bluuebunny/crossref_metadata_2025_split huggingface dataset:
Early Development of Locomotion in the Term Piglet Model: Does Size Matter?
Authors: Aerts Peter , Mielke Falk , Vanden Hole Charlotte , Van Gorp Merel J W , Van Ginneken Chris 
Published: June 2023

Synopsis
Intrauterine undernutrition in humans typically results in low birth weight ([small for gestational age] SGA) and delayed postnatal neuromotor maturation. Since SGA and intrauterine growth retardation are also common in domestic pigs, piglets are premised as models to study delayed motor development. Applied to the locomotor paradigm, however, questions emerge: (i) how to map the developmental time scale of the precocial model onto the altricial target species and (ii) how to distinguish size from maturation effects? Gait data were collected at self-selected voluntary walking speed during early development (0–96 hours postpartum; pp) for SGA- and normal ([appropriate for gestational age] AGA) piglets. Dimensionless spatiotemporal gait characteristics (according to dynamic similarity) become invariant already after 4 hours pp, suggesting rapid postnatal neuromotor maturation. Moreover, dimensionless gait data are largely identical for SGA- and AGA-siblings, indicating that primarily size effects explain absolute locomotor differences. This is further supported by (i) normalized force-generating capacity of limb muscles, (ii) joint kinematics (&lt;10 hours pp), and (iii) normalized ground reaction forces (&lt;5 days pp) being indifferent between SGA- and AGA- piglets. Furthermore, predictive modeling based on limb joint kinematics is unable to discern the majority of SGA- from AGA-piglets (&lt;10 hours pp). All this leads to the conclusion that, although smaller than the AGA piglets in absolute terms, SGA-piglets mature (neuromechanically speaking) just like, and equally fast as their AGA littermates. Yet, it remains a fact that early SGA piglets are reported to be less mobile, less vital, and less competitive than their AGA siblings (even often die before day 3 pp). This conspicuous difference likely results from the energy level (blood glucose and glycogen) and its mobilization being considerably different between the piglet categories during early development.
Remaining safe conducting Field work While Black (FWB), and Tips for PIs, Universities, and Employers of Black Individuals
Authors: Troutman Alex 
Published: June 2023

Synopsis
Field work is essential to the career of many biologists; however, when working in the field while black (FWB), everyday tasks conducted while in the field can be life-threatening. As a Black individual or as the principal investigator supervising Black individuals, safety in the field requires you to not only navigate weather and wildlife but also your fellow humans. In this article, I address some of the challenges faced by Black scientists in the field, as well as within conservation agencies, universities, and neighboring towns of field sites. I will also discuss how PIs, universities, and employers can ensure a safer, more inclusive experience for their Black friends, colleagues, and students while conducting fieldwork.
Avoiding Recursion in the Representation of Subsenses and Subentries in Dictionaries
Authors: Měchura Michal 
Published: June 2023

Abstract
Recursion, and recursion-like design patterns, are used in the entry schemas of dictionaries to model subsenses and subentries. Recursion occurs when elements of a given type, such as sense, are allowed to contain elements of the same or similar type, such as sense or subsense. This article argues that recursion unnecessarily increases the computational complexity of entries, making dictionaries less easily processable by machines. The article will show how entry schemas can be simplified by re-engineering subsenses and subentries as relations (like in a relational database) such that we only have flat lists of senses and entries, while the is-subsense-of and is-subentry-of relations are encoded using pairs of unique identifiers. This design pattern losslessly records the same information as recursion (including – importantly – the listing order of items inside an entry) but decreases the complexity of the entry structure and makes dictionary entries more easily machine-processable.
Simultaneous diagonalization of nearly commuting Hermitian matrices: do-one-then-do-the-other
Authors: Sutton Brian D 
Published: June 2023

Abstract
Commuting Hermitian matrices may be simultaneously diagonalized by a common unitary matrix. However, the numerical aspects are delicate. We revisit a previously rejected numerical approach in a new algorithm called ‘do-one-then-do-the-other’. One of two input matrices is diagonalized by a unitary similarity, and then the computed eigenvectors are applied to the other input matrix. Additional passes are applied as necessary to resolve invariant subspaces associated with repeated eigenvalues and eigenvalue clusters. The algorithm is derived by first developing a spectral divide-and-conquer method and then allowing the method to break the spectrum into, not just two invariant subspaces, but as many as safely possible. Most computational work is delegated to a black-box eigenvalue solver, which can be tailored to specific computer architectures. The overall running time is a small multiple of a single eigenvalue-eigenvector computation, even on difficult problems with tightly clustered eigenvalues. The article concludes with applications to a structured eigenvalue problem and a highly sensitive eigenvector computation.
Error analysis for the numerical approximation of the harmonic map heat flow with nodal constraints
Authors: Bartels Sören , Kovács Balázs , Wang Zhangxian 
Published: June 2023

Abstract
An error estimate for a canonical discretization of the harmonic map heat flow into spheres is derived. The numerical scheme uses standard finite elements with a nodal treatment of linearized unit-length constraints. The analysis is based on elementary approximation results and only uses the discrete weak formulation.
Non-asymptotic estimates for TUSLA algorithm for non-convex learning with applications to neural networks with ReLU activation function
Authors: Lim Dong-Young , Neufeld Ariel , Sabanis Sotirios , Zhang Ying 
Published: June 2023

Abstract
We consider nonconvex stochastic optimization problems where the objective functions have super-linearly growing and discontinuous stochastic gradients. In such a setting, we provide a nonasymptotic analysis for the tamed unadjusted stochastic Langevin algorithm (TUSLA) introduced in Lovas et al. (2020). In particular, we establish nonasymptotic error bounds for the TUSLA algorithm in Wasserstein-1 and Wasserstein-2 distances. The latter result enables us to further derive nonasymptotic estimates for the expected excess risk. To illustrate the applicability of the main results, we consider an example from transfer learning with ReLU neural networks, which represents a key paradigm in machine learning. Numerical experiments are presented for the aforementioned example, which support our theoretical findings. Hence, in this setting, we demonstrate both theoretically and numerically that the TUSLA algorithm can solve the optimization problem involving neural networks with ReLU activation function. Besides, we provide simulation results for synthetic examples where popular algorithms, e.g., ADAM, AMSGrad, RMSProp and (vanilla) stochastic gradient descent algorithm, may fail to find the minimizer of the objective functions due to the super-linear growth and the discontinuity of the corresponding stochastic gradient, while the TUSLA algorithm converges rapidly to the optimal solution. Moreover, we provide an empirical comparison of the performance of TUSLA with popular stochastic optimizers on real-world datasets, as well as investigate the effect of the key hyperparameters of TUSLA on its performance.
Effect and application of proline metabolism-related gene CgMCUR1 on stress tolerance of Candida glycerinogenes and Saccharomyces cerevisiae
Authors: Chu Chu , Zong Hong , Zhuge Bin , Lu Xinyao 
Published: June 2023

Abstract

Aims
To investigate the effect of CgMCUR1 on the phenotype of Candida glycerinogenes and Saccharomyces cerevisiae.

Methods and results
Inhibition of CgMCUR1 expression reduced acetate, H2O2, and high temperature tolerance of C. glycerinogenes. Expression of CgMCUR1 resulted in better acetic acid, H2O2, and high temperature tolerance in recombinant S. cerevisiae. Meanwhile, CgMCUR1 was able to enhance intracellular proline accumulation. The qRT-PCR analysis revealed that overexpression of CgMCUR1 affected proline metabolism in recombinant S. cerevisiae. The overexpression strain also showed reduced levels of cellular lipid peroxidation and an altered ratio of saturated fatty acid (SFA) to unsaturated fatty acid (UFA) in the cell membrane. The ethanol production of recombinant S. cerevisiae at high temperature was 30.9 g l−1, obtaining an increase of 12%, and the conversion rate was increased by 12%. In the undetoxified cellulose hydrolysate, the ethanol yield was 14.7 g l−1 at 30 h with an improvement of 18.5%, and the conversion rate was increased by 15.3%.

Conclusions
Overexpression of CgMCUR1 rendered the acetic acid, H2O2, and high temperature tolerant of recombinant S. cerevisiae and enhanced the ethanol fermentation performance of recombinant S. cerevisiae under high temperature stress and in undetoxified cellulose hydrolysate by improving intracellular proline accumulation and by changing cellular physiological metabolism.
Development and Antibacterial Investigation of Linezolid-Loaded SPIONs and HPLC Method Development for Quantitative Analysis of Linezolid
Authors: Warsi Musarrat Husain , Mohapatra Sharmistha , Asfer Mohammed , Yusuf Mohammad , Ali Abuzer , Rahman Mohammad Akhlaquer , Ali Amena , Qadir Abdul , Jain Gaurav K 
Published: June 2023

Abstract

Background
Linezolid (LNZ) is extremely prone to resistance. The development of resistance to LNZ should be taken into consideration when selecting this drug as a therapeutic option. It is well established that reactive oxygen species (ROS) generated by iron oxide nanoparticles (MNPs) could kill the infecting bacteria. So, we hypothesized the synergistic antibacterial effect of iron oxide nanoparticles and LNZ.

Objective
To study the release and antibacterial effects of LNZ-loaded superparamagnetic iron oxide nanoparticles (SPIONs) on Staphylococcus aureus and Streptococcus pneumoniae.

Method
Ferrofluid containing SPIONs was synthesized via chemical co-precipitation method and stabilized by sodium lauryl sulphate (SLS). SPIONs were then loaded with LNZ and characterized for particle size, FT-IR, XRD, and entrapment efficiency. Further antibacterial activity of SPIONs and LNZ-loaded SPIONs was investigated. For the in vitro release findings, HPLC analytical method development and validation were performed.

Results
Isolation of LNZ was accomplished on a C-18 column with methanol–TBHS (tetra butyl ammonium hydrogen sulphate, 50:50, v/v). The eluate was monitored at 247 nm with a retention time of 4.175 min. The MNP’s DLS measurement revealed monodispersed particles with an average size of 16.81 ± 1.07 nm and PDI 0.176 ± 0.012. In optimized formulation, 25 ± 1.75% (w/w) of the drug was found to be entrapped. XRD revealed uniform coating of oleic acid covering the entire magnetic particles’ surface with no change in its crystallinity. An effective antimicrobial activity was observed at the lowered dose of drug.

Conclusions
A robust HPLC method was developed to quantify the LNZ in MNPs, and outcomes showed that the reduced dose of LNZ incorporated in SPIONs was able to show similar activity as the marketed product.

Highlights
Successfully reduction of the dose of LNZ was established with the aid of biocompatible MNPs to attain the equivalent antibacterial activity.
Inter-domain interaction of ferredoxin-NADP+ reductase important for the negative cooperativity by ferredoxin and NADP(H)
Authors: Kimata-Ariga Yoko , Shinkoda Rina , Abe Ryuya 
Published: June 2023

Summary (Abstract)
Ferredoxin-NADP+ reductase (FNR) in plants receives electrons from ferredoxin (Fd) and converts NADP+ to NADPH. The affinity between FNR and Fd is weakened by the allosteric binding of NADP(H) on FNR, which is considered as a part of negative cooperativity. We have been investigating the molecular mechanism of this phenomenon and proposed that the NADP(H)-binding signal is transferred to the Fd-binding region across the two domains of FNR, NADP(H)-binding domain and FAD-binding domain. In this study, we analyzed the effect of altering the inter-domain interaction of FNR on the negative cooperativity. Four site-directed FNR mutants at the inter-domain region were prepared, and their NADPH-dependent changes in the Km for Fd and physical binding ability to Fd were investigated. Two mutants, in which an inter-domain hydrogen bond was changed to a disulfide bond (FNR D52C/S208C) and an inter-domain salt bridge was lost (FNR D104N), were shown to suppress the negative cooperativity by using kinetic analysis and Fd-affinity chromatography. These results showed that the inter-domain interaction of FNR is important for the negative cooperativity, suggesting that the allosteric NADP(H)-binding signal is transferred to Fd-binging region by conformational changes involving inter-domain interactions of FNR.
Effects of artificial diet rearing during all instars on silk secretion and gene transcription in Bombyx mori (Lepidoptera: Bombycidae)
Authors: Yin Xingcan , Zhang Yuli , Yu Dongliang , Li Guoli , Wang Xilei , Wei Yuting , He Chunhui , Liu Yanwei , Li Yizhe , Xu Kaizun , Zhang Guizheng 
Published: June 2023

Abstract
Silkworms (Bombyx mori) reared on artificial diets during all instars have the advantages of simplicity and efficiency, year-round production, and reduced risk of poisoning. However, low silk yield remains a challenge, limiting its industrial application. To address this issue, the spinning behavior, nutrient absorption, and transcriptomics of silkworms were investigated. Compared with silkworms reared on mulberry leaves during all instars, those fed with artificial diets showed significantly lower cocoon weight, cocoon shell weight, cocoon shell rate, and silk gland tissue somatic index at the end of the fifth instar (P &lt; 0.01). The spinning duration and crawling distance of silkworms reared on artificial diets were also significantly lower than those reared on mulberry leaves (P &lt; 0.01). Regarding nutrient absorption, the dietary efficiency indexes of silkworms fed with artificial diets were significantly lower than those fed with mulberry leaves, except for the efficiency conversion of digesta to cocoon (P &lt; 0.01). Further RNA-Seq analysis revealed 386 differentially transcribed genes between the 2 groups, with 242 upregulated and 144 downregulated genes. GO enrichment analysis showed that differential transcriptional genes were mainly enriched in organic acid metabolism, oxidation–reduction, and drug catabolism. KEGG enrichment analysis showed that differential transcriptional genes were mainly enriched in genetic information processing and metabolism pathways. Our findings provide new insights into the silk secretion and can serve as a reference for future research and application of silkworms fed with artificial diets.
Optimizing a rapid LAMP assay for discrimination of Drosophila suzukii (Diptera: Drosophilidae) from common drosophilids captured in monitoring traps from the Midwest, United States
Authors: Hong Zihan , Michel Andrew P , Long Elizabeth Y 
Published: June 2023

Abstract
Spotted-wing Drosophila, Drosophila suzukii, is an economically important pest of small fruits worldwide. Currently, the timing of management strategies relies on detection of adult flies captured in baited monitoring traps; however, identifying D. suzukii in trap catch based on morphology can be challenging for growers. DNA-based diagnostic methods such as loop-mediated isothermal amplification (LAMP) have the potential to improve D. suzukii detection. This study evaluated a LAMP assay as a diagnostic tool to discriminate between D. suzukii and closely related drosophilid species found commonly in monitoring traps in the Midwestern United States. Targeting the mitochondrial cytochrome oxidase I (COI) gene, we found the LAMP assay accurately detected D. suzukii with as little as 0.1 ng/μl of DNA at 63 °C for 50 min. Under these optimal incubation conditions, D. suzukii could be discriminated from D. affinis and D. simulans consistently, when specimens collected from liquid monitoring traps were tested independently. Compared to other DNA-based diagnostic tools for D. suzukii, LAMP offers unique benefits: DNA extraction is not required, testing occurs at one temperature in less than 1 h, and positive results are visible as a colorimetric change from pink to yellow. The LAMP assay for D. suzukii can reduce reliance on morphological identification, enhance the adoption of monitoring tools, and improve accuracy of detection. Further optimization can be conducted to evaluate the accuracy and sensitivity of results when a mixture of DNA from both D. suzukii and congener flies are tested in a single LAMP reaction.
Marking Identity: The Debate on the Śrīvaiṣṇavas’ Forehead Marks
Authors: Akepiyapornchai Manasicha 
Published: June 2023

Abstract
Marking one’s forehead plays a role in identifying one’s identity in various sectarian traditions in India, from the premodern period to the modern day. One such tradition is the Śrīvaiṣṇava tradition, the most influential Vaiṣṇava tradition of South India, of which the practice of marking one’s forehead was well established since the premodern time. In this article, I investigate the meanings of forehead marks or the ūrdhvapuṇḍra within the Śrīvaiṣṇava tradition. In particular, I compare the premodern discussions in the Sanskrit texts from the time of the most influential Śrīvaiṣṇava ācārya, Rāmānuja (traditional dates ca. 1017–1137), to the time of one of the most significant post-Rāmānuja ācāryas, Vedāntadeśika (traditional dates ca. 1268­­–1369), and the contemporary positions presented by Prativādi Bhayaṅkaram Aṇṇaṅkarācārya (1891–1983) in his Satsaṃpradāyārthasāranidhi (1947). I argue that the premodern debate on the superiority of the ūrdhvapuṇḍra among the sectarian marks of the Vaiṣṇavas and Śaivas was transformed into the dispute between the two Śrīvaiṣṇava subcommunities, the Teṉkalais and Vaṭakalais, in the present context. Moreover, the arguments and authoritative sources of the premodern authors differ markedly from what we find in the modern text, the Satsaṃpradāyārthasāranidhi. Despite this difference, marking one’s forehead has always been a way for the Śrīvaiṣṇava tradition to indicate their religious identity and sectarian belonging from the past to the present.
Logical reduction of relations: From relational databases to Peirce’s reduction thesis
Authors: Koshkin Sergiy 
Published: June 2023

Abstract
We study logical reduction (factorization) of relations into relations of lower arity by Boolean or relative products that come from applying conjunctions and existential quantifiers to predicates, i.e. by primitive positive formulas of predicate calculus. Our algebraic framework unifies natural joins and data dependencies of database theory and relational algebra of clone theory with the bond algebra of C.S. Peirce. We also offer new constructions of reductions, systematically study irreducible relations and reductions to them and introduce a new characteristic of relations, ternarity, that measures their ‘complexity of relating’ and allows to refine reduction results. In particular, we refine Peirce’s controversial reduction thesis, and show that reducibility behaviour is dramatically different on finite and infinite domains.
Temperature influences lipid content in the red harvester ant, Pogonomyrmex barbatus
Authors: Roeder Diane V , Remy Samantha , Roeder Karl A 
Published: June 2023

Abstract
Temperature is one of the most important environmental conditions affecting physiological processes in ectothermic organisms like ants. Yet, we often lack information on how certain physiological traits covary with temperature across time. Here, we test predictions on how one trait—lipid content—covaries with temperature using a conspicuous, ground-dwelling harvester ant. We focus on lipid content as fat bodies are metabolically active tissues that are important for storing and releasing energy in response to demand, which could be vital for survival under variable temperatures. From March to November, we extracted lipids from surface workers of 14 colonies while simultaneously recording ground temperature. We first assessed if lipid content was highest during cooler temperatures when ants were less active and less metabolically stressed. In doing so, we found that lipid content of ants declined almost 70% from cool months (November lipid content = 14.6%) to hot months (August lipid content = 4.6%). We next assessed if lipid levels from a group of ants collected at a single time point could change by placing individuals into environmental chambers set at 10, 20, and 30°C (i.e., the approximate span of average temperatures from March to November). Temperature again had a significant impact such that after 10 days, lipid content of ants in the hottest chamber (30°C) had decreased by more than 75%. While intraspecific variation in physiological traits often follows seasonal patterns, our results suggest fluctuations in temperature may account for a portion of the variance observed in traits like lipid content.
Prediction of secondary electron yield for metal materials using deep learning
Authors: Kusumi Masahiro , Inoue Bunta , Hirai Yoshihiko , Yasuda Masaaki 
Published: June 2023

Abstract
This article describes a neural network system for predicting the secondary electron yield of metallic materials. For bulk metals, experimental values are used as training data. Due to the strong correlation between the secondary electron yield and the work function, deep learning predicts the secondary electron yield with relatively high accuracy even with a small amount of training data. Our approach demonstrates the importance of the work function in predicting the secondary electron yield. For the secondary electron yield of thin metal films on metal substrates, deep learning predictions are generated using training data obtained by Monte Carlo simulations. The accuracy of the secondary yield predictions of thin films on substrates could be improved by adding experimental values of bulk metals to the training data.