cell-specific markers, indicate that Cactus silencing triggers granulocyte differentiation into megacytes, a process mediated by the Rel1 transcription factor of the Toll pathway. Megacytes are very plastic cells that can extend long filopodia, tend to form clusters in vivo, and are massively recruited to the basal midgut surface in response to bacterial feeding and Plasmodium infection. We show that hemocyte differentiation to the megacyte lineage greatly enhances mosquito immunity against Plasmodium.
Systemic influences of mammary cancer on monocytes in mice
Authors: Robinson A , Burgess M , Webb S , Louwe PA , Ouyang Z , Skola D , Han CZ , Batada NN , González-Huici V , Cassetta L , Glass CK , Jenkins SJ , Pollard JW 
Published: December 2021

AbstractThere is a growing body of evidence that cancer causes systemic changes. These influences are most evident in the bone marrow and blood, particularly the myeloid compartment. Here we show using mouse models of breast cancer caused by the mammary epithelial expression of the Polyoma middle T antigen that there is an increase in the number of circulating and splenic monocytes. In the circulation, cancer does not affect ratios of classical to non-classical populations monocytes nor their halflives. Single cell RNA sequencing also indicates that cancer does not induce any new monocyte populations. In the bone marrow cancer does not change monocytic progenitor number is unaffected but the proliferation rate of monocytes is higher thus providing an explanation for expansion in the circulating number. Deep RNA sequencing of these monocytic populations reveals cancer causes changes in the classical monocyte compartment with changes evident in bone marrow monocytes but more in the blood suggesting influences in both compartments. Down regulation of interferon type 1 signalling and antigen presentation were the most prominent. Consistent with this analysis down regulated genes are enriched with STAT1/STAT2 binding sites in their promoter, transcription factors required for type 1 interferon signalling. However, these transcriptome changes in mice did not replicate those found in patients with breast cancer. Consequently, mouse models of cancer may be insufficient to study the systemic influences of human cancer.
Phenotyping single-cell motility in microfluidic confinement
Authors: Bentley Samuel A. , Anagnostidis Vasileios , Schlogelhofer Hannah Laeverenz , Gielen Fabrice , Wan Kirsty Y. 
Published: December 2021

AbstractAt all scales, the movement patterns of organisms serve as dynamic read-outs of their behaviour and physiology. We devised a novel droplet microfluidics assay to encapsulate single algal microswimmers inside closed arenas, and comprehensively studied their roaming behaviour subject to a large number of environmental stimuli. We compared two model species,Chlamydomonas reinhardtii(freshwater alga, 2 cilia), andPyramimonas octopus(marine alga, 8 cilia), and detailed their highly-stereotyped behaviours and the emergence of a trio of macroscopic swimming states (smooth-forward, quiescent, tumbling or excitable backward). Harnessing ultralong timeseries statistics, we reconstructed the species-dependent reaction network that underlies the choice of locomotor behaviour in these aneural organisms, and discovered the presence of macroscopic non-equilibrium probability fluxes in these active systems. We also revealed for the first time how microswimmer motility changes instantaneously when a chemical is added to their microhabitat, by inducing deterministic fusion between paired droplets - one containing a trapped cell, and the other, a pharmacological agent that perturbs cellular excitability. By coupling single-cell entrapment with unprecedented tracking resolution, speed and duration, our approach offers unique and potent opportunities for diagnostics, drug-screening, and for querying the genetic basis of micro-organismal behaviour.
LotuS2: An ultrafast and highly accurate tool for amplicon sequencing analysis
Authors: Özkurt Ezgi , Fritscher Joachim , Soranzo Nicola , Ng Duncan Y. K. , Davey Robert P. , Bahram Mohammad , Hildebrand Falk 
Published: December 2021

AbstractBackgroundAmplicon sequencing is an established and cost-efficient method for profiling microbiomes. However, many available tools to process this data require both bioinformatics skills and high computational power to process big datasets. Furthermore, there are only few tools that allow for long read amplicon data analysis. To bridge this gap, we developed the LotuS2 (Less OTU Scripts 2) pipeline, enabling user-friendly, resource friendly, and versatile analysis of raw amplicon sequences.ResultsIn LotuS2, six different sequence clustering algorithms as well as extensive pre- and post-processing options allow for flexible data analysis by both experts, where parameters can be fully adjusted, and novices, where defaults are provided for different scenarios. We benchmarked three independent gut and soil datasets, where LotuS2 was on average 29 times faster compared to other pipelines - yet could better reproduce the alpha- and beta-diversity of technical replicate samples. Further benchmarking a mock community with known taxa composition showed that, compared to the other pipelines, LotuS2 recovered a higher fraction of correctly identified genera and species (98% and 57%, respectively). At ASV/OTU level, precision and F-score were highest for LotuS2, as was the fraction of correctly reconstructed 16S sequences.ConclusionLotuS2 is a lightweight and user-friendly pipeline that is fast, precise and streamlined. High data usage rates and reliability enable high-throughput microbiome analysis in minutes.AvailabilityLotuS2 is available from GitHub, conda or via a Galaxy web interface, documented at http://lotus2.earlham.ac.uk/.
Selfee: Self-supervised Features Extraction of animal behaviors
Authors: Jia Yinjun , Li Shuaishuai , Guo Xuan , Hu Junqiang , Xu Xiao-Hong , Zhang Wei 
Published: December 2021

ABSTRACTFast and accurately characterizing animal behaviors is crucial for neuroscience research. Deep learning models are efficiently used in laboratories for behavior analysis. However, it has not been achieved to use a fully unsupervised method to extract comprehensive and discriminative features directly from raw behavior video frames for annotation and analysis purposes. Here, we report a self-supervised feature extraction (Selfee) convolutional neural network with multiple downstream applications to process video frames of animal behavior in an end-to-end way. Visualization and classification of the extracted features (Meta-representations) validate that Selfee processes animal behaviors in a comparable way of human understanding. We demonstrate that Meta-representations can be efficiently used to detect anomalous behaviors that are indiscernible to human observation and hint in-depth analysis. Furthermore, time-series analyses of Meta-representations reveal the temporal dynamics of animal behaviors. In conclusion, we present a self-supervised learning approach to extract comprehensive and discriminative features directly from raw video recordings of animal behaviors and demonstrate its potential usage for various downstream applications.
A neural correlate of individual odor preference inDrosophila
Authors: Churgin Matthew A. , Lavrentovich Danylo O. , Smith Matthew A. , Gao Ruixuan , Boyden Edward S. , de Bivort Benjamin 
Published: December 2021

AbstractBehavior varies even among genetically identical animals raised in the same environment. However, little is known about the circuit or anatomical origins of this individuality. Here, we demonstrate a neural correlate ofDrosophilaodor preference behavior in the olfactory sensory periphery. Namely, idiosyncratic calcium responses in projection neuron (PN) dendrites and densities of the presynaptic protein Bruchpilot in olfactory receptor neuron (ORN) axon terminals correlate with individual preferences in a choice between two aversive odorants. The ORN-PN synapse appears to be a locus of individuality where microscale variation gives rise to idiosyncratic behavior. Simulating microscale stochasticity in ORN-PN synapses of a 3,062 neuron model of the antennal lobe recapitulates patterns of variation in PN calcium responses matching experiments. Conversely, stochasticity in other compartments of this circuit does not recapitulate those patterns. Our results demonstrate how physiological and microscale structural circuit variations can give rise to individual behavior, even when genetics and environment are held constant.
Diverse Protein Architectures and α-N-Methylation Patterns Define Split Borosin RiPP Biosynthetic Gene Clusters
Authors: Imani Aman S. , Lee Aileen R. , Vishwanathan Nisha , de Waal Floris , Freeman Michael F. 
Published: December 2021

AbstractBorosins are ribosomally synthesized and post-translationally modified peptides (RiPPs) with α-N-methylations installed on the peptide backbone that impart unique properties like proteolytic stability to these natural products. The borosin RiPP family was initially reported only in fungi until our recent discovery and characterization of a Type IV split borosin system in the metal-respiring bacterium Shewanella oneidensis. Here, we used hidden Markov models and sequence similarity networks to identify over 1,600 putative pathways that show split borosin biosynthetic gene clusters are widespread in bacteria. Noteworthy differences in precursor and α-N-methyltransferase open reading frame sizes, architectures, and core peptide properties allow further subdivision of the borosin family into six additional discrete structural types, of which five have been validated in this study.Abstract Figure
Quality financial inclusion and its determinants in South Africa: evidence from survey data
Authors: Chipunza Kudakwashe Joshua , Fanta Ashenafi 
Published: December 2021

PurposeThe study measured quality financial inclusion, a more comprehensive measure of financial inclusion, and examined its determinants at a consumer level in South Africa.Design/methodology/approachThis study leveraged on FinScope 2015 survey data to compute a quality financial inclusion index using polychoric principal component analysis. Subsequently, a heteroscedasticity consistent ordinary least squares regression model was employed to assess determinants of quality financial inclusion.FindingsThe empirical findings indicated that gender, education, financial literacy, income, location and geographical proximity determine quality financial inclusion. These findings could inform policymakers and financial services providers on how quality financial inclusion can be promoted through tailoring financial products for various socio-demographic groups.Research limitations/implicationsDue to data limitations, the study was confined to South Africa and did not capture digital financial inclusion. Hence, future studies could replicate the study in Sub-Saharan Africa's context and compute an index that captures digital financial inclusion.Practical implicationsThese findings could inform policymakers and financial services providers on how quality financial inclusion can be promoted through tailoring financial products for various socio-demographic groups.Originality/valueThis study proposed a more comprehensive measure of quality financial inclusion from a demand-side perspective by accounting for important dimensions that include diversity, affordability, appropriateness and flexibility of financial products and services.
Analysis on the related factors of China's technological innovation ability using greyness relational degree
Authors: Li Li , Li Xican 
Published: December 2021

PurposeIn order to make grey relational analysis applicable to the interval grey number, this paper discusses the model of grey relational degree of the interval grey number and uses it to analyze the related factors of China's technological innovation ability.Design/methodology/approachFirst, this paper gives the definitions of the lower bound domain, the value domain, the upper bound domain of interval grey number and the generalized measure and the generalized greyness of interval grey number. Then, based on the grey relational theory, this paper proposes the model of greyness relational degree of the interval grey number and analyzes its relationship with the classical grey relational degree. Finally, the model of greyness relational degree is applied to analyze the related factors of China's technological innovation ability.FindingsThe results show that the model of greyness relational degree has strict theoretical basis, convenient calculation and easy programming and can be applied to the grey number sequence, real number sequence and grey number and real number coexisting sequence. The relational order of the four related factors of China's technological innovation ability is research and development (R&D) expenditure, R&D personnel, university student number and public library number, and it is in line with the reality.Practical implicationsThe results show that the sequence values of greyness relational degree have large discreteness, and it is feasible and effective to analyze the related factors of China's technological innovation ability.Originality/valueThe paper succeeds in realizing both the model of greyness relational degree of interval grey number with unvalued information distribution and the order of related factors of China's technological innovation ability.
Investigating the climate-adaptive design strategies of residential earth-sheltered buildings in Iran
Authors: Mirabi Elahe , Akrami Abarghuie Fatemeh 
Published: December 2021

PurposeThe earth-sheltered building is an adaptive strategy reducing energy consumption as well as increasing thermal comfort of the residents. Although this idea historically implemented in the city of Yazd, Iran, its effects on thermal comfort have not been studied thoroughly. This paper aims to discuss and analyze energy performance, in terms of parameters such as orientation, underground depth, nocturnal ventilation and its subsequent effects on thermal comfort in earth-sheltered buildings in Yazd.Design/methodology/approachUsing EnergyPlus software, the obtained numeric data are precisely modeled, simulated and analyzed.FindingsResults show that there is a direct relationship between depth of construction and energy consumption savings. The more construction depth of earth-sheltered buildings, the more percentage of energy consumption savings, that is of a higher rate in comparison to the aboveground ones. However, in south orientation, energy saving significantly reduces from depth of 2 m downwards and the annual indoor temperature fluctuation decreases by 50%. This subsequently yields to experiencing indoor thermal comfort for a significant number of days throughout the year. Considering the effects of orientation factor, the south orientation regardless of the depth provides the most desired outcome regarding energy savings.Originality/valueSimulating the model generalized to the sunken courtyard can approve that the results of this research can be applied to the other models.
Cash holding and performance analysis of mutual funds: a case of an emerging financial market
Authors: Khan Faisal , Shah Syed Hamid Ali , Bangash Romana 
Published: December 2021

PurposeThis study is about the determinants of cash holding and impact of cash holding on mutual funds’ performance. In addition, the study analyzes the impact of performance-related determinants of cash holding on funds' performance.Design/methodology/approachPanel data of ten years of 190 open-end mutual funds are analyzed through fixed effect regression technique. The risk-adjusted funds' performance of cash based portfolios is computed through capital asset pricing model (CAPM) (1964), Fama and French (1993) and Carhart (1997) models.FindingsThe results indicate that small size funds, high charging front-end load funds, high turnover ratio funds, high 12-month fund returns run up, high dividend paying funds and high redemption level funds hold more cash for precautionary purpose to avoid costs of cash short-falls. Further, monthly average raw returns and risk-adjusted performance of funds with the lowest raw and residual cash holding are found higher than the funds with the highest cash holding. An increase in cash is found to dilute performance.Originality/valueThis is a pioneer study in a corporate environment with shallow capital market, reliance of businesses on bank credit, firms exposed to agency issues, wealth expropriations and existence of business groups with political linkages but with opportunities of investments due to expected favorable geo-socio-political situation. The study generates outcomes relevant for other similar economies.
Asymmetric financial reporting quality and firm size: conditional evidence from an emerging market
Authors: Saji T.G. 
Published: December 2021

PurposeThe mandatory adoption/convergence of IFRS has increased the information quality of reported earnings in equity markets across the globe. The purpose of the study is to explore whether the mandatory convergence of Indian Accounting Standards (Ind AS) with International Financial Reporting Standards (IFRS) affect the financial reporting quality of listed firms in India.Design/methodology/approachThe sample includes 355 non-financial publicly listed firms on National Stock Exchange (NSE) of India with 1,065 firm-year observations. The authors use models similar to Jones (1991), and DeFond and Jiambalvo (1994) to investigate value relevance in the period “1st January 2017 to 31st December 2019”. The study uses the quantile regression (QR) analysis to verify our hypothesis.FindingsThe findings suggest that IFRS convergence process adds value to accounting quality of reported earnings in Indian stock market. The authors' QR estimations produce collaborating evidence on the uneven impact of IFRS across quantiles and the financial reporting quality skewed in favour of investors of high-valued firms.Research limitations/implicationsThe effects of convergence with IFRS in value relevance of financial statements could be reinforced by considering alternate accrual models and incorporating more accounting measures on an expanded sample of stocks from several global markets.Practical implicationsPresently, convergence of local accounting standards to IFRS in India is only partial. The findings may produce useful insights for regulators and standard setters to further increase the value relevance of financial reports whilst they move towards full convergence.Originality/valueThe study explores the information quality of reported earnings of Indian listed firms in post-IFRS convergence period, which is not properly investigated in the literature. Moreover, the research is unique in terms of applying QR estimations to examine the value relevance of IFRS-converged financial reporting from the emerging market perspective.