bluuebunny/crossref_metadata_2025_split huggingface dataset:
Artificial coarse aggregate from waste materials, fly ash and Msand dust through geopolymerization
Authors: Mathew Gifty Mary , Binu Grace Susan , joice Geo George , Biju Leni Ann , Mathew Mini 
Published: October 2023

Abstract
Coarse aggregate is considered the most vital aspect, providing quantity and strength to the concrete. The aggregates are obtained mainly from natural resources by quarrying rocks or riverbeds. Each year, construction industries use large amounts of natural aggregates, resulting in the depletion of raw materials. Different methods, such as sintering, cold bombing, autoclaving, and geopolymerization, can prepare artificial coarse aggregates. Geopolymerization is a chemical reaction between an alkali solution and source materials containing alumina and silicate. The main objective of this study is to develop artificial aggregates with M sand dust and fly ash by geo polymerization. The ratio of Fly ash to M Sand Dust adopted is 40:60 by weight. Different molarities of sodium hydroxide was used for making the artificial aggregates with a solution-to-binder (S/B) ratio of 3.5 and a sodium silicate-to-sodium hydroxide ratio of 2.5. The mechanical properties of the developed lightweight aggregate are determined as per the specification requirement in IS 9142 (1979) for artificial lightweight aggregates for concrete masonry units. By comparison, these geopolymer aggregates are sustainable, and aggregates with 12 molarity NaOH showed better properties than other molarity NaOH aggregates based on its mechanical properties.
Blockchain Powered IoT Platform for Autonomous Drone Operations in Smart Farming for Environment Sustainability
Authors: Aruna Devi K , Ranjitha M , Divya M O 
Published: October 2023

Abstract
A blockchain based platform can be decentralized, meaning that it is not controlled by a single entity or organization. This can help to cut down the risk of data manipulation or fraud, and can also make the platform more resilient to cyber-attacks or other security threats. By automating many of the processes involved in data collection and analysis, blockchain technology can assist farmers to decrease their costs and increase profitability. Architecture for blockchain powered IoT platform for autonomous drone operations in smart farming is proposed. It has three layers which include data acquistion and encryption in IoT layer and creation and management of ledger in the blockchain layer and service provider layer that include user interaction and farming software. Agriculture integrates many of the new automation technologies already in their routine. The proposed architecture enriches the functioning of farming without affecting the current framework. Overall, the blockchain powered IoT platform for autonomous drone operations in smart farming can help farmers improve their efficiency, increase transparency and security, reduce costs, and ultimately achieve more environment sustainability and profitable farming practices.
3D printing of solid polymer electrolytes by fused filament fabrication: challenges towards in-space manufacturing
Authors: Bourseau Félix , Grugeon Sylvie , Lafont Ugo , Dupont Loïc 
Published: October 2023

Abstract
A new chapter of space exploration is opening with future long-duration space missions toward the Moon and Mars. In this context, the European Space Agency is developing out-of-the-earth manufacturing abilities, to overcome the absence of regular supplies for astronauts’ vital needs (food, health, housing, energy). Additive manufacturing is at the heart of this evolution because it allows the fabrication of tailorable and complex shapes, with a considerable ease of process. Fused filament fabrication (FFF), the most generalized 3D printing technique, has been integrated into the International Space Station to produce polymer parts in microgravity. Filament deposition printing has also a key role to play in Li-ion battery (LIB) manufacturing. Indeed, it could reduce manufacturing cost & time, through one-shot printing of LIB, and improve battery performances with suitable 3D architectures. Thus, additive manufacturing via FFF of LIB in microgravity would open the way to in-space manufacturing of energy storage devices. However, as liquid and volatile species are not compatible with a space station-confined environment, solvent-free 3D printing of polymer electrolytes (PEs) is a necessary step to make battery printing in microgravity feasible. This is a challenging stage because of a strong opposition between the mechanical requirements of the feeding filament and electrochemical properties. Nowadays, PE manufacturing remains a hot topic and lots of strategies are currently being studied to overcome their poor ionic conductivity at room temperature. This work firstly gives a state of the art on the 3D printing of LIBs by FFF. Then, a summary of ionic conduction mechanisms in PEs permits to understand the several strategies studied to enhance PEs performances. Thanks to the confrontation with the specifications of FFF printing and the microgravity environment, polymer blends and composite electrolytes turn out to be the most suitable strategies to 3D print a lithium-ion polymer battery in microgravity.
Incidence of Stomach, Liver, and Colorectal Cancers by Geography and Social Vulnerability Among American Indian and Alaska Native Populations, 2010–2019
Authors: Melkonian Stephanie C , Jim Melissa A , Reza Avid , Peipins Lucy A , Haverkamp Donald , Said Nathania , Sharpe J Danielle 
Published: October 2023

Abstract
Social determinants of health and associated systems, policies, and practices are important drivers of health disparities. American Indian and Alaska Native (AI/AN) populations in the United States have elevated incidence rates of stomach, liver, and colorectal cancers compared with other racial/ethnic groups. In this study, we examined incidence rates of 3 types of gastrointestinal cancer among non-Hispanic AI/AN (NH-AI/AN) and non-Hispanic White (NHW) populations by geographic region and Social Vulnerability Index (SVI) score. Incident cases diagnosed during 2010–2019 were identified from population-based cancer registries linked with the Indian Health Service patient registration databases. Age-adjusted incidence rates (per 100,000 population) for stomach, liver, and colorectal cancers were compared within NH-AI/AN populations and between the NH-AI/AN and NHW populations by SVI score. Rates were higher among NH-AI/AN populations in moderate– and high–SVI-score counties in Alaska, the Southern Plains, and the East than in low-SVI counties. Incidence rates among NH-AI/AN populations were elevated when compared with NHW populations by SVI category. Results indicated that higher social vulnerability may drive elevated cancer incidence among NH-AI/AN populations. Additionally, disparities between NH-AI/AN and NHW populations persist even when accounting for SVI. Exploring social vulnerability can aid in designing more effective interventions to address root causes of cancer disparities among AI/AN populations.
Aggression rates increase around seasonally exploited resources in a primarily grass-eating primate
Authors: Jarvey Julie C , Low Bobbi S , Azanaw Haile Abebaw , Chiou Kenneth L , Snyder-Mackler Noah , Lu Amy , Bergman Thore J , Beehner Jacinta C , Schneider-Crease India A 
Published: October 2023

Abstract
Female social relationships are often shaped by the distribution of dietary resources. Socioecological models predict that females should form strict linear dominance hierarchies when resources are clumped and exhibit more egalitarian social structures when resources are evenly distributed. While many frugivores and omnivores indeed exhibit dominance hierarchies accompanied by differential resource access, many folivores deviate from the expected pattern and display dominance hierarchies despite evenly distributed resources. Among these outliers, geladas (Theropithecus gelada) present a conspicuous puzzle; females exhibit aggressive competition and strict dominance hierarchies despite feeding primarily on non-monopolizable grasses. However, these grasses become scarce in the dry season and geladas supplement their diet with underground storage organs that require relatively extensive energy to extract. We tested whether female dominance hierarchies provide differential access to underground storage organs by assessing how rank, season, and feeding context affect aggression in geladas under long-term study in the Simien Mountains National Park, Ethiopia. We found that the likelihood of receiving aggression was highest when feeding belowground and that the inverse relationship between rank and aggression was the most extreme while feeding belowground in the dry season. These results suggest that aggression in geladas revolves around belowground foods, which may mean that underground storage organs are an energetically central dietary component (despite being consumed less frequently than grasses), or that even “fallback” foods can influence feeding competition and social relationships. Further work should assess whether aggression in this context is directly associated with high-ranking usurpation of belowground foods from lower-ranking females following extraction.
Modeling effects of habitat structure on intraguild predation frequency and spatial coexistence between jaguars and ocelots
Authors: Richards Sean , Gámez Siria , Harris Nyeema C 
Published: October 2023

Abstract
Species within the same ecological guild exhibit niche attributes that vary in association with their diet, spatial occupancy, and temporal activity to reduce competition. In the case of the tropical felid community, many species exhibit substantial overlap in these niche dimensions. Consequently, jaguars (Panthera onca) will sometimes kill the smaller ocelot (Leopardus pardalis) competitor in a phenomenon called intraguild predation (IGP), which is a major structuring force in tropical forests. We developed a spatially explicit agent-based model to understand IGP with the expectation that ocelots employ spatial avoidance strategies using available forest canopy as the more arboreal species. We parameterized model agents with realistic behaviors to replicate the real-world environment. Jaguar and ocelot agents were allowed to move, hunt, and reproduce with varying numbers, heights, and canopy thickness of trees as we recorded IGP events and ocelot canopy occupancy. We used structural equation modeling (SEM) to demonstrate how the number and height of trees significantly affected IGP occurrence. In accordance with our hypothesis, we found that the main contributor mediating coexistence between the two species was spatial avoidance of jaguars by ocelots by using available canopy refuges. Our modeling approach has broad application to different environments with similar intraguild interactions to predict the importance of forest structure and can inform policy directed toward forest management and habitat conservation.
Qmatey: an automated pipeline for fast exact matching-based alignment and strain-level taxonomic binning and profiling of metagenomes
Authors: Adams Alison K , Kristy Brandon D , Gorman Myranda , Balint-Kurti Peter , Yencho G Craig , Olukolu Bode A 
Published: October 2023

Abstract
Metagenomics is a powerful tool for understanding organismal interactions; however, classification, profiling and detection of interactions at the strain level remain challenging. We present an automated pipeline, quantitative metagenomic alignment and taxonomic exact matching (Qmatey), that performs a fast exact matching-based alignment and integration of taxonomic binning and profiling. It interrogates large databases without using metagenome-assembled genomes, curated pan-genes or k-mer spectra that limit resolution. Qmatey minimizes misclassification and maintains strain level resolution by using only diagnostic reads as shown in the analysis of amplicon, quantitative reduced representation and shotgun sequencing datasets. Using Qmatey to analyze shotgun data from a synthetic community with 35% of the 26 strains at low abundance (0.01–0.06%), we revealed a remarkable 85–96% strain recall and 92–100% species recall while maintaining 100% precision. Benchmarking revealed that the highly ranked Kraken2 and KrakenUniq tools identified 2–4 more taxa (92–100% recall) than Qmatey but produced 315–1752 false positive taxa and high penalty on precision (1–8%). The speed, accuracy and precision of the Qmatey pipeline positions it as a valuable tool for broad-spectrum profiling and for uncovering biologically relevant interactions.
Comment on ‘rigorous benchmarking of T cell receptor repertoire profiling methods for cancer RNA sequencing’
Authors: Davydov Alexey N , Bolotin Dmitry A , Poslavsky Stanislav V , Chudakov Dmitry M 
Published: October 2023

Abstract
Transcriptome sequencing has become common in cancer research, resulting in the generation of a substantial volume of RNA sequencing (RNA-Seq) data. The ability to extract immune repertoires from these data is crucial for obtaining information on infiltrating T- and B-lymphocyte clones when dedicated amplicon T-cell/B-cell receptors sequencing (TCR-Seq/BCR-Seq) methods are unavailable. In response to this demand, several dedicated computational methods have been developed, including MiXCR, TRUST and ImRep. In the recent publication in Briefings in Bioinformatics, Peng et al. have conducted an intensive, systematic comparison of the three previously mentioned tools. Although their effort is commendable, we do have a few constructive critiques regarding technical elements of their analysis.
Accurately identifying nucleic-acid-binding sites through geometric graph learning on language model predicted structures
Authors: Song Yidong , Yuan Qianmu , Zhao Huiying , Yang Yuedong 
Published: October 2023

Abstract
The interactions between nucleic acids and proteins are important in diverse biological processes. The high-quality prediction of nucleic-acid-binding sites continues to pose a significant challenge. Presently, the predictive efficacy of sequence-based methods is constrained by their exclusive consideration of sequence context information, whereas structure-based methods are unsuitable for proteins lacking known tertiary structures. Though protein structures predicted by AlphaFold2 could be used, the extensive computing requirement of AlphaFold2 hinders its use for genome-wide applications. Based on the recent breakthrough of ESMFold for fast prediction of protein structures, we have developed GLMSite, which accurately identifies DNA- and RNA-binding sites using geometric graph learning on ESMFold predicted structures. Here, the predicted protein structures are employed to construct protein structural graph with residues as nodes and spatially neighboring residue pairs for edges. The node representations are further enhanced through the pre-trained language model ProtTrans. The network was trained using a geometric vector perceptron, and the geometric embeddings were subsequently fed into a common network to acquire common binding characteristics. Finally, these characteristics were input into two fully connected layers to predict binding sites with DNA and RNA, respectively. Through comprehensive tests on DNA/RNA benchmark datasets, GLMSite was shown to surpass the latest sequence-based methods and be comparable with structure-based methods. Moreover, the prediction was shown useful for inferring nucleic-acid-binding proteins, demonstrating its potential for protein function discovery. The datasets, codes, and trained models are available at https://github.com/biomed-AI/nucleic-acid-binding.
Autoantibodies to beta tubulin in autoimmune liver diseases—Relation to pANCA and clinical relevance
Authors: Preuß Beate , Frank Amelie , Terjung Birgit , Spengler Ulrich , Berg Christoph , Klein Reinhild 
Published: October 2023

Abstract
There was evidence that perinuclear antineutrophil cytoplasmic antibodies (pANCA) in autoimmune liver diseases react with human beta-tubulin-5 (TBB5). Here, we reevaluate the specificity and clinical relevance of anti-TBB5 antibodies.
Patients with untreated autoimmune hepatitis (AIH; n = 53), AIH under immunosuppressive therapy (AIH-IS; n = 125), primary sclerosing cholangitis (PSC; n = 40), primary biliary cholangitis (PBC; n = 250), nonautoimmune liver diseases (n = 158), inflammatory bowel diseases (IBD; n = 30), and healthy individuals (n = 62) were tested by enzyme-linked immunosorbent assay for IgG- and IgA-antibodies against recombinant human TBB5. pANCA were detected by immunofluorescence test. Sera were absorbed with TBB5 coupled to cyanogen bromide-activated sepharose.
Prevalence and reactivity of IgG anti-TBB5 were significantly higher in patients with untreated AIH (68%; arbitrary units [AU] median: 369) than in PSC (28%; AU median: 84, P &lt; 0.001), other liver diseases (14%; AU median: 185, P &lt; 0.0001), IBD (3%; AU median: 111, P &lt; 0.0001), and healthy controls (3%; AU median: 135; P &lt; 0.0001). Anti-TBB5 did not correlate with pANCA, and immunoprecipitation with TBB5 did not abolish pANCA reactivity. In untreated AIH, anti-TBB5-reactivity was significantly higher than in AIH-IS. Transaminases decreased under IS preferentially in anti-TBB5-negative patients. There was no correlation between anti-TBB5-reactivity and histological stages. IgA-anti-TBB5 was mainly found in alcohol-associated liver disease (ALD; 39%).
Our data do not support TBB5 as an autoantigenic target of pANCA. However, IgG-anti-TBB5 showed high specificity for (untreated) AIH. While they did not correlate with histological and laboratory parameters, their presence may indicate a poor response to IS.
Temporal association activates projections from the perirhinal cortex and ventral CA1 to the prelimbic cortex and from the prelimbic cortex to the basolateral amygdala
Authors: Santos Thays B , Kramer-Soares Juliana C , Coelho Cesar A O , Oliveira Maria G M 
Published: October 2023

Abstract
In trace fear conditioning, the prelimbic cortex exhibits persistent activity during the interval between the conditioned and unconditioned stimuli, which maintains a conditioned stimulus representation. Regions cooperating for this function or encoding the conditioned stimulus before the interval could send inputs to the prelimbic cortex, supporting learning. The basolateral amygdala has conditioned stimulus- and unconditioned stimulus-responsive neurons, convergently activated. The prelimbic cortex could directly project to the basolateral amygdala to associate the transient memory of the conditioned stimulus with the unconditioned stimulus. We investigated the neuronal circuit supporting temporal associations using contextual fear conditioning with a 5-s interval, in which 5 s separates the contextual conditioned stimulus from the unconditioned stimulus. Injecting retrobeads, we quantified c-Fos in prelimbic cortex- or basolateral amygdala-projecting neurons from 9 regions after contextual fear conditioning with a 5-s interval or contextual fear conditioning, in which the conditioned and unconditioned stimuli overlap. The contextual fear conditioning with a 5-s interval activated ventral CA1 and perirhinal cortex neurons projecting to the prelimbic cortex and prelimbic cortex neurons projecting to basolateral amygdala. Both fear conditioning activated ventral CA1 and lateral entorhinal cortex neurons projecting to basolateral amygdala and basolateral amygdala neurons projecting to prelimbic cortex. The perirhinal cortex → prelimbic cortex and ventral CA1 → prelimbic cortex connections are the first identified prelimbic cortex afferent projections participating in temporal associations. These results help to understand time-linked memories, a process required in episodic and working memories.
Impact of a Purified Microbiome Therapeutic on Abundance of Antimicrobial Resistance Genes in Patients With RecurrentClostridioides difficileInfection
Authors: Straub Timothy J , Lombardo Mary-Jane , Bryant Jessica A , Diao Liyang , Lodise Thomas P , Freedberg Daniel E , Wortman Jennifer R , Litcofsky Kevin D , Hasson Brooke R , McGovern Barbara H , Ford Christopher B , Henn Matthew R 
Published: October 2023

AbstractBackgroundThe gastrointestinal microbiota is an important line of defense against colonization with antimicrobial resistant (AR) bacteria. In this post hoc analysis of the phase 3 ECOSPOR III trial, we assessed impact of a microbiota-based oral therapeutic (fecal microbiota spores, live; VOWST Oral Spores [VOS], formerly SER-109]; Seres Therapeutics) compared with placebo, on AR gene (ARG) abundance in patients with recurrent Clostridioides difficile infection (rCDI).MethodsAdults with rCDI were randomized to receive VOS or placebo orally for 3 days following standard-of-care antibiotics. ARG and taxonomic profiles were generated using whole metagenomic sequencing of stool at baseline and weeks 1, 2, 8, and 24 posttreatment.ResultsBaseline (n = 151) and serial posttreatment stool samples collected through 24 weeks (total N = 472) from 182 patients (59.9% female; mean age: 65.5 years) in ECOSPOR III as well as 68 stool samples obtained at a single time point from a healthy cohort were analyzed. Baseline ARG abundance was similar between arms and significantly elevated versus the healthy cohort. By week 1, there was a greater decline in ARG abundance in VOS versus placebo (P = .003) in association with marked decline of Proteobacteria and repletion of spore-forming Firmicutes, as compared with baseline. We observed abundance of Proteobacteria and non–spore-forming Firmicutes were associated with ARG abundance, while spore-forming Firmicutes abundance was negatively associated.ConclusionsThis proof-of-concept analysis suggests that microbiome remodeling with Firmicutes spores may be a potential novel approach to reduce ARG colonization in the gastrointestinal tract.
Interspecific competitive effects and annual differences in predation of Empoasca onukii (Hemiptera: Cicadellidae) by wandering spiders
Authors: Chen Shiyan , Cheng Honghao , Cai Junjie , Zou Yunding , Cheng Xian , Bi Shoudong 
Published: October 2023

Abstract
Empoasca onukii Matsuda is an important pest widely distributed in tea areas in China, which greatly affects tea production and quality. The long-term use of chemical control measures will cause environmental pollution. To better utilize wandering spiders that have strong competitive effects on the predation of E. onukii, we conducted a path analysis between the populations of E. onukii and wandering spiders in 3 tea plantations in 2020 and 2021. The wandering spider species that had the greatest direct and indirect effects on the population of E. onukii were analyzed by the magnitude of the path coefficient. Then, a gray system analysis was conducted to determine the closeness of the populations of different wandering spiders to E. onukii by the magnitude of gray correlation coefficient. Finally, the competition coefficients were calculated to determine the competitiveness of wandering spiders. In addition, considering the influence of the number of E. onukii on the interspecific competition of wandering spiders, the gray correlation coefficient and competition coefficient were combined to derive the competition intensity index, which was used to analyze the competitiveness of wandering spiders in a comprehensive manner. The highest competition coefficients in 2020 and 2021 were found for Ebrechtella tricuspidata Fabricius (Araneae: Thomisidae) (X2, 0.5329) and Clubiona reichlini Fabricius (Araneae: Clubionidae) (X4, 0.8475), respectively. The magnitude of the competition intensity index showed that the most competitive wandering spider in 2020 and 2021 was E. tricuspidata (X2, 0.5692) and C. reichlini (X4, 0.8892), respectively. The least competitive spider in both years was Plexippus setipes Karsch (Araneae: Salticidae) (X7). The more competitive the wandering spider is, the closer it is to E. onukii in terms of numbers, and the more dominant it is in feeding on E. onukii. By reasonably protecting and utilizing the competitive E. tricuspidata (X2) and C. reichlini (X4), we can achieve sustainable and effective control of E. onukii.