bluuebunny/crossref_metadata_2025_split huggingface dataset:
Physical activity of mice on dietary sulfur amino acid restriction is influenced by age of diet initiation and biological sex
Authors: Cooke Diana , Ables Gene P. 
Published: November 2023

Abstract Please use the attached pdf file for corrections.Sulfur amino acid restriction (SAAR)—the reduction of methionine and cysteine concentrations either in the diet or by genetic manipulation—promotes health span and extends lifespan, but its effects on physical activity remain unclear. We investigated whether age of diet initiation and biological sex could influence physical activity in mice fed either a control diet (CF, 0.86% methionine w/w) or SAAR (0.12% methionine w/w). Quadriceps femoris muscle mass is smaller in SAAR than in CF mice. Young mice fed a chronic SAAR diet at 8 weeks of age exhibited improved wire hang and running wheel activities compared to young CF mice, while aged mice showed comparable results. The effects of chronic SAAR on physical activity was mildly influenced by sex as observed in middle-aged male SAAR mice who showed minor improvements than CF males while middle-aged females displayed no discernible effects. Muscle mass is minimally affected by changes in markers of protein synthesis, autophagy and atrophy. Improvements to physical activity in young SAAR mice could be partially attributed to increased skeletal muscle mitochondrial activity. Furthermore, SAAR in C2C12 myotubes increased citrate synthase protein expression and enhanced succinyl dehydrogenase enzyme activity compared to CF myotubes. Overall, our data reveal that SAAR can improve mouse physical activity without compromising muscle proteostasis. This is partially due to enhanced mitochondrial activity, but the effects are influenced by age of diet initiation and sex.
Insight into age-related changes of the human facial skeleton based on medieval European osteological collection
Authors: Walczak Anna , Krenz-Niedbała Marta , Łukasik Sylwia 
Published: November 2023

AbstractAging changes in the facial skeleton are concentrated mostly in orbits, maxilla and mandible. The aim of this study was to analyze metric traits of the adult viscerocranium in a medieval sample from Cedynia (Poland, Central Europe) and confront the results with literature data for modern populations. It was assumed that diet-related greater biomechanical forces generated during mastication in medieval versus modern times led to slower rate of bone resorption with age. 3D models of the facial skeleton are created for 230 individuals, categorized into young, middle and old adults, and a subgroup of edentulous middle adults is distinguished. Orbits, piriform aperture, maxilla and mandible are measured using Geomagic Studio 12 and analyzed among age categories as well as dentate and edentulous subgroups. The values of the orbital and piriform aperture measurements tend to increase with age and reached statistical significance in males (right orbit height, left orbit width, piriform aperture surface area). In females, maxillary height significantly decrease at right first premolar and first molar, together with height of the right mandibular ramus. In edentulous individuals of both sexes the orbits are wider, and maxillary and mandibular heights are lower than in dentate individuals. This study reveals similar character and direction of the aging process of the facial skeleton in medieval and modern adults, however slower rate of resorptive changes is found in the former sample, which suggests, that diet-related biomechanical forces can influence intensification of the aging processes in the facial skeleton.
Study on the factors of hydrogen sulfide production from lignite bacterial sulfate reduction based on response surface method
Authors: Deng Qigen , Li Shuai , Yao Mengmeng , Liu Chaosi , Zhang Zhecheng , Xiang Sisi 
Published: November 2023

AbstractBacterial sulfate reduction (BSR) is one of the key factors leading to the anomalous accumulation of hydrogen sulphide in coal mines. Environmental factors such as temperature and pH play a crucial role in the metabolism and degradation of coal by sulfate-reducing bacteria (SRB). In this study, coal samples were selected from Shengli Coal Mine, and SRB strains were isolated and purified from mine water using a dilution spread-plate anaerobic cultivation method. Based on single-factor experiments and response surface methodology (RSM), the impact of temperature, pH, oxidation–reduction potential (ORP), chemical oxygen demand to sulfate ratio (COD/SO42−) on the generation of hydrogen sulphide during brown coal BSR was analyzed. The results showed that the anaerobic degradation of coal by SRB was inhibited by either too high or too low a temperature to produce hydrogen sulfide, and the greatest production of hydrogen sulfide occurred at a temperature of about 30 °C; The greatest production of hydrogen sulfide occurred at an initial ambient pH of 7.5; COD/SO42− ratio of around 2.0 is most conducive to hydrogen sulphide generation; the lower ORP value is more favorable for hydrogen sulfide generation. The optimal conditions obtained by RSM were: temperature of 30.37 °C, pH of 7.64 and COD/SO42− of 1.96. Under these conditions, the hydrogen sulfide concentration was 56.79 mg/L, the pH value was 8.40, the ORP value was −274 mV, and the SO42− utilization rate was 58.04%. The RSM results showed that temperature, ambient pH and COD/SO42− had a significant effect on hydrogen sulfide production, and the degree of effect was: ambient pH > temperature > COD/SO42−.
Morphotype induced changes in the life history and population dynamics of an hippolytid shrimp
Authors: Anastasiadou Chryssa , Liasko Roman , Leonardos Ioannis 
Published: November 2023

AbstractOne of the most exceptional, loud paradigm of shape polymorphisms constitutes the “rostral loss” condition in hippolytid shrimps. The intertidal shrimp Hippolyte sapphica includes two conspecific morphotypes, one of which demonstrates a neotenic rostrum (morph-B). Morphs’ rostral elongation is controlled by a single genetic locus, with long rostra (morph-A) representing the recessive state and short, larval-like ones the completely dominant state. Geometrics morphometry on the species morphotypes revealed also the homozygous/heterozygous state of the gene site along with some induced body’ adaptations, which compete the micro-evolutionary disadvantage of the “rostral loss”. We found recently that females’ viability and maternal energy investment selectively favors morph-A. The present contribution detects and discuss comparatively demographic and reproductive traits in species mixed (both morphs) and unmixed populations. Our results show that this sharp dimorphic rostral condition is a sex-related marker and that the species is gonochoric. Presence of morph-B results to (a) lower egg production (b) higher seasonally males’ percentage (c) morph-A females’ earlier maturation and (d) higher fecundity in morph-A mixed populations. It seems that the “rostral loss” state induces complex adaptations between the two morphotypes through sex ratios equilibria, morphotypes’ growth rates, and morphs’ fecundity differentiate inputs throughout the seasons.
Multi-scale measurement of stiffness in the developing ferret brain
Authors: Walter Christopher , Balouchzadeh Ramin , Garcia Kara E. , Kroenke Christopher D. , Pathak Amit , Bayly Philip V. 
Published: November 2023

AbstractCortical folding is an important process during brain development, and aberrant folding is linked to disorders such as autism and schizophrenia. Changes in cell numbers, size, and morphology have been proposed to exert forces that control the folding process, but these changes may also influence the mechanical properties of developing brain tissue. Currently, the changes in tissue stiffness during brain folding are unknown. Here, we report stiffness in the developing ferret brain across multiple length scales, emphasizing changes in folding cortical tissue. Using rheometry to measure the bulk properties of brain tissue, we found that overall brain stiffness increases with age over the period of cortical folding. Using atomic force microscopy to target the cortical plate, we found that the occipital cortex increases in stiffness as well as stiffness heterogeneity over the course of development and folding. These findings can help to elucidate the mechanics of the cortical folding process by clarifying the concurrent evolution of tissue properties.
Nucleotide excision repair deficiency is a targetable therapeutic vulnerability in clear cell renal cell carcinoma
Authors: Prosz Aurel , Duan Haohui , Tisza Viktoria , Sahgal Pranshu , Topka Sabine , Klus Gregory T. , Börcsök Judit , Sztupinszki Zsofia , Hanlon Timothy , Diossy Miklos , Vizkeleti Laura , Stormoen Dag Rune , Csabai Istvan , Pappot Helle , Vijai Joseph , Offit Kenneth , Ried Thomas , Sethi Nilay , Mouw Kent W. , Spisak Sandor , Pathania Shailja , Szallasi Zoltan 
Published: November 2023

AbstractDue to a demonstrated lack of DNA repair deficiencies, clear cell renal cell carcinoma (ccRCC) has not benefitted from targeted synthetic lethality-based therapies. We investigated whether nucleotide excision repair (NER) deficiency is present in an identifiable subset of ccRCC cases that would render those tumors sensitive to therapy targeting this specific DNA repair pathway aberration. We used functional assays that detect UV-induced 6–4 pyrimidine-pyrimidone photoproducts to quantify NER deficiency in ccRCC cell lines. We also measured sensitivity to irofulven, an experimental cancer therapeutic agent that specifically targets cells with inactivated transcription-coupled nucleotide excision repair (TC-NER). In order to detect NER deficiency in clinical biopsies, we assessed whole exome sequencing data for the presence of an NER deficiency associated mutational signature previously identified in ERCC2 mutant bladder cancer. Functional assays showed NER deficiency in ccRCC cells. Some cell lines showed irofulven sensitivity at a concentration that is well tolerated by patients. Prostaglandin reductase 1 (PTGR1), which activates irofulven, was also associated with this sensitivity. Next generation sequencing data of the cell lines showed NER deficiency-associated mutational signatures. A significant subset of ccRCC patients had the same signature and high PTGR1 expression. ccRCC cell line-based analysis showed that NER deficiency is likely present in this cancer type. Approximately 10% of ccRCC patients in the TCGA cohort showed mutational signatures consistent with ERCC2 inactivation associated NER deficiency and also substantial levels of PTGR1 expression. These patients may be responsive to irofulven, a previously abandoned anticancer agent that has minimal activity in NER-proficient cells.
YFDM: YOLO for detecting Morse code
Authors: Wei Zhenhua , Li Zijun , Han Siming 
Published: November 2023

AbstractWith the increasing complexity of the shortwave communication environment, the efficiency and accuracy of the manual detection of Morse code no longer meet actual needs. Therefore, this paper proposes a Morse code detection algorithm called YFDM. For the time–frequency image of the received signal, a combination module of deformable convolution and C3 is used to enhance the backbone network’s attention to the abstract semantics and location information of Morse code. GSConv and VOV-GSCSP modules are used to build a lightweight neck network. Finally, the confidence propagation cluster (CP-Cluster) algorithm is used to filter the detection frame. In an ablation experiment, the parameters and giga floating-point operations per second (GFLOPs) of YFDM were 5.961 M and 9.74 G, respectively, 15.11% and 38.9% less than those of YOLOv5. Moreover, when WIoUv1 was used as the loss function of the bounding box, the AP0.5:0.95 and frames per second (FPS) values of the algorithm reached the highest values, 0.68 and 72.4. The experimental results indicate that the algorithm can effectively reduce the weight of the model while ensuring the detection accuracy and inference speed.
Efficacy and safety of second-line cabozantinib after immuno-oncology combination therapy for advanced renal cell carcinoma: Japanese multicenter retrospective study
Authors: Sazuka Tomokazu , Matsushita Yuto , Sato Hiroaki , Osawa Takahiro , Hinata Nobuyuki , Hatakeyama Shingo , Numakura Kazuyuki , Ueda Kosuke , Kimura Takahiro , Takahashi Masayuki , Tanaka Hajime , Kawasaki Yoshihide , Kurahashi Toshifumi , Kato Takuma , Fujita Kazutoshi , Miyake Makito , Kojima Takahiro , Kitamura Hiroshi , Miyake Hideaki , Ichikawa Tomohiko 
Published: November 2023

AbstractImmuno-oncology (IO) combination therapy is utilized as a first-line systemic treatment for advanced renal cell carcinoma. However, evidence supporting the use of cabozantinib after IO combination therapy is lacking. We retrospectively analyzed patients who received second-line cabozantinib after IO combination therapy using the Japanese Urological Oncology Group (JUOG) database. In total, 254 patients were enrolled in the JUOG global study, and 118 patients who received second-line cabozantinib comprised the study cohort. The objective response rate, disease control rate, second-line cabozantinib progression-free survival (PFS), and overall survival from second-line for overall were 32%, 75%, 10.5 months, and not reached, respectively, for first-line IO-IO therapy were 37%, 77%, 11.1 months, and not reached, respectively, versus 24%, 71%, 8.3 months, and not reached, respectively, for first-line IO-tyrosine kinase inhibitor therapy. In univariate and multivariate analyses, discontinuation of first-line treatment because of progressive disease and liver metastasis were independent risk factors for PFS. All-grade adverse events occurred in 72% of patients, and grade 3 or higher adverse events occurred in 28% of patients. Second line-cabozantinib after first-line IO combination therapy for advanced renal cell carcinoma was expected to be effective after either IO-IO or IO-TKI treatment and feasible in real-world practice.
Parapapillary choroidal microvasculature dropout in eyes with primary open-angle glaucoma
Authors: Igarashi Ryoko , Ochiai Shun , Akagi Tadamichi , Miyamoto Daiki , Sakaue Yuta , Iikawa Ryu , Fukuchi Takeo 
Published: November 2023

AbstractThe purpose of this study was to evaluate how various parameters are related to microvasculature dropout (MvD) area measured using optical coherence tomography angiography (OCTA). We measured the area of MvD in 55 patients with primary open-angle glaucoma (POAG). Using OCTA, MvD area and peripapillary choroidal atrophy (PPA) area were assessed in a 4.5 mm × 4.5 mm region. The following were examined: circumpapillary nerve fiber layer (cpRNFL) thickness, optic disc area, optic disc cupping area, optic disc rim area, Humphrey Field Analyzer (HFA) 24/10–2 mean deviation (MD), and pattern standard deviation (PSD). The relationship between MvD area and each parameter was evaluated using Spearman’s rank correlation coefficient analysis. Mean MvD area and PPA area were 0.18 ± 0.17 mm2 and 1.13 ± 0.72 mm2, respectively. MvD area was significantly correlated with optic disc rim area (p = 0.0017), cpRNFL (p = 0.0027), HFA 24/10–2 MD, and PSD (p < 0.001). In eyes with POAG, MvD area indicates the severity of glaucoma, which might be associated with structural changes in the peripapillary vasculature around the optic disc.
Exploring complexity of class-A Beta-lactamase family using physiochemical-based multiplex networks
Authors: Bhadola Pradeep , Deo Nivedita 
Published: November 2023

AbstractThe Beta-lactamase protein family is vital in countering Beta-lactam antibiotics, a widely used antimicrobial. To enhance our understanding of this family, we adopted a novel approach employing a multiplex network representation of its multiple sequence alignment. Each network layer, derived from the physiochemical properties of amino acids, unveils distinct insights into the intricate interactions among nodes, thereby enabling the identification of key motifs. Nodes with identical property signs tend to aggregate, providing evidence of the presence of consequential functional and evolutionary constraints shaping the Beta-lactamase family. We further investigate the distribution of evolutionary links across various layers. We observe that polarity manifests the highest number of unique links at lower thresholds, followed by hydrophobicity and polarizability, wherein hydrophobicity exerts dominance at higher thresholds. Further, the combinations of polarizability and volume, exhibit multiple simultaneous connections at all thresholds. The combination of hydrophobicity, polarizability, and volume uncovers shared links exclusive to these layers, implying substantial evolutionary impacts that may have functional or structural implications. By assessing the multi-degree of nodes, we unveil the hierarchical influence of properties at each position, identifying crucial properties responsible for the protein’s functionality and providing valuable insights into potential targets for modulating enzymatic activity.
Discriminating mixed qubit states with collective measurements
Authors: Conlon Lorcán O. , Eilenberger Falk , Lam Ping Koy , Assad Syed M. 
Published: November 2023

AbstractIt is a central fact in quantum mechanics that non-orthogonal states cannot be distinguished perfectly. In general, the optimal measurement for distinguishing such states is a collective measurement. However, to the best our knowledge, collective measurements have not been used to enhance quantum state discrimination to date. One of the main reasons for this is the fact that, in the usual state discrimination setting with equal prior probabilities, at least three copies of a quantum state are required to be measured collectively to outperform separable measurements. This is very challenging experimentally. In this work, by considering unequal prior probabilities, we propose and experimentally demonstrate a protocol for distinguishing two copies of single qubit states using collective measurements which achieves a lower probability of error than can be achieved by any non-entangling measurement. Additionally, we implemented collective measurements on three and four copies of the unknown state and found they performed poorly.
Genomic evidence that microbial carbon degradation is dominated by iron redox metabolism in thawing permafrost
Authors: Romanowicz Karl J , Crump Byron C , Kling George W 
Published: November 2023

Abstract
Microorganisms drive many aspects of organic carbon cycling in thawing permafrost soils, but the compositional trajectory of the post-thaw microbiome and its metabolic activity remain uncertain, which limits our ability to predict permafrost–climate feedbacks in a warming world. Using quantitative metabarcoding and metagenomic sequencing, we determined relative and absolute changes in microbiome composition and functional gene abundance during thaw incubations of wet sedge tundra collected from northern Alaska, USA. Organic soils from the tundra active-layer (0–50 cm), transition-zone (50–70 cm), and permafrost (70+ cm) depths were incubated under reducing conditions at 4 °C for 30 days to mimic an extended thaw duration. Following extended thaw, we found that iron (Fe)-cycling Gammaproteobacteria, specifically the heterotrophic Fe(III)-reducing Rhodoferax sp. and chemoautotrophic Fe(II)-oxidizing Gallionella sp., increased by 3–5 orders of magnitude in absolute abundance within the transition-zone and permafrost microbiomes, accounting for 65% of community abundance. We also found that the abundance of genes for Fe(III) reduction (e.g., MtrE) and Fe(II) oxidation (e.g., Cyc1) increased concurrently with genes for benzoate degradation and pyruvate metabolism, in which pyruvate is used to generate acetate that can be oxidized, along with benzoate, to CO2 when coupled with Fe(III) reduction. Gene abundance for CH4 metabolism decreased following extended thaw, suggesting dissimilatory Fe(III) reduction suppresses acetoclastic methanogenesis under reducing conditions. Our genomic evidence indicates that microbial carbon degradation is dominated by iron redox metabolism via an increase in gene abundance associated with Fe(III) reduction and Fe(II) oxidation during initial permafrost thaw, likely increasing microbial respiration while suppressing methanogenesis in wet sedge tundra.
Transient‐based radio frequency fingerprinting with adaptive ensemble of transforms and convolutional neural network
Authors: Baldini Gianmarco 
Published: November 2023

AbstractRadio Frequency Fingerprinting (RFF) has been recently investigated by the research community to enhance wireless security. This letter proposes an RFF approach based only on the complex ramp‐up transient portion of the transmitted frame. The well known issues in literature with the use of the transients for RFF is that they have very short duration, they are strongly non‐stationary and their analysis is sensitive to noise. Then, this letter proposes the application of an ensemble of transforms to the original complex time domain representation in combination with Convolution Neural Network (CNN) to address these issues. To avoid the computing demanding calculation of all the considered transforms, a pre‐processing step based on feature extraction and filter feature selection is implemented to select the most discriminating transforms to reduce the input data to the CNN. The approach is applied to two public RFF data sets, where the complex transient ramp‐up have been extracted. The result shows that the proposed approach is able to obtain a classification accuracy higher than the baseline based on the original signal or selected transforms across various values of Signal to Noise Ratio (SNR).
GSTGAT: Gated spatiotemporal graph attention network for traffic demand forecasting
Authors: Yao Shuilin , Zhang Huizhen , Wang Chenxi , Zeng Dan , Ye Ming 
Published: November 2023

AbstractUrban traffic demand forecasting is an important component in the implementation of intelligent transport systems (ITS). Urban traffic demand data is a spatiotemporal data, describing the amount of traffic demand generated by different areas or stations within a city along the time dimension. Although there has been considerable research work, researchers still face several challenges in predicting accurately, including the capture of hidden features in the temporal dimension of such spatiotemporal data, and the capture of dynamic dependent changes in the spatial dimension. These are even more difficult for long‐time series prediction tasks. This paper designs a multivariate temporal forecasting model specifically adapted to traffic demand to address these challenges, called the Gated Spatiotemporal Graph Attention Network (GSTGAT). GSTGAT is based on the Transformer framework and the whole model is used in an end‐to‐end manner. First of all, it uses the gated self‐attention to extract temporal features in the sequence. Secondly, graph attention is used to capture the spatial dependencies among different variables in the unstructured space. Finally, the use of gated recurrent units in combination with hidden spatial states is proposed to capture multiple levels of spatial dependencies. Experimental results on the taxi dataset in New York and the bicycle dataset in San Francisco Bay Area show that the authors’ proposed model outperforms other state‐of‐the‐art models and improves the prediction accuracy.