bluuebunny/crossref_metadata_2025_split huggingface dataset:
Simulated digestions of free oligosaccharides and mucin-type O-glycans reveal a potential role for Clostridium perfringens
Authors: McDonald Andrew G. , Lisacek Frédérique 
Published: January 2024

AbstractThe development of a stable human gut microbiota occurs within the first year of life. Many open questions remain about how microfloral species are influenced by the composition of milk, in particular its content of human milk oligosaccharides (HMOs). The objective is to investigate the effect of the human HMO glycome on bacterial symbiosis and competition, based on the glycoside hydrolase (GH) enzyme activities known to be present in microbial species. We extracted from UniProt a list of all bacterial species catalysing glycoside hydrolase activities (EC 3.2.1.-), cross-referencing with the BRENDA database, and obtained a set of taxonomic lineages and CAZy family data. A set of 13 documented enzyme activities was selected and modelled within an enzyme simulator according to a method described previously in the context of biosynthesis. A diverse population of experimentally observed HMOs was fed to the simulator, and the enzymes matching specific bacterial species were recorded, based on their appearance of individual enzymes in the UniProt dataset. Pairs of bacterial species were identified that possessed complementary enzyme profiles enabling the digestion of the HMO glycome, from which potential symbioses could be inferred. Conversely, bacterial species having similar GH enzyme profiles were considered likely to be in competition for the same set of dietary HMOs within the gut of the newborn. We generated a set of putative biodegradative networks from the simulator output, which provides a visualisation of the ability of organisms to digest HMO and mucin-type O-glycans. B. bifidum, B. longum and C. perfringens species were predicted to have the most diverse GH activity and therefore to excel in their ability to digest these substrates. The expected cooperative role of Bifidobacteriales contrasts with the surprising capacities of the pathogen. These findings indicate that potential pathogens may associate in human gut based on their shared glycoside hydrolase digestive apparatus, and which, in the event of colonisation, might result in dysbiosis. The methods described can readily be adapted to other enzyme categories and species as well as being easily fine-tuneable if new degrading enzymes are identified and require inclusion in the model.
Brain control of bimanual movement enabled by recurrent neural networks
Authors: Deo Darrel R. , Willett Francis R. , Avansino Donald T. , Hochberg Leigh R. , Henderson Jaimie M. , Shenoy Krishna V. 
Published: January 2024

AbstractBrain-computer interfaces have so far focused largely on enabling the control of a single effector, for example a single computer cursor or robotic arm. Restoring multi-effector motion could unlock greater functionality for people with paralysis (e.g., bimanual movement). However, it may prove challenging to decode the simultaneous motion of multiple effectors, as we recently found that a compositional neural code links movements across all limbs and that neural tuning changes nonlinearly during dual-effector motion. Here, we demonstrate the feasibility of high-quality bimanual control of two cursors via neural network (NN) decoders. Through simulations, we show that NNs leverage a neural ‘laterality’ dimension to distinguish between left and right-hand movements as neural tuning to both hands become increasingly correlated. In training recurrent neural networks (RNNs) for two-cursor control, we developed a method that alters the temporal structure of the training data by dilating/compressing it in time and re-ordering it, which we show helps RNNs successfully generalize to the online setting. With this method, we demonstrate that a person with paralysis can control two computer cursors simultaneously. Our results suggest that neural network decoders may be advantageous for multi-effector decoding, provided they are designed to transfer to the online setting.
Integrated image and sensor-based food intake detection in free-living
Authors: Ghosh Tonmoy , Han Yue , Raju Viprav , Hossain Delwar , McCrory Megan A. , Higgins Janine , Boushey Carol , Delp Edward J. , Sazonov Edward 
Published: January 2024

AbstractThe first step in any dietary monitoring system is the automatic detection of eating episodes. To detect eating episodes, either sensor data or images can be used, and either method can result in false-positive detection. This study aims to reduce the number of false positives in the detection of eating episodes by a wearable sensor, Automatic Ingestion Monitor v2 (AIM-2). Thirty participants wore the AIM-2 for two days each (pseudo-free-living and free-living). The eating episodes were detected by three methods: (1) recognition of solid foods and beverages in images captured by AIM-2; (2) recognition of chewing from the AIM-2 accelerometer sensor; and (3) hierarchical classification to combine confidence scores from image and accelerometer classifiers. The integration of image- and sensor-based methods achieved 94.59% sensitivity, 70.47% precision, and 80.77% F1-score in the free-living environment, which is significantly better than either of the original methods (8% higher sensitivity). The proposed method successfully reduces the number of false positives in the detection of eating episodes.
Regnase-2 inhibits glioblastoma cell proliferation
Authors: Sowinska Weronika , Wawro Mateusz , Kochan Jakub , Solecka Aleksandra , Polak Jarosław , Kwinta Borys , Kasza Aneta 
Published: January 2024

AbstractRegnase-2 (Reg-2/MCPIP2/ZC3H12B) is uniquely expressed at a high level in the healthy brain and down-regulated in samples from patients with glioma, reaching the lowest level in high-grade glioblastoma multiforme (GBM). This RNase is involved in the regulation of neuroinflammation through the degradation of IL-6 and IL-1 mRNAs, key pro-inflammatory cytokines for GBM pathology. Reg-2 is a strong inhibitor of the proliferation of human glioblastoma cell lines and blocks their potential to form colonies. Here, we describe that overexpression of Reg-2 stalls glioblastoma cells in the G1 phase of the cell cycle and reduces the level of transcripts implicated in cell cycle progression. These newly identified targets include CCND1, CCNE1, CCNE2, CCNA2, CCNB1, and CCNB2, encoding the cyclins as well as AURKA and PLK1, encoding two important mitosis regulators. By RNA immunoprecipitation we confirmed the direct interaction of Reg-2 with the investigated transcripts. We also tested mRNA regions involved in their interaction with Reg-2 on the example of CCNE2. Reg-2 interacts with the 3’UTR of CCNE2 in a dose-dependent manner. In conclusion, our results indicate that Reg-2 controls key elements in GBM biology by restricting neuroinflammation and inhibiting cancer cell proliferation.
Biodiesel production potential of Eichhornia crassipes (Mart.) Solms: comparison of collection sites and different alcohol transesterifications
Authors: Leite Aricely Aparecida Silva , Weber Luciana Vincenzi , Correa João Paulo Aquino , de Castro Thiago Luis Aguayo , da Silva Carmem Cícera Maria , da Costa e Silva Rosangela Maria Ferreira , Cardoso Claudia Andrea Lima , Konradt-Moraes Leila Cristina 
Published: January 2024

AbstractRenewable resources have stood out as raw materials in producing biofuels. This study aimed to evaluate the parameters of alcohol transesterification (ethanol and methanol) and localization of collection of aquatic macrophyte Eichhornia crassipes (Mart.) Solms in the production of biodiesel by in situ transesterification. E. crassipes was collected in Dourados and Corumbá (Brazil) municipalities. The fatty acid ester composition of the biodiesel was characterized and quantified by gas chromatography. The biodiesel properties were estimated using the BiodieselAnalyzer© program prediction. The ethyl transesterification resulted in higher yields, but the localization of collection was the most relevant parameter in biodiesel production according to the Permutation Multivariate Analysis of Variance. The simulation and comparison of the physical–chemical properties of E. crassipes biodiesel and BD 100 (commercial biodiesel) were promising for commercial application.
Modelling the impact of sublingual immunotherapy versus subcutaneous immunotherapy on patient travel time and CO2 emissions in Sweden
Authors: Cardell Lars-Olaf , Sterner Thomas , Ahmed Waqas , Slættanes Andreas Kallsoy , Svärd Mikael , Pollock Richard F. 
Published: January 2024

AbstractIn Sweden, allergy immunotherapy (AIT) is available as either subcutaneous immunotherapy (SCIT) injections or sublingual immunotherapy (SLIT) tablets and is used to treat moderate-severe allergic rhinitis (AR). This study sought to determine treatment-related CO2 emissions and travel times in Swedish patients receiving either SCIT or SLIT-tablets. A list of specialized Swedish AR clinics that administer AIT was determined, and respective co-ordinates retrieved. Swedish municipality population data were obtained from a national database. The mean distance from each Swedish municipality to the nearest AR clinic was calculated, adjusted using a detour index, and weighted by estimated patient population size. Transport modality data were obtained from a Swedish urban transport study and CO2 emissions were obtained from Government sources. The mean number of annual SLIT-tablets and SCIT doses required were calculated based on product labels and clinical expert input. The annual number of healthcare professional interactions were layered into the model to estimate changes in mean patient travel time, distance, and travel-related CO2 emissions associated with using SCIT versus SLIT-tablets. Mean annual travel-related CO2 emissions were 410 tonnes (to two significant figures [s.f.]; standard deviation [SD] 90) with SLIT-tablets, versus 1700 tonnes (SD 380) for SCIT, resulting in mean annual savings of approximately 1300 tonnes (SD 290) of CO2 if all AIT patients were to receive SLIT-tablets instead of SCIT, over 380 times greater than 2021 average Swedish CO2 emissions per capita. Approximate mean annual travel times for patients taking SLIT-tablets were 66,500 h (three s.f.; SD 14,400), and 278,000 h (SD 60,200) for SCIT, resulting in mean annual savings of 211,000 h (SD 45,800) if all AIT patients were to receive SLIT-tablets instead of SCIT. Compared with SCIT injections, SLIT-tablets led to substantial reductions in treatment-related CO2 emissions and travel times for Swedish patients.
AI-based shape optimization of galloping micro-power generators: exploring the benefits of curved surfaces
Authors: Alhussein Hussam , Dalaq Ahmed S. , Daqaq Mohammed 
Published: January 2024

AbstractThe advent of flow micro-power generation has resparked the interest in researching the galloping instability with the objective of determining the shape of the bluff body that is most prone to galloping. Such shape, which is sought to maximize the efficacy of galloping micro-power generators (GMPGs), must possess a very low cut-in flow speed while achieving large-amplitude steady-state oscillations beyond it. Additionally, since GMPGs can operate in environments with fluctuating flow conditions, the optimal shape must also have a very short rise time to its steady-state amplitude. In this work, we utilize computational fluid dynamics in conjunction with machine learning to optimize the shape of the bluff body of GMPGs for both steady-state and transient performance. We investigate a continuum shape description which encapsulates most of the cases studied earlier in the literature. The continuum has a straight frontal and dorsal faces with varying lengths, and side faces described by surfaces of different curvatures. The optimization study reveals that a curved-trapezoidal bluff body with the highest side surface curvature and frontal-to-dorsal ratio is the perfect shape for steady flow conditions. On the other hand, a square profile with the highest side surface curvature is the ideal choice for highly-fluctuating flow conditions because of its shortest rise time. The theoretical findings are replicated experimentally using wind tunnel tests.
Assessing the reliability of paleomagnetic datasets using the R package PmagDiR
Authors: Dallanave Edoardo 
Published: January 2024

AbstractPaleomagnetism is the most important source of information for determining the position of tectonic plates in the geological past. Over the last few decades significant advancements have been made in improving the reliability of paleomagnetic data, ranging from analytical methods to statistical assessments. Here I present the first version of PmagDiR, an R-based open-source package which displays, assesses the reliability, and, when possible, corrects given paleomagnetic directions distributions. The main functions of the package are to: plot paleomagnetic directions, their averages and confidence boundaries; apply different direction cut-offs to identify and filter outliers; perform a test for antipodality; compare the distribution shape with the one predicted by a widely accepted paleosecular variation model; correct flawed distributions for paleomagnetic inclination flattening; and correct for strain-derived paleomagnetic directions deviations when the strain fabric is known. Furthermore, directions can be converted in virtual geomagnetic poles and plotted on a spherical projection for comparison with reference apparent polar wander paths. All main functions of the PmagDiR package return results as comma separated value text files as well as vector graphic files (pdf), optimized for publication purpose with minimal manipulation.
ATF4 expression in thermogenic adipocytes is required for cold-induced thermogenesis in mice via FGF21-independent mechanisms
Authors: Bjorkman Sarah H. , Marti Alex , Jena Jayashree , García-Peña Luis Miguel , Weatherford Eric T. , Kato Kevin , Koneru Jivan , Chen Jason , Sood Ayushi , Potthoff Matthew J. , Adams Christopher M. , Abel E. Dale , Pereira Renata O. 
Published: January 2024

AbstractIn brown adipose tissue (BAT), short-term cold exposure induces the activating transcription factor 4 (ATF4), and its downstream target fibroblast growth factor 21 (FGF21). Induction of ATF4 in BAT in response to mitochondrial stress is required for thermoregulation, partially by increasing FGF21 expression. In the present study, we tested the hypothesis that Atf4 and Fgf21 induction in BAT are both required for BAT thermogenesis under physiological stress by generating mice selectively lacking either Atf4 (ATF4 BKO) or Fgf21 (FGF21 BKO) in UCP1-expressing adipocytes. After 3 days of cold exposure, core body temperature was significantly reduced in ad-libitum-fed ATF4 BKO mice, which correlated with Fgf21 downregulation in brown and beige adipocytes, and impaired browning of white adipose tissue. Conversely, despite having reduced browning, FGF21 BKO mice had preserved core body temperature after cold exposure. Mechanistically, ATF4, but not FGF21, regulates amino acid import and metabolism in response to cold, likely contributing to BAT thermogenic capacity under ad libitum-fed conditions. Importantly, under fasting conditions, both ATF4 and FGF21 were required for thermogenesis in cold-exposed mice. Thus, ATF4 regulates BAT thermogenesis under fed conditions likely in a FGF21-independent manner, in part via increased amino acid uptake and metabolism.
Cell cycle specific, differentially tagged ribosomal proteins to measure phase specific transcriptomes from asynchronously cycling cells
Authors: Cochran Jesse D. , Leathers Tess A. , Maldosevic Emir , Siejda Klara W. , Vitello Julian , Lee Haesol , Bradley Leigh A. , Young Alex , Jomaa Ahmad , Wolf Matthew J. 
Published: January 2024

AbstractAsynchronously cycling cells pose a challenge to the accurate characterization of phase-specific gene expression. Current strategies, including RNAseq, survey the steady state gene expression across the cell cycle and are inherently limited by their inability to resolve dynamic gene regulatory networks. Single cell RNAseq (scRNAseq) can identify different cell cycle transcriptomes if enough cycling cells are present, however some cells are not amenable to scRNAseq. Therefore, we merged two powerful strategies, the CDT1 and GMNN degrons used in Fluorescent Ubiquitination-based Cell Cycle Indicator (FUCCI) cell cycle sensors and the ribosomal protein epitope tagging used in RiboTrap/Tag technologies to isolate cell cycle phase-specific mRNA for sequencing. The resulting cell cycle dependent, tagged ribosomal proteins (ccTaggedRP) were differentially expressed during the cell cycle, had similar subcellular locations as endogenous ribosomal proteins, incorporated into ribosomes and polysomes, and facilitated the recovery of cell cycle phase-specific RNA for sequencing. ccTaggedRP has broad applications to investigate phase-specific gene expression in complex cell populations.
Ecological determinants of Cope’s rule and its inverse
Authors: Roy Shovonlal , Brännström Åke , Dieckmann Ulf 
Published: January 2024

AbstractCope’s rule posits that evolution gradually increases the body size in lineages. Over the last decades, two schools of thought have fueled a debate on the applicability of Cope’s rule by reporting empirical evidence, respectively, for and against Cope’s rule. The apparent contradictions thus documented highlight the need for a comprehensive process-based synthesis through which both positions of this debate can be understood and reconciled. Here, we use a process-based community-evolution model to investigate the eco-evolutionary emergence of Cope’s rule. We report three characteristic macroevolutionary patterns, of which only two are consistent with Cope’s rule. First, we find that Cope’s rule applies when species interactions solely depend on relative differences in body size and the risk of lineage extinction is low. Second, in environments with higher risk of lineage extinction, the recurrent evolutionary elimination of top predators induces cyclic evolution toward larger body sizes, according to a macroevolutionary pattern we call the recurrent Cope’s rule. Third, when interactions between species are determined not only by their body sizes but also by their ecological niches, the recurrent Cope’s rule may get inverted, leading to cyclic evolution toward smaller body sizes. This recurrent inverse Cope’s rule is characterized by highly dynamic community evolution, involving the diversification of species with large body sizes and the extinction of species with small body sizes. To our knowledge, these results provide the first theoretical foundation for reconciling the contrasting empirical evidence reported on body-size evolution.
A 19‐GHz low‐phase‐noise frequency synthesizer for a K‐band FMCW radar sensor of detecting micro unmanned aerial vehicles
Authors: Lee Jayol , Park Kyung Hwan , Koo Bon Tae 
Published: January 2024

AbstractA 19‐GHz low‐phase‐noise PLL‐frequency synthesizer is presented in this letter that is intended to be used in a K‐band FMCW radar which requires strict phase noise for detecting a small unmanned aerial vehicle. The 17.9 to 19.5‐GHz PLL includes a Darlington cross‐coupled capacitive‐degeneration VCO which presents higher maximum attainable oscillation frequency (ƒtrans) and larger negative transconductance (gm), thus resulting in low phase noise. Manufactured using the SiGe BiCMOS process, the K‐band synthesizer demonstrates −114 dBc/Hz at 1 MHz offset and −138 dBc/Hz at 10 MHz offset from 19.456 GHz locking carrier frequency.
Vibration feature extraction and fault detection method for transmission towers
Authors: Zhao Long , Liu Zhicheng , Yuan Peng , Wen Guanru , Huang Xinbo 
Published: January 2024

AbstractThis paper presents a novel bolt looseness detection method for power transmission towers based on vibration signal analysis. The proposed method utilizes pulse excitation to extract the vibration signal of the tower, which is then adaptively decomposed using the Variational Mode Decomposition of Spider Wasp optimizer (SWVMD). This overcomes limitations of traditional Variational Mode Decomposition methods by leveraging bio‐inspired optimization to improve signal decomposition. Simulated signals processed with different optimization methods verify the superiority of the SWO approach. Field tests on a 110‐kV transmission tower further demonstrate the effectiveness of the proposed SWVMD technique for analyzing on‐site vibration data. A new improved intrinsic multiscale sample entropy feature is also introduced for bolt state characterization. A Spider Wasp Support Vector Machine classifier is developed to realize accurate bolt loosening monitoring using the extracted features. Dynamic response tests under varying bolt conditions show that the method can identify early loosening and reduce tower damage risks compared to conventional techniques. This novel vibration‐based detection framework presents an innovative application of nature‐inspired computing for power infrastructure health monitoring.
Die Zukunft der Homöopathie – eine
persönliche Sicht
Authors: Walach Harald 
Published: January 2024

ZusammenfassungDieser Artikel gibt den Vortrag wieder, den Herr Prof. Dr. Dr. Harald Walach bei
der 171. Jahrestagung des DZVhÄ am 20.05.2023 zum Abschluss des
Kongresses hielt.
Self-consistent phonon calculations and quartic anharmonic lattice thermal conductivity in 2D InS monolayer
Authors: Andharia Eesha , Alqurashi Hind , Pandit Abhiyan , Hamad Bothina 
Published: January 2024

Low lattice thermal conductivity (κl) is a crucial factor for higher figure-of merit and hence the efficiency of thermoelectric generators. There are several reports on intrinsically low κl values in two-dimensional (2D) van der Waals materials using density functional theory and molecular dynamics simulations. In general, phonon dispersions are studied at absolute zero temperature using the finite-displacement approach within harmonic approximations. In addition, the κlis calculated using the third-order cubic interatomic force constants (IFCs) by solving the Boltzmann transport equation for phonons. In these calculations, we use quartic IFCs to solve self-consistent phonon equations to obtain dynamical dispersion relations at a finite temperature of 300 K using finite-temperature Green’s function for Bosonic systems in 2D indium sulfide (InS) monolayer. The cubic and quartic IFCs are calculated using machine learning algorithms, namely, the ordinary least square fitting and the least absolute shrinkage and selection operator. It was found that there is a lowering of the renormalized anharmonic phonon frequencies in the dispersion relations at 300 K upon the inclusion of quartic IFCs and anharmonic terms in the case of the InS monolayer. Thus, the κlvalue is reduced to 0.6 W/mK as compared to 0.9 W/mK obtained using cubic IFCs.