bluuebunny/crossref_metadata_2025_split huggingface dataset:
Pervasive downstream RNA hairpins dynamically dictate start-codon selection
Authors: Xiang Yezi , Huang Wenze , Tan Lianmei , Chen Tianyuan , He Yang , Irving Patrick S. , Weeks Kevin M. , Zhang Qiangfeng Cliff , Dong Xinnian 
Published: September 2023

AbstractTranslational reprogramming allows organisms to adapt to changing conditions. Upstream start codons (uAUGs), which are prevalently present in mRNAs, have crucial roles in regulating translation by providing alternative translation start sites1–4. However, what determines this selective initiation of translation between conditions remains unclear. Here, by integrating transcriptome-wide translational and structural analyses during pattern-triggered immunity in Arabidopsis, we found that transcripts with immune-induced translation are enriched with upstream open reading frames (uORFs). Without infection, these uORFs are selectively translated owing to hairpins immediately downstream of uAUGs, presumably by slowing and engaging the scanning preinitiation complex. Modelling using deep learning provides unbiased support for these recognizable double-stranded RNA structures downstream of uAUGs (which we term uAUG-ds) being responsible for the selective translation of uAUGs, and allows the prediction and rational design of translating uAUG-ds. We found that uAUG-ds-mediated regulation can be generalized to human cells. Moreover, uAUG-ds-mediated start-codon selection is dynamically regulated. After immune challenge in plants, induced RNA helicases that are homologous to Ded1p in yeast and DDX3X in humans resolve these structures, allowing ribosomes to bypass uAUGs to translate downstream defence proteins. This study shows that mRNA structures dynamically regulate start-codon selection. The prevalence of this RNA structural feature and the conservation of RNA helicases across kingdoms suggest that mRNA structural remodelling is a general feature of translational reprogramming.
Surveillance of Vermont wildlife in 2021–2022 reveals no detected SARS-CoV-2 viral RNA
Authors: Despres Hannah W. , Mills Margaret G. , Schmidt Madaline M. , Gov Jolene , Perez Yael , Jindrich Mars , Crawford Allison M. L. , Kohl Warren T. , Rosenblatt Elias , Kubinski Hannah C. , Simmons Benjamin C. , Nippes Miles C. , Goldenberg Anne J. , Murtha Kristina E. , Nicoloro Samantha , Harris Mia J. , Feeley Avery C. , Gelinas Taylor K. , Cronin Maeve K. , Frederick Robert S. , Thomas Matthew , Johnson Meaghan E. , Murphy James , Lenzini Elle B. , Carr Peter A. , Berger Danielle H. , Mehta Soham P. , Floreani Christopher J. , Koval Amelia C. , Young Aleah L. , Fish Jess H. , Wallace Jack , Chaney Ella , Ushay Grace , Ross Rebecca S. , Vostal Erin M. , Thisner Maya C. , Gonet Kyliegh E. , Deane Owen C. , Pelletiere Kari R. , Rockafeller Vegas C. , Waterman Madeline , Barry Tyler W. , Goering Catriona C. , Shipman Sarah D. , Shiers Allie C. , Reilly Claire E. , Duff Alanna M. , Madruga Sarah L. , Shirley David J. , Jerome Keith R. , Pérez-Osorio Ailyn C. , Greninger Alexander L. , Fortin Nick , Mosher Brittany A. , Bruce Emily A. 
Published: September 2023

AbstractPrevious studies have documented natural infections of SARS-CoV-2 in various domestic and wild animals. More recently, studies have been published noting the susceptibility of members of the Cervidae family, and infections in both wild and captive cervid populations. In this study, we investigated the presence of SARS-CoV-2 in mammalian wildlife within the state of Vermont. 739 nasal or throat samples were collected from wildlife throughout the state during the 2021 and 2022 harvest season. Data was collected from red and gray foxes (Vulpes vulples and Urocyon cineroargentus, respectively), fishers (Martes pennati), river otters (Lutra canadensis), coyotes (Canis lantrans), bobcats (Lynx rufus rufus), black bears (Ursus americanus), and white-tailed deer (Odocoileus virginianus). Samples were tested for the presence of SARS-CoV-2 via quantitative RT-qPCR using the CDC N1/N2 primer set and/or the WHO-E gene primer set. Surprisingly, we initially detected a number of N1 and/or N2 positive samples with high cycle threshold values, though after conducting environmental swabbing of the laboratory and verifying with a second independent primer set (WHO-E) and PCR without reverse transcriptase, we showed that these were false positives due to plasmid contamination from a construct expressing the N gene in the general laboratory environment. Our final results indicate that no sampled wildlife were positive for SARS-CoV-2 RNA, and highlight the importance of physically separate locations for the processing of samples for surveillance and experiments that require the use of plasmid DNA containing the target RNA sequence. These negative findings are surprising, given that most published North America studies have found SARS-CoV-2 within their deer populations. The absence of SARS-CoV-2 RNA in populations sampled here may provide insights in to the various environmental and anthropogenic factors that reduce spillover and spread in North American’s wildlife populations.
Adapting blockchain’s proof-of-work mechanism for multiple traveling salesmen problem optimization
Authors: Sabry Nareman , Shabana Bahaa , Handosa Mohamed , Rashad M. Z. 
Published: September 2023

AbstractThe blockchain network uses a Proof-of-Work (PoW) mechanism to validate transactions and keep the blockchain growth safe against tampering, but it is hugely energy-consuming with no benefit to the peer-to-peer network participants. In this paper, we proposed a blockchain network for distributing products to different locations based on the use of the Proof of Useful Work mechanism, in which miners use computing resources to optimize the traveling salesman problem (TSP) as an alternative to solving mathematical problems that represent the basis of the traditional PoW mechanism to get a new block. According to this proposed blockchain, it not only receives and securely stores the distribution locations but also improves the paths for salesmen when traveling between different locations during the transportation process. This strategy aims to take advantage of the miners’ efforts to minimize the traveled distance by applying the clustering technique and computing the shortest path by Guided Local Search (GLS) for each cluster at the same time. According to the tested results on TSP-LIB instances, the used strategy works efficiently with an average of 0.08 compared to the rest of the meta-heuristics, and the proposed architecture reduced total distances with an average of 0.025%. In addition, the block generation time in the blockchain decreased by 11.11% compared to other works.
The effect of N-arachidonoylethanolamide administration on energy and fat metabolism of early lactating dairy cows
Authors: Schwerdtfeger Jessica , Sauerwein Helga , Albrecht Elke , Mazzuoli-Weber Gemma , von Soosten Dirk , Dänicke Sven , Kuhla Björn 
Published: September 2023

AbstractThe aim of the study was to investigate the effect of N-arachidonoylethanolamide (AEA), an endocannabinoid with orexigenic characteristics, on plasma endocannabinoid concentrations, feed intake, energy balance, lipomobilisation, and hepatic lipid metabolism of early-lactating dairy cows. The experiment involved 10 pairs of Holstein half-sibling cows (end of 2nd–3rd pregnancy). Half-sibs of each pair were randomly assigned to either AEA (n = 10) or control (CON) group (n = 10). From day 1 to 30 postpartum, the AEA group received 5 intraperitoneal injections per week of 3 µg/kg body weight AEA and the CON group 0.9% NaCl. In week 1–3 postpartum, AEA administration had no effect on dry matter intake, body weight, or lipomobilisation, but increased plasma triglyceride concentration on d 21 p.p. and mRNA abundances of genes related to hepatic triglyceride synthesis. In week 4 postpartum, the AEA group showed reduced feed intake and whole-body carbohydrate oxidation, but increased whole-body fat oxidation and hepatic lipid accumulation, likely as a result of a counter-regulatory leptin increase. In conclusion, the present study shows a tissue-specific AEA insensitivity and may point to a leptin-controlled regulation of the ECS in early-lactation.
Different environmental response strategies in sympatric corals from Pacific Islands
Authors: Porro Barbara , Zamoum Thamilla , Forcioli Didier , Gilson Eric , Poquet Adrien , Di Franco Eugenio , Barnay-Verdier Stéphanie , Lombard Fabien , Voolstra Christian R. , Hume Benjamin C. C. , Galand Pierre E. , Moulin Clémentine , Boissin Emilie , Bourdin Guillaume , Iwankow Guillaume , Poulain Julie , Romac Sarah , Agostini Sylvain , Banaigs Bernard , Boss Emmanuel , Bowler Chris , de Vargas Colomban , Douville Eric , Flores Michel , Pesant Stéphane , Reynaud Stéphanie , Sullivan Matthew B. , Sunagawa Shinichi , Thomas Olivier P. , Troublé Romain , Thurber Rebecca Vega , Wincker Patrick , Zoccola Didier , Planes Serge , Allemand Denis , Röttinger Eric , Furla Paola 
Published: September 2023

AbstractCoral reefs are severely threatened by global and local environmental changes. However, susceptibility to perturbations and subsequent mortality varies among coral species. In this study, we tested the contribution of genetic and environmental conditions to coral’s phenotypic response inPocilloporaspp. andPoritesspp. sampled together at a large ecological and temporal scale throughout the Pacific Ocean. We assessed coral phenotype signatures using a multi-biomarker approach (animal and symbiont biomasses, protein carbonylation and ubiquitination and total antioxidant capacities). In both genera, we highlighted a strong anticorrelation between the redox state and the animal and symbiont biomasses. In addition,Pocilloporaexhibited high phenotypic plasticity, responding to various environmental variables such as temperature, nutrients, phosphate, and carbonate chemistry. In contrast,Poritesdisplayed more robust phenotypes influenced by both genetics and past climate events. In conclusion, co-located coral species display different phenotypic response strategies that are influenced by different environmental conditions.
Increased amplitude of atmospheric rivers and associated extreme precipitation in ultra-high-resolution greenhouse warming simulations
Authors: Nellikkattil Arjun Babu , Lee June-Yi , Guan Bin , Timmermann Axel , Lee Sun-Seon , Chu Jung-Eun , Lemmon Danielle 
Published: September 2023

AbstractAtmospheric rivers play an integral role in the global water cycle, but predicting their future changes remains uncertain due to inter-model and inter-detection-method differences. Using ultra-high-resolution Community Earth System Model simulations and a novel detection algorithm based on geometric shape extraction, we quantify global changes in atmospheric rivers and the associated precipitation events in response to doubling and quadrupling of atmospheric CO2 concentrations. We find that, atmospheric rivers are projected to become more frequent and more likely to be associated with extreme precipitation events, increasing their contribution to global mean precipitation. While the water vapor transport within these structures follow Clausius-Clapeyron scaling, the changes in maximum precipitation intensity resemble other saturated atmospheric environments like tropical cyclone cores. The increased amplitude of atmospheric rivers and the associated increase in mean and extreme precipitation have important implications for future water management and adaptation policies.
Development patterns, material metabolism, and greenhouse gas emissions of high-speed railway in China
Authors: Mao Ruichang , Wu Yankun , Chen Jian , Chen Peng , Li Xiaodong 
Published: September 2023

AbstractChina built the longest high-speed railway system by consuming massive construction materials. However, characterization material metabolism in HSR system remains less explored. Here we conducted a bottom-up material metabolism study and revealed the material stocks, flows, and greenhouse gas emissions from 2008 to 2035 in China’s high-speed railway. We show that material stocks temporally amount from 0.6 gigatons in 2010 to 3.7 gigatons in 2020, dominated by aggregate and cement. Spatially, material stock distribution gaps across Chinese provinces are becoming more narrowed. Material flows wise, growing high-speed railway speed increased resource demands, but construction technology and material production advances could offset these increases. Our results demonstrate the carbon replacement value of 1008 megatons by 2020 and the operational emissions of 31 megatons annually. Compared with road and aviation passenger transport, we highlighted the environmental benefits of high-speed railway for informing green transitions.
Secondary flow in contour currents controls the formation of moat-drift contourite systems
Authors: Wilckens Henriette , Eggenhuisen Joris T. , Adema Pelle H. , Hernández-Molina F. Javier , Jacinto Ricardo Silva , Miramontes Elda 
Published: September 2023

AbstractOcean currents control seafloor morphology and the transport of sediments, organic carbon, nutrients, and pollutants in deep-water environments. A better connection between sedimentary deposits formed by bottom currents (contourites) and hydrodynamics is necessary to improve reconstructions of paleocurrent and sediment transport pathways. Here we use physical modeling in a three-dimensional flume tank to analyse the morphology and hydrodynamics of a self-emerging contourite system. The sedimentary features that developed on a flat surface parallel to a slope are an elongated depression (moat) and an associated sediment accumulation (drift). The moat-drift system can only form in the presence of a secondary flow near the seafloor that transports sediment from the slope toward the drift. The secondary flow increases with higher speeds and steeper slopes, leading to steeper adjacent drifts. This study shows how bottom currents shape the morphology of the moat-drift system and highlights their potential to estimate paleo-ocean current strength.
Predictors of Functional Communication Outcomes in Children With Idiopathic Motor Speech Disorders
Authors: Namasivayam Aravind K. , Shin Hyunji , Nisenbaum Rosane , Pukonen Margit , van Lieshout Pascal 
Published: September 2023

Purpose:
The purpose of the study was to investigate child- and intervention-level factors that predict improvements in functional communication outcomes in children with motor-based speech sound disorders.

Method:

Eighty-five preschool-age children with childhood apraxia of speech (
n
= 37) and speech motor delay (
n
= 48) participated. Multivariable logistic regression models estimated odds ratios and 95% confidence intervals for the association between minimal clinically important difference in the Focus on the Outcomes of Communication Under Six scores and multiple child-level (e.g., age, sex, speech intelligibility, Kaufman Speech Praxis Test diagnostic rating scale) and intervention-level predictors (dose frequency and home practice duration).

Results:
Overall, 65% of participants demonstrated minimal clinically important difference changes in the functional communication outcomes. Kaufman Speech Praxis Test rating scale was significantly associated with higher odds of noticeable change in functional communication outcomes in children. There is some evidence that delivering the intervention for 2 times per week for 10 weeks provides benefit.

Conclusion:
A rating scale based on task complexity has the potential for serving as a screening tool to triage children for intervention from waitlist and/or determining service delivery for this population.
The Korean Speech Recognition Sentences: A Large Corpus for Evaluating Semantic Context and Language Experience in Speech Perception
Authors: Song Jieun , Kim Byungjun , Kim Minjeong , Iverson Paul 
Published: September 2023

Purpose:
The aim of this study was to develop and validate a large Korean sentence set with varying degrees of semantic predictability that can be used for testing speech recognition and lexical processing.

Method:

Sentences differing in the degree of final-word predictability (predictable, neutral, and anomalous) were created with words selected to be suitable for both native and nonnative speakers of Korean. Semantic predictability was evaluated through a series of cloze tests in which native (
n
= 56) and nonnative (
n
= 19) speakers of Korean participated. This study also used a computer language model to evaluate final-word predictabilities; this is a novel approach that the current study adopted to reduce human effort in validating a large number of sentences, which produced results comparable to those of the cloze tests. In a speech recognition task, the sentences were presented to native (
n
= 23) and nonnative (
n
= 21) speakers of Korean in speech-shaped noise at two levels of noise.

Results:
The results of the speech-in-noise experiment demonstrated that the intelligibility of the sentences was similar to that of related English corpora. That is, intelligibility was significantly different depending on the semantic condition, and the sentences had the right degree of difficulty for assessing intelligibility differences depending on noise levels and language experience.

Conclusions:
This corpus (1,021 sentences in total) adds to the target languages available in speech research and will allow researchers to investigate a range of issues in speech perception in Korean.

Supplemental Material:

https://doi.org/10.23641/asha.24045582
Evidence-Based Guidance for Alphabet Knowledge Across Service Delivery Models
Authors: Pfeiffer Danika L. , Pavelko Stacey L. 
Published: September 2023

Purpose:The purposes of this alphabet knowledge (AK) tutorial are to provide (a) a description of its developmental sequence, (b) evidence-based assessment considerations, (c) evidence-based intervention guidance, and (d) a discussion of three service delivery models that speech-language pathologists (SLPs) can use when providing intervention that supports AK skills.Method:The tutorial begins with a description of AK's developmental progression, followed by evidence-based assessment considerations, guidance for evidence-based intervention, and a discussion of three service delivery models. Finally, an example is provided of a preschool student with developmental language disorder (DLD) to demonstrate how an SLP could collaborate with a general education teacher to provide intervention addressing AK skills. The application of three different service delivery models is discussed: pull-out, collaborative-consultation, and classroom-based.Conclusions:SLPs should consider a variety of service delivery models, which may include both direct and indirect services, when planning intervention targeting emergent literacy skills for children with DLD. Although these models can be challenging to implement due to barriers such as time and resistance from other professionals, they have the potential to positively impact children's outcomes and educators' knowledge and skills. SLP training programs should incorporate interprofessional education experiences to provide student SLPs with the interprofessional knowledge and skills required to collaborate effectively with other educators in schools.
SCGformer: Smart contract vulnerability detection based on control flow graph and transformer
Authors: Gong KeXin , Song Xiangmei , Wang Na , Wang Chunyang , Zhu Huijuan 
Published: September 2023

AbstractThe security of smart contract has always been one of the significant problems in blockchain. As shown in previous studies, vulnerabilities in smart contracts can lead to unpredictable losses. With the rapid growth of the number of smart contracts, more and more data driven detection technologies based on machine learning have been proposed. However, some state‐of‐the‐art approaches mainly rely on the source code of smart contract. These methods are limited by the openness of the source code and the version of the programming language. To address this problem, we propose a novel vulnerability detection method based on transformer by constructing the control flow graph (CFG) of smart contracts operation codes (opcodes), which shields the difference of various versions of program language. Extensive experiments are conducted to evaluate the effectiveness of the proposed method on the authors' own collected dataset. The experimental results show that the proposed method achieves 94.36% accuracy in vulnerability detection, which performs better than other state‐of‐the‐art methods.
Optimal placement of resistive superconducting fault current limiter by considering short‐circuit current and transient stability of power system
Authors: Hafidz Isa , Mahendra Rafin Aqsa Izza , Pujiantara Margo , Priyadi Ardyono , Purnomo Mauridhi Hery 
Published: September 2023

AbstractHigh level of fault currents has become one of the most challenging issues, along with increased electrical energy consumption and power grid expansion. However, some of the previous work was limited to installing limiters on designs and installing them on small plans. Here, the optimal placement of a resistive‐type superconducting fault current limiter (RSFCL) to achieve good power system transient stability is proposed. The proposed method has several advantages. First, procedure fault analysis is applied to consider the magnitude of the short‐circuit currents and the line located close to the generator for the placement of the device. Compared with other methods, it can directly find the exact line to be installed RSFCL. Second, the stability assessment is validated using the time domain simulation by installing limiters with varying capacities in any location. Third, parameters were analysed to evaluate the proposed method's effectiveness, including angular speed, rotor angular velocity, and generator rotor angle in a multi‐machine system. The result reveals that the placement of the limiter on the line with the most significant short‐circuits value on the line closest to the generator increases the power system stability more than the placement in other locations.
Optimal placement and coordination of the protection devices simultaneous with optimal allocation of the DGs
Authors: Fatemi Seyed Salman , Samet Haidar 
Published: September 2023

AbstractOptimal coordination of the protection devices (PDs) is performed here simultaneous with optimal allocation of them and the DGs. The PDs are a set of directional overcurrent relays (DOCRs) and voltage relays, each with its own fast switch (FS). In previous optimal DG placement studies the coordination of the PDs has been considered as a constraint. So, it was not possible to optimal coordination of the PDs simultaneously. In the present study, the coordination between the PDs is considered in calculating the value of the energy not supplied (ENS) that is a part of an overall cost function. The cost function considered here includes cost of purchase, installation, and maintenance of the DGs and the PDs, cost of the energy losses, cost of the ENS, cost of the purchased energy from the main grid and the DGs, and the penalty cost for emitting environmental pollutants. Here, output of the renewable DGs and the network loads during the year, in a 96‐h model, has been considered as variable. To solve the desired optimization problem, an algorithm based on evolutionary algorithms such as genetic algorithm (GA) is proposed. Finally, various cases have been simulated by considering a standard 33‐bus radial network.