bluuebunny/crossref_metadata_2025_split huggingface dataset:
Milti-Scale Detrended Partial Cross-Correlation Analysis of Tree Ring Width and Climate Variations: Revealing Heat and Drought Stress Resilience Factors in a Forest Ecosystem
Authors: Bogachev Mikhail I. , Gafurov Artur M. , Iskandirov Pavel Y. , Kaplun Dmitrii I. , Kayumov Airat R. , Lyanova Asya I. , Pyko Nikita S. , Pyko Svetlana A. , Safonova Anastasia N. , Sinitca Aleksandr M. , Usmanov Bulat M. , Tishin Denis V. 
Published: June 2023

AbstractIn a changing climate, forest ecosystems become increasingly vulnerable to the continuously exacerbating heat and drought stress conditions. Climate stress resilience is governed by a complex interplay of global, regional and local factors, with hydrological conditions among the key roles. Using a modified detrended partial cross-correlation analysis (DPCCA), we analyse the interconnections between long-term tree-ring width (TRW) data and regional climate variations at various scales and time lags. By comparing dendrochronological series of Scots pine trees near the southern edge of the boreal ecotone, we investigate how local hydrological conditions affect heat- and drought stress resilience of the forest ecosystem. While TRW are negatively correlated with spring and summer temperatures and positively cor-related with the Palmer drought severety index (PDSI) in the same year indicating that heatwaves and droughts represent the limiting factors, at interannual scales remarkable contrasts can be observed between areas with different local hydrological conditions. In particular, for the sphagnum bog area positive TRW trends over several consecutive years tend to follow negative PDSI trends and positive spring and summer temperature trends of the same duration with a time lag between one and three years, indicating that prolonged dry periods, as well as warmer springs and summers appear beneficial for the increased annual growth. In contrast, for the surrounding elevated dry land area a reversed tendency can be observed, with pronounced negative long-term correlations with temperature and positive correlations with PDSI. Moreover, by combining detrending models and partial correlation analysis, we show expicitly that the long-term temperature dependence could be partially attributed to the spurious correlations induced by coinciding trends of the trees ageing and climate warming, while contrasts in correlations between TRW and PDSI become only further highlighted, indicating the major impact of the local hydrological conditions on the drought stress resilience.Graphical AbstractHighlightsClimate stress resilience of forest ecosystems is largely driven by local hydrologyMultiscale analysis reveals reversed climate stress response in dry and wetland areasWarmer springs and summers are favorable for tree growth under nondrought conditionsWarm and dry periods improve trees growth in the peat bog area with 1-3 year time lagClimate stress response and ageing effects can be understood from partial correlation
Decoding fMRI Data: A Comparison Between Support Vector Machines and Deep Neural Networks
Authors: Liang Yun , Bo Ke , Meyyappan Sreenivasan , Ding Mingzhou 
Published: June 2023

AbstractMultivoxel pattern analysis (MVPA) examines the differences in fMRI activation patterns associated with different cognitive conditions and provides information not possible with the conventional univariate analysis. Support vector machines (SVMs) are the predominant machine learning method in MVPA. SVMs are intuitive and easy to apply. The limitation is that it is a linear method and mainly suitable for analyzing data that are linearly separable. Convolutional neural networks (CNNs), a class of AI models originally developed for object recognition, are known to have the ability to approximate nonlinear relationships. CNNs are rapidly becoming an alternative to SVMs. The purpose of this study is to compare the two methods when they are applied to the same datasets. Two datasets were considered: (1) fMRI data collected from participants during a cued visual spatial attention task (the attention dataset) and (2) fMRI data collected from participants viewing natural images containing varying degrees of affective content (the emotion dataset). We found that (1) both SVM and CNN are able to achieve above chance level decoding accuracies for attention control and emotion processing in both the primary visual cortex and the whole brain with, (2) the CNN decoding accuracies are consistently higher than that of the SVM, (3) the SVM and CNN decoding accuracies are generally not correlated with each other, and (4) the heatmaps derived from SVM and CNN are not significantly overlapping. These results suggest that (1) there are both linearly separable features and nonlinearly separable features in fMRI data that distinguish cognitive conditions and (2) applying both SVM and CNN to the same data may yield a more comprehensive understanding of neuroimaging data.Key pointsWe compared the performance and characteristics of SVM and CNN, two major methods in MVPA analysis of neuroimaging data, by applying them to the same two fMRI datasets.Both SVM and CNN achieved decoding accuracies above chance level for both datasets in the chosen ROIs and the CNN decoding accuracies were consistently higher than those of SVM.The heatmaps derived from SVM and CNN, which assess the contribution of voxels or brain regions to MVPA decoding performance, showed no significant overlap, providing evidence that the two methods depend on distinct brain activity patterns for decoding cognitive conditions.
A comparison of the binding sites of antibodies and single-domain antibodies
Authors: Gordon Gemma L. , Capel Henriette L. , Guloglu Bora , Richardson Eve , Stafford Ryan L. , Deane Charlotte M. 
Published: June 2023

AbstractAntibodies are the largest class of biotherapeutics. However, in recent years, single-domain antibodies have gained traction due to their smaller size and comparable binding affinity. Antibodies (Abs) and single-domain antibodies (sdAbs) differ in the structures of their binding sites: most significantly, single-domain antibodies lack a light chain and so have just three CDR loops. Given this inherent structural difference, it is important to understand whether Abs and sdAbs are distinguishable in how they engage a binding partner and thus, whether they are suited to different types of epitopes. In this study, we use non-redundant sequence and structural datasets to compare the paratopes, epitopes and antigen interactions of Abs and sdAbs. We demonstrate that even though sd-Abs have smaller paratopes, they target epitopes of equal size to those targeted by Abs. To achieve this, the paratopes of sdAbs contribute more interactions per residue than the paratopes of Abs. Additionally, we find that conserved framework residues are of increased importance in the paratopes of sd-Abs, suggesting that they include non-specific interactions to achieve comparable affinity. Further-more, the epitopes of sdAbs and Abs cannot be distinguished by their shape. For our datasets, sd-Abs do not target more concave epitopes than Abs: we posit that this may be explained by differences in the orientation and compaction of sdAb and Ab CDR-H3 loops. Overall, our results have important implications for the engineering and humanization of sdAbs, as well as the selection of the best modality for targeting a particular epitope.
Correlation between antibacterial activity of twoArtemisiasp. extracts and their plant characteristics
Authors: Mashraqi Abdullah , Al Abboud Mohamed A. , Ismail Khatib Sayeed , Modafer Yosra , Sharma Mukul , El-Shabasy A. 
Published: June 2023

AbstractThe present study evaluated the potential antibacterial activity ofArtemisia absinthiumL. andArtemisia herba-albaAsso. extracts through different organic and aqueous solvents. The tested bacteria were pathogenic types;Listeria monocytogenes,Pseudomonas aeruginosa, Salmonella enterica andStaphylococcus aureus. There were different affinities for the studied organic solvents besides aqueous one. The comparative study was accomplished with comparing to the morphological, anatomical and palynological characters. The similarity parameter is obtained. ANOVA test analyzed MIC values for both plant extracts. Pearson Correlation Coefficients were determined for all both plant traits. MIC and MBC values were confirmed on using butanol and diethyl ether extracts besides butanol and chloroform extracts forArtemisia absinthiumL. andArtemisia hera albaAsso against tested pathogenic bacteria respectively as an alternative natural antibacterial inhibitor agent.
PROTOCOL FOR THE DEVELOPMENT OF A CORE OUTCOME SET FOR RESPECTFUL MATERNAL AND NEWBORN CARE IN A LOW-MIDDLE INCOME SETTING
Authors: Marenga Farai , Dube Kushupika , Goshomi Unice , Bedwell Carol , Kirkham Jamie J 
Published: June 2023

ABSTRACTIntroductionDisrespect and abuse have been seen as a real hindrance to achieving universal coverage for skilled delivery. Improving respectful maternal and newborn care (RMNC) and quality of care around the time of birth has been identified as a key strategy in low- and middle-income countries (LMICs) for reducing the rates of stillbirths and maternal and newborn mortality and morbidity rates (Bohren et al., 2017). Currently, there is no core outcome set (COS) on RMNC, resulting in reporting of various study outcomes from different studies which hinders the improvement of maternal and neonatal health.ObjectiveTo develop a COS for RMNC that can be used in research studies and clinical practice in LMICs.Methods /DesignAn exploratory sequential mixed methods evidence synthesis design will be adopted for the study. This design will enable the utilisation of the COS methodology in three stages: (1) A systematic review and secondary analysis of qualitative interviews of women who utilise maternal care services in order to generate a list of outcomes (2) The list of outcomes will be used in a Delphi study with multiple stakeholder groups which include women and their partners, women representative groups, parents, health workers and researchers. Each person will score the outcomes in terms of the defined criteria. (3) The results of the Delphi will be summarised and discussed at a virtual consensus meeting with representation from all stakeholder groups where the final COS will be decided.DiscussionThe COS will predominantly be developed for use in a LMIC setting to measure and improve the quality of RMNC services.
Silicosis, tuberculosis and silica exposure among artisanal and small-scale miners: A systematic review and modelling paper
Authors: Howlett Patrick , Mousa Hader , Said Bibie , Mbuya Alexander , Kon Onn Min , Mpagama Stellah George , Feary Johanna 
Published: June 2023

AbstractBackgroundAn estimated 44 million artisanal and small-scale miners (ASM), largely based in developing economies, face significant occupational risks for respiratory diseases. We aimed to review studies that describe silicosis and tuberculosis prevalence and respirable crystalline silica (RCS) exposures among ASM and use background evidence to attempt to understand the relationship between exposures and disease outcomes.MethodsWe searched PubMed, Web of Science, Scopus and Embase for studies published before the 24thMarch 2023. Our primary outcome of interest was silicosis or tuberculosis among ASM. Secondary outcomes included measurements of respirable dust or silica, spirometry and prevalence of respiratory symptoms. A systematic review and narrative synthesis was performed and risk of bias assessed using the Joanna Briggs Prevalence Critical Appraisal Tool. Logistic and Poisson regression models with predefined parameters were used to estimate silicosis prevalence and tuberculosis incidence at different distributions of cumulative silica exposure.ResultsWe identified 18 eligible studies that included 29,562 miners from 13 distinct populations in 10 countries. Silicosis prevalence ranged from 11 to 37%, despite four of five studies reporting an average median duration of mining of <6 years. Tuberculosis prevalence was high; microbiologically confirmed disease ranged from 1.8 to 12% and clinical disease 3.0 to 17%. Average RCS intensity was very high (range 0.19-89.5 mg/m3) and respiratory symptoms were common. Our modelling demonstrated decreases in RCS result in reductions in silicosis and tuberculosis, with greater effects at higher mean exposures.DiscussionDespite potential selection and measurement bias, prevalence of silicosis and tuberculosis were high in the studies identified in this review. Our modelling demonstrated the greatest respiratory health benefits of reducing RCS are in those with highest exposures. ASM face a high occupational respiratory disease burden which can be reduced by low-cost and effective reductions in RCS.
Automatic speaker diarization for natural conversation analysis in autism clinical trials
Authors: O’Sullivan James , Bogaarts Guy , Schoenenberger Philipp , Tillmann Julian , Slater David , Mesgarani Nima , Eule Eckhart , Kilchenmann Timothy , Murtagh Lorraine , Hipp Joerg , Lindemann Michael , Lipsmeier Florian , Cheng Wei-Yi , Nobbs David , Chatham Christopher 
Published: June 2023

AbstractChallenges in social communication is one of the core symptom domains in autism spectrum disorder (ASD). Novel therapies are under development to help individuals with these challenges, however the ability to show a benefit is dependent on a sensitive and reliable measure of treatment effect. Currently, measuring these deficits requires the use of time-consuming and subjective techniques. Objective measures extracted from natural conversations could be more ecologically relevant, and administered more frequently – perhaps giving them added sensitivity to change. While several studies have used automated analysis methods to study autistic speech, they require manual transcriptions. In order to bypass this time-consuming process, an automated speaker diarization algorithm must first be applied. In this paper, we are testing whether a speaker diarization algorithm can be applied to natural conversations between autistic individuals and their conversational partner in a natural setting at home over the course of a clinical trial. We calculated the average duration that a participant would speak for within their turn. We found a significant correlation between this feature and the Vineland Adaptive Behaviour Scales (VABS) expressive communication score (r=0.51, p=7 × 10-5). Our results show that natural conversations can be used to obtain measures of talkativeness, and that this measure can be derived automatically, thus showing the promise of objectively evaluating communication challenges in ASD.Index Termsspeaker diarization, autism spectrum disorder, talkativeness, natural conversations, mean length of utterance
Rice biological nitrification inhibition efficiency depends on plant genotype exudation rate
Authors: Kaur-Bhambra Jasmeet , Rajakulendran Joy Ebenezer , Bodington Dylan , Jaspars Marcel , Gubry-Rangin Cécile 
Published: June 2023

AbstractNitrification largely contributes to global nitrogen (N) fertiliser loss and nitrous oxide emissions in agricultural soils, including rice cultivation, Asia’s largest fertiliser consumer. One promising mitigation strategy to achieve greener agriculture involves biological nitrification inhibition (BNI) by plant-derived compounds. Future implementation of this nature-based approach in agricultural settings requires a better understanding of the impact of plant physiological traits on BNI efficiency and nitrification dynamics. We targeted those objectives in five rice genotypes grown in greenhouse conditions. The BNI efficiency was variable among the five plant genotypes, with a stronger inhibition of the ammonia-oxidiser in the rhizosphere than in the bulk soil. We identified that the root mass, root exudation rate and chemical composition are factors explaining the distinct BNI efficiencies in the rice genotypes, with plants having a high BNI efficiency having a small root mass and a high root exudation rate. Using the BNI efficiency assay of root exudates on multiple AO cultures, we demonstrated that AO bioassay could accurately represent the BNI variability in the soil. Finally, we identified a novel BNI compound,N-butyldodecane-1-amine (NBDA), in two high-BNI genotypes. NBDA specifically inhibited ammonia oxidisers by inhibiting enzymes involved in the ammonia oxidation pathway. These findings demonstrate that BNI research integrating plant physiology, microbial ecology, and chemistry has a strong potential for providing more sustainable agriculture.
Rhizoctonia solanidisease suppression: addition of keratin-rich soil amendment leads to functional shifts in soil microbial communities
Authors: Russ Lina , Andreo Jimenez Beatriz , Nijhuis Els , Postma Joeke 
Published: June 2023

AbstractPromoting soil suppressiveness against soil borne pathogens could be a promising strategy to manage crop diseases. One way to increase pathogen suppression would be the addition of soil organic amendments, however the mechanism behind this effect remains unexplored. The presented study will focus onRhizoctonia solanidisease in sugar beet grown in two different soils. We aim to find how microbial communities and their molecular functions can be linked toRhizoctonia solanidisease suppression in sugar beet seedlings after soil is amended with a keratin-rich side stream from the farming industry. Amended soil samples were analyzed using shotgun metagenomics sequencing, and the disease score of plants infected withRhizoctoniaand grown in the same soil was collected. Results showed that both keratin-rich amended soils were rich in bacteria from the Flavobacteriaceae, Sphingobacteriaceae, Boseaceae, Phyllobacteriaceae, Caulobacteraceae, Oxalobacteraceae, Comamonadaceae, Rhodanobacteraceae and Steroidobacteraceae, as well as taxa from the phylum Bdellovibrionota, containing obligate predatory bacteria. The only fungal group that increased significantly was the Mortierellaceae family. Keratinases were abundant in the keratin-rich amended samples. Pfam domain enrichment analysis showed a decline in domains that could be annotated in both keratin-rich amended soils (Lisse ∼18% and Vredepeel ∼30%), showing an increase in unknown proteins. Among proteins that were enriched were those potentially involved in the production of secondary metabolites/antibiotics, proteins involved in motility, keratin-degradation, and contractile secretion system proteins (mostly type VI secretion system). These results could show that keratin-rich soil amendments can support the transformation into a disease suppressive soil by stimulating the same taxa that have been found in other disease suppressive soils. We hypothesize that these taxa are responsible for the suppression effect due to their genomic potential to produce antibiotics, secrete effectors via the contractile secretion system, and degrade oxalate, which is considered a virulence factor ofR. solani, while simultaneously possessing the ability to metabolize keratin.
The lipid flippase ATP10B enables cellular lipid uptake under stress conditions
Authors: Wouters Rosanne , Beletchi Igor , Van den Haute Chris , Baekelandt Veerle , Martin Shaun , Eggermont Jan , Vangheluwe Peter 
Published: June 2023

AbstractPathogenic ATP10B variants have been described in patients with Parkinson’s disease and dementia with Lewy body disease, and we previously established ATP10B as a late endo-/lysosomal lipid flippase transporting both phosphatidylcholine (PC) and glucosylceramide (GluCer) from the lysosomal exoplasmic to cytoplasmic membrane leaflet. Since several other lipid flippases regulate cellular lipid uptake, we here examined whether also ATP10B impacts cellular lipid uptake. Transient co-expression of ATP10B with its obligatory subunit CDC50A stimulated the uptake of fluorescently (NBD-) labeled PC in HeLa cells. This uptake is dependent on the transport function of ATP10B, is impaired by disease-associated variants and appears specific for NBD-PC. Uptake of non-ATP10B substrates, such as NBD-sphingomyelin or NBD-phosphatidylethanolamine is not increased. Remarkably, in stable cell lines co-expressing ATP10B/CDC50A we only observed increased NBD-PC uptake following treatment with rotenone, a mitochondrial complex I inhibitor that induces transport-dependent ATP10B phenotypes. Conversely, Im95m and WM-115 cells with endogenous ATP10B expression, present a decreased NBD-PC uptake following ATP10B knockdown, an effect that is exacerbated under rotenone stress. Our data show that the endo-/lysosomal lipid flippase ATP10B contributes to cellular PC uptake under specific cell stress conditions.
Associative memory neurons of encoding multi-modal signals are recruited by neuroligin-3 mediated new synapse formation
Authors: Xu Yang , Cui Tian-Liang , Li Jia-Yi , Chen Bingchen , Wang Jin-Hui 
Published: June 2023

AbstractThe joint storage and reciprocal retrieval of leant associated signals are presumably encoded by associative memory cells. In the accumulation and enrichment of memory contents in lifespan, a signal often becomes a core signal associatively shared for other signals. One specific group of associative memory neurons that encode this core signal likely interconnects multiple groups of associative memory neurons that encode these other signals for their joint storage and reciprocal retrieval. We have examined this hypothesis in a mouse model of associative learning by pairing the whisker tactile signal sequentially with the olfactory signal, the gustatory signal and the tail-heating signal. Mice experienced this associative learning show the whisker fluctuation induced by olfactory, gustatory and tail-heating signals, or the other way around, i.e., memories to multi-modal associated signals featured by their reciprocal retrievals. Barrel cortical neurons in these mice become able to encode olfactory, gustatory and tail-heating signals alongside the whisker signal. Barrel cortical neurons interconnect piriform, S1-Tr and gustatory cortical neurons. With the barrel cortex as the hub, the indirect activation occurs among piriform, gustatory and S1-Tr cortices for the second-order associative memory. These associative memory neurons recruited to encode multi-modal signals in the barrel cortex for associative memory are downregulated byneuroligin-3knockdown. Thus, associative memory neurons can be recruited as the core cellular substrate to memorize multiple associated signals for the first-order and the second-order of associative memories by neuroligin-3-mediated synapse formation, which constitutes neuronal substrates of cognitive activities in the field of memoriology.HighlightThe coactivity of cerebral cortices during associative learning induces their interconnections.Interconnections endorse the first order and the second order of associative memory.Associative memory cells in cerebral cortices are recruited by mutual synapse innervations.Neuroligin-3 mediates the recruitment of associative memory cells for associative memory.