bluuebunny/crossref_metadata_2025_split huggingface dataset:
Retention of p-Chip microtransponders and posttagging survival of small-bodied stream fishes
Authors: Spooner Joseph , Spurgeon Jonathan 
Published: June 2024

Abstract

Objective
Obtaining demographic rates often requires complex open-population capture–mark–recapture (CMR) study designs. Conducting such studies for small-bodied fishes has been limited in part by excessive mortality after tagging procedures and poor tag retention. As new tag types emerge, information regarding fish survival and tag retention over varying time scales may benefit resource managers to effectively plan future CMR studies. The p-Chip microtransponder is a 500- × 500- × 100-μm tag that is inserted subcutaneously and is read with a handheld laser. Each tag contains a nine-digit unique identification number. P-Chip microtransponder tags have been used on a limited number of small-bodied fishes, with relatively high rates observed for fish survival and tag retention. Information on posttagging survival and retention of p-Chip microtransponder tags across a range of small-bodied fish species and tagging locations is needed to inform their effectiveness in future CMR studies.

Methods
We quantified survival and tag retention after p-Chip microtransponder implantation in Creek Chub Semotilus atromaculatus and Northern Pearl Dace Margariscus nachtriebi in a laboratory environment, and retention of p-Chip microtransponder tags in Northern Pearl Dace was also quantified over a year-long field study. We marked 56 Creek Chub and 9 Northern Pearl Dace in the laboratory with p-Chip microtransponder tags and compared them to an equal number of unmarked individuals over 90 days. We marked 1990 Northern Pearl Dace and conducted recapture events through four seasons (June, September, and October 2022 and June 2023) in four headwater streams of Nebraska.

Result
Survival for Creek Chub was 85% (standard error [SE] = 5.9) and did not differ from control fish survival (95%; SE = 3.2) in the 90-day laboratory experiment. Survival for Northern Pearl Dace was 89% (SE = 11.0) and did not differ from that of control fish (100%) in the laboratory experiment. Tag retention was 89% (SE = 4.6) for Creek Chub and 100% for Northern Pearl Dace in the laboratory. The p-Chip microtransponder performed well during the CMR field study, with tag retention for Northern Pearl Dace at 94% across 374 days.

Conclusion
Our results suggest that the p-Chip microtransponder minimally affected small-bodied fish survival and had high tag retention in both the laboratory and field studies. Thus, the p-Chip microtransponder tag may be appropriate for use in small-bodied fishes when individual identification is needed in a CMR study.
Enhancing nutritional formula expiry monitoring: A quality improvement project in a tertiary‐level hospital in Riyadh, Saudi Arabia
Authors: Albalawi Sawsan , AlObari Rania , AlMidani Eyad , Malkawi Rafat , Abosaleh Dima , Qarni Sozan , Subrayan Sasikalan , Almuteiry Saif , Abel‐Reyes Leodevina , Alhazaa Bader , Alhuthil Raghad 
Published: June 2024

AbstractBackgroundNutrition is a vital part of any treatment plan. This may include providing nutritional formulas during hospitalization and afterward. However, reported incidents showed that we had issues with nutritional formula expiry monitoring at our hospital with low compliance to Joint Commission International Standards (MMU.3.1): “There is a process for storage of medications and nutritional products that require special consideration.” Therefore, a “Nutritional Formula Expiry Monitoring” project was created to decrease hospital safety incidents related to expired nutritional formulas from an average of 28 in 2015 to zero by 2018.Materials and MethodsA quality improvement model was developed to map the existing formula processes. Several proposed ideas were tested including performing a hospital‐wide audit to examine possible risks and practices, developing a hospital policy, flow charts, forms, and audit tools, and providing educational presentations.ResultsA total of 40 units in the hospital were included in the implementation. After implementing all the change ideas, the system for monitoring the expiry of the nutritional formula was standardized, and the number of reported incidents related to the nutritional formula decreased from 28 in the third quarter of 2015 to one in the first quarter of 2018.ConclusionThis project provided step‐by‐step instructions for improving storing, delivering, and monitoring of nutritional formula. Consequently, the incidences of expired formula and cost wasting were successfully decreased, which increased safe administration and prevented patients from receiving expired nutritional formula. This project can be implemented in various healthcare settings.
Instead of with a rowboat, search for the north star by navigating a sailboat through turbulent times
Authors: Hoedemakers Juri , de Bruin Cardoso Isabel , van Overbeeke Philine , Meijs Lucas 
Published: June 2024

AbstractWe respond to von Schnurbein and Ahmad's (2019) metaphor of rowing to elucidate the inflexibility of foundations. We suggest that perhaps a sailboat would be more appropriate to finding the north star and add a fifth proposition: a participatory decision‐making process that includes balanced feedback. This approach, though not new, can pose risks such as misaligned priorities and ineffective decisions. To navigate these challenges, the introduction of a "court jester" role is proposed, encouraging open dialogue and critical self‐reflection. The flexibility akin to sailing, where adjustments are made based on feedback, is advocated for effective and dynamic foundation governance.
Auxiliary model maximum likelihood gradient‐based iterative identification for feedback nonlinear systems
Authors: Liu Lijuan , Li Fu , Ma Junxia , Xia Huafeng 
Published: June 2024

AbstractThis article considers the iterative identification problems for a class of feedback nonlinear systems with moving average noise. The model contains both the dynamic linear module and the static nonlinear module, which brings challenges to the identification. By utilizing the key term separation technique, the unknown parameters from both linear and nonlinear modules are included in a parameter vector. Furthermore, an auxiliary model maximum likelihood gradient‐based iterative algorithm is derived to estimate the unknown parameters. In addition, an auxiliary model maximum likelihood stochastic gradient algorithm is derived as a comparison. The numerical simulation results indicate that the auxiliary model maximum likelihood gradient‐based iterative algorithm can effectively estimate the parameters of the feedback nonlinear systems and get more accurate parameter estimates than the auxiliary model maximum likelihood stochastic gradient algorithm.
Osteogenic and angiogenic dual small molecule loaded chitosan nanoparticles for vascularized bone regeneration
Authors: Büyük Nisa İrem , Torun Köse Gamze 
Published: June 2024

AbstractIn recent years, the preference for small molecules has increasingly overshadowed growth factors. In this study, an osteogenic factor, DIPQUO, and an angiogenic factor, a VEGF inducer, GS4012, were encapsulated in chitosan nanoparticles (NPs) to provide vascularized bone regeneration. The encapsulation efficiencies of DIPQUO and GS4012 were 79% and 75%, respectively. The release profiles were 69% and 41% within the first 3 h, followed by 13 days to complete the release of all materials. The synthesis of NPs was validated via FT‐IR analysis, while their thermal properties were assessed via Differential scanning calorimetry (DSC). For in vitro osteogenesis, mesenchymal stem cells isolated from rat bone marrow were investigated by MTS, ALP, and various histological stains (H&E, alizarin red, and von Kossa). In the context of angiogenesis, endothelial cells derived from the peripheral blood of rats were isolated, characterized, and their capabilities to migrate and form vessels assessed. This study demonstrated that two different small molecules act synergistically to enable bone differentiation and may contribute to vascularized bone regeneration.
A fully bio‐based epoxy resin with excellent mechanical properties combines flame retardancy and degradability
Authors: Chen Yuquan , Ren Bin , Li Xuemei , Rao Suhan , Guo Zhangyi , Li Yufei , Huang Ying , Kang Ming , Li Xiuyun 
Published: June 2024

AbstractTraditional epoxy resins are made from non‐renewable fossil resources, which are difficult to reprocess and recycle, and their flammability makes them unsafe during use. In this experiment, an epoxy resin containing Schiff base (TA‐VAN‐EP) was synthesized successfully with biomass‐derived raw materials. This new material not only had favorable mechanical properties but also had good flame retardancy and degradation properties. The chemical structure of TA‐VAN‐EP was characterized by Fourier transform infrared (FTIR) spectroscopy and 1H nuclear magnetic resonance (NMR) spectroscopy. Its mechanical properties, thermal stability, flame‐retardant properties, and other properties were tested. The results showed that, compared with the pure epoxy resin (EP), the mechanical properties of TA‐VAN‐EP were significantly improved, and the glass transition temperature (Tg) was increased from 152°C to 190°C. Additionally, TA‐VAN‐EP reached a V‐1 rating during the UL‐94 test, and the limited oxygen index (LOI) value increased from 24.7% to 28.4%. Also, the total heat release (THR), smoke production rate (SPR), and total smoke release (TSR) decreased extremely. Moreover, TA‐VAN‐EP demonstrated good degradation performance under acidic conditions. In conclusion, this work provided a new idea for the production of bio‐based flame‐retardant epoxy resin with promising degradable abilities and mechanical properties.
Mechanical and thermal properties of fumed silica‐incorporated silane‐terminated urethane/epoxy‐interpenetrating polymer network nanocomposites
Authors: Akın Emre , Çakır Mustafa , Kartal İlyas 
Published: June 2024

AbstractIn this study, it was aimed to improve the mechanical and thermal properties of epoxy materials based on diglycidyl ether of bisphenol‐A‐based. For this purpose, three different nanocomposite materials were prepared at various ratios including a fumed silica nanoparticle‐reinforced epoxy nanocomposite (FSN), an epoxy/silane‐terminated urethane (STU) hybrid interpenetrating polymer network (IPN) nanocomposite (SHIN), and a fumed silica‐reinforced epoxy/STU hybrid IPN nanocomposite (FSHIN). While synthesizing SHIN, 3‐isocyanato propyl trimethoxy silane (ICPTMS) and poly (hexamethylene carbonate) diol were used. The synthesized STU polymer chains were crosslinked by reacting them with TEOS via the sol–gel process. Therefore, hybrid networks were obtained. Moreover, fumed silica nanoparticles were incorporated into the hybrid networks via the sol–gel process for FSHINs. The three different nanocomposite materials exhibited much more improved properties than the neat epoxy. The most prominent nanocomposite was FSHIN. In comparison with the neat epoxy, Young's modulus, ultimate tensile strength, and Izod impact resistance values increased at ratios of 53%, 50%, and 223%, respectively. Glass transition temperature values and char yield values increased substantially in all nanocomposites. However, thermal decomposition temperatures increased only for FSNs. Moreover, these values for FSHINs that were very close to those of the neat epoxy were considerably higher than those of SHINs.Highlights
Fumed silica‐incorporated silane‐terminated urethane/epoxy IPN nanocomposites.
Substantially improved mechanical properties and impact resistance.
Improved thermal stability.
Genome wide association studies on seven yield‐related traits of 183 rice varieties in Bangladesh
Authors: Roy Nilanjan , Kabir Acramul Haque , Zahan Nourin , Mouna Shahba Tasmiya , Chakravarty Sakshar , Rahman Atif Hasan , Bayzid Md. Shamsuzzoha 
Published: June 2024

AbstractRice genetic diversity is regulated by multiple genes and is largely dependent on various environmental factors. Uncovering the genetic variations associated with the diversity in rice populations is the key to breed stable and high yielding rice varieties. We performed genome wide association studies (GWASs) on seven rice yielding traits (grain length, grain width, grain weight, panicle length, leaf length, leaf width, and leaf angle) based on a population of 183 rice landraces of Bangladesh. Our GWASs reveal various chromosomal regions and candidate genes that are associated with different traits in Bangladeshi rice varieties. Noteworthy was the recurrent implication of chromosome 10 in all three grain‐shape‐related traits (grain length, grain width, and grain weight), indicating its pivotal role in shaping rice grain morphology. Our study also underscores the involvement of transposon gene families across these three traits. For leaf related traits, chromosome 10 was found to harbor regions that are significantly associated with leaf length and leaf width. The results of these association studies support previous findings as well as provide additional insights into the genetic diversity of rice. This is the first known GWAS study on various yield‐related traits in the varieties of Oryza sativa available in Bangladesh—the fourth largest rice‐producing country. We believe this study will accelerate rice genetics research and breeding stable high‐yielding rice in Bangladesh.
DNA barcoding of terrestrial invasive plant species in Southwest Michigan
Authors: Nath Sneha , VanSlambrouck Joshua T. , Yao Janelle W. , Gullapalli Ashika , Razi Fayyaz , Lu Yan 
Published: June 2024

AbstractBecause of the detrimental effects of terrestrial invasive plant species (TIPS) on native species, ecosystems, public health, and the economy, many countries have been actively looking for strategies to prevent the introduction and minimize the spread of TIPS. Fast and accurate detection of TIPS is essential to achieving these goals. Conventionally, invasive species monitoring has relied on morphological attributes. Recently, DNA‐based species identification (i.e., DNA barcoding) has become more attractive. To investigate whether DNA barcoding can aid in the detection and management of TIPS, we visited multiple nature areas in Southwest Michigan and collected a small piece of leaf tissue from 91 representative terrestrial plant species, most of which are invasive. We extracted DNA from the leaf samples, amplified four genomic loci (ITS, rbcL, matK, and trnH‐psbA) with PCR, and then purified and sequenced the PCR products. After careful examination of the sequencing data, we were able to identify reliable DNA barcode regions for most species and had an average PCR‐and‐sequencing success rate of 87.9%. We found that the species discrimination rate of a DNA barcode region is inversely related to the ease of PCR amplification and sequencing. Compared with rbcL and matK, ITS and trnH‐psbA have better species discrimination rates (80.6% and 63.2%, respectively). When ITS and trnH‐psbA are simultaneously used, the species discrimination rate increases to 97.1%. The high species/genus/family discrimination rates of DNA barcoding indicate that DNA barcoding can be successfully employed in TIPS identification. Further increases in the number of DNA barcode regions show little or no additional increases in the species discrimination rate, suggesting that dual‐barcode approaches (e.g., ITS + trnH‐psbA) might be the efficient and cost‐effective method in DNA‐based TIPS identification. Close inspection of nucleotide sequences at the four DNA barcode regions among related species demonstrates that DNA barcoding is especially useful in identifying TIPS that are morphologically similar to other species.
A Third of Organic Carbon Is Mineral Bound in Permafrost Sediments Exposed by the World's Largest Thaw Slump, Batagay, Siberia
Authors: Thomas Maxime , Jongejans Loeka L. , Strauss Jens , Vermylen Chloé , Calcus Sacha , Opel Thomas , Kizyakov Alexander , Wetterich Sebastian , Grosse Guido , Opfergelt Sophie 
Published: June 2024

ABSTRACTOrganic carbon (OC) in permafrost interacts with the mineral fraction of soil and sediments, representing < 1% to ~80% of the total OC pool. Quantifying the nature and controls of mineral–OC interactions is therefore crucial for realistic assessments of permafrost‐carbon‐climate feedbacks, especially in ice‐rich regions facing rapid thaw and the development of thermo‐erosion landforms. Here, we analyzed sediment samples from the Batagay megaslump in East Siberia, and we present total element concentrations, mineralogy, and mineral–OC interactions in its different stratigraphic units. Our findings indicate that up to 34 ± 8% of the OC pool interacts with mineral surfaces or elements. Interglacial deposits exhibit enhanced OC–mineral interactions, where OC has undergone greater microbial transformation and has likely low degradability. We provide a first‐order estimate of ~12,000 tons of OC mobilized annually downslope of the headwall (i.e., the approximate mass of 30 large aircrafts), with a maximum of 38% interacting with OC via complexation with metals or associations to poorly crystalline iron oxides. These data imply that over one‐third of the OC exposed by the slump is not readily available for mineralization, potentially leading to prolonged OC residence time in soil and sediments under stable physicochemical conditions.
Ignition and energy release performance of dual‐oxidant Al/MnO2/CuO ternary thermites under rapid heating conditions
Authors: Liu Zhaohu , He Chuan , Zhuang Zhihua , Li Shukui , Feng Xinya , Liu Jinxu 
Published: June 2024

AbstractTailoring the energy release performance of the thermites is crucial for their application in various fields. In this article, dual‐oxidant Al/MnO2/CuO ternary thermites with varying compositions were prepared and systematically evaluated. The ignition delay time, heat of reaction, self‐sustained burning rate, and pressure performance of the thermites were evaluated. As the Al/CuO content increased, the ignition delay time and heat of reaction decreased, while the reaction efficiency, burning rate, pressure peak, and pressurization rate increased. Furthermore, the synergistic addition of the MnO2 and CuO led to enhanced relative flame intensity and maximum flame temperature in the ternary thermite. Our work demonstrates an effective strategy for regulating the energy performance of the thermites by co‐adding of metal oxides. This approach opens avenues for tailoring thermite properties to meet the diverse requirements of various applications.
Knot or not? Identifying unknotted proteins in knotted families with sequence‐based Machine Learning model
Authors: Sikora Maciej , Klimentova Eva , Uchal Dawid , Sramkova Denisa , Perlinska Agata P. , Nguyen Mai Lan , Korpacz Marta , Malinowska Roksana , Nowakowski Szymon , Rubach Pawel , Simecek Petr , Sulkowska Joanna I. 
Published: June 2024

AbstractKnotted proteins, although scarce, are crucial structural components of certain protein families, and their roles continue to be a topic of intense research. Capitalizing on the vast collection of protein structure predictions offered by AlphaFold (AF), this study computationally examines the entire UniProt database to create a robust dataset of knotted and unknotted proteins. Utilizing this dataset, we develop a machine learning (ML) model capable of accurately predicting the presence of knots in protein structures solely from their amino acid sequences. We tested the model's capabilities on 100 proteins whose structures had not yet been predicted by AF and found agreement with our local prediction in 92% cases. From the point of view of structural biology, we found that all potentially knotted proteins predicted by AF can be classified only into 17 families. This allows us to discover the presence of unknotted proteins in families with a highly conserved knot. We found only three new protein families: UCH, DUF4253, and DUF2254, that contain both knotted and unknotted proteins, and demonstrate that deletions within the knot core could potentially account for the observed unknotted (trivial) topology. Finally, we have shown that in the majority of knotted families (11 out of 15), the knotted topology is strictly conserved in functional proteins with very low sequence similarity. We have conclusively demonstrated that proteins AF predicts as unknotted are structurally accurate in their unknotted configurations. However, these proteins often represent nonfunctional fragments, lacking significant portions of the knot core (amino acid sequence).
How arginine inhibits substrate‐binding domain 2 elucidated using molecular dynamics simulations
Authors: Kienlein Maximilian , Zacharias Martin 
Published: June 2024

AbstractThe substrate‐binding domain 2 (SBD2) is an important part of the bacterial glutamine (GLN) transporter and mediates binding and delivery of GLN to the transporter translocation subunit. The SBD2 consists of two domains, D1 and D2, that bind GLN in the space between domains in a closed structure. In the absence of ligand, the SBD2 adopts an open conformation with larger space between domains. The GLN binding and closing are essential for the subsequent transport into the cell. Arginine (ARG) can also bind to SBD2 but does not induce closing and inhibits GLN transport. We use atomistic molecular dynamics (MD) simulations in explicit solvent to study ARG binding in the presence of the open SBD2 structure and observed reversible binding to the native GLN binding site with similar contacts but no transition to a closed SBD2 state. Absolute binding free energy simulations predict a considerable binding affinity of ARG and GLN to the binding site on the D1 domain. Free energy simulations to induce subsequent closing revealed a strong free energy penalty in case of ARG binding in contrast to GLN binding that favors the closed SBD2 state but still retains a free energy barrier for closing. The simulations allowed the identification of the molecular origin of the closing penalty in case of bound ARG and suggested a mutation of lysine at position 373 to alanine that strongly reduced the penalty and allowed closing even in the presence of bound ARG. The study offers an explanation of the molecular mechanism of how ARG competitively inhibits GLN from binding to SBD2 and from triggering the transition to a closed conformation. The proposed Lys373Ala mutation shows promise as a potential tool to validate whether a conformational mismatch between open SBD2 and the translocator is responsible for preventing ARG uptake to the cell.