bluuebunny/crossref_metadata_2025_split huggingface dataset:
A GHz chirped amplitude-modulated laser for high-contrast plasma gratings
Authors: Valdman Michael , Hen Amir , Marcus Gilad 
Published: November 2023

AbstractThe generation and control of large amplitude plasma gratings and other plasma structures is of paramount importance for the realization of plasma photonics. Autoresonant excitation of such structures by means of chirped amplitude-modulated lasers has been recently discussed and analyzed theoretically. Here we discuss the parameter space for the realization of such a scheme and describe the laser system that was built towards this goal. We also expand our earlier theoretical study to account for the more realistic case of a moderately focused laser beam, instead of the simplified plane wave approximation.
EXPERIMENTAL OBSERVATIONS ON PROCESSING LEATHER, SKIN, AND PARCHMENT FOR RADIOCARBON DATING
Authors: Davis Margaret A , Culleton Brendan J , Rosencrance Richard L , Jazwa Christopher S 
Published: November 2023

ABSTRACTSkin-based samples (leather, skin, and parchment) in archaeological, historic and museum settings are among the most challenging materials to radiocarbon (14C) date in terms of removing exogenous carbon sources—comparable to bone collagen in many respects but with much less empirical study to guide pretreatment approaches. In the case of leather, the 14C content of materials used in manufacturing the leather can vary greatly. The presence of leather manufacturing chemicals before pretreatment and their absence afterward is difficult to demonstrate, and the accuracy of dates depends upon isolating the original animal proteins and removing exogenous carbon. Parchments differ in production technique from leather but include similar unknowns. It is not clear that lessons learned in the treatment of one are always salient for treating the other. We measured the 14C content of variously pretreated leather, parchment, skin samples, and extracts, producing apparent ages that varied by hundreds or occasionally thousands of years depending upon sample pretreatment. Fourier Transform Infrared Spectroscopy (FTIR) and C:N ratios provided insight into the chemical composition of carbon reservoirs contributing to age differences. The results of these analyses demonstrated that XAD column chromatography resulted in the most accurate 14C dates for leather and samples of unknown tannage, and FTIR allowed for the detection of contamination that might have otherwise been overlooked.
Characterization of the complete mitochondrial genomes of the zoonotic parasites Bolbosoma nipponicum and Corynosoma villosum (Acanthocephala: Polymorphida) and the molecular phylogeny of the order Polymorphida
Authors: Li Dai-Xuan , Yang Rui-Jia , Chen Hui-Xia , Kuzmina Tetiana A. , Spraker Terry R. , Li Liang 
Published: November 2023

AbstractAcanthocephalans of the order Polymorphida mainly parasitic in birds and mammals, are of veterinary, medical and economic importance. However, the evolutionary relationships of its 3 families (Centrorhynchidae, Polymorphidae and Plagiorhynchidae) remain under debate. Additionally, some species of Polymorphida (i.e. Bolbosoma spp. and Corynosoma spp.) are recognized as zoonotic parasites, associated with human acanthocephaliasis, but the mitochondrial genomes for representatives of Bolbosoma and Corynosoma have not been reported so far. In the present study, the complete mitochondrial genomes B. nipponicum and C. villosum (Acanthocephala: Polymorphidae) are reported for the first time, which are 14 296 and 14 241 bp in length, respectively, and both contain 36 genes [including 12 PCGs, 22 tRNA genes and 2 rRNA genes] and 2 non-coding regions (NCR1 and NCR2). The gene arrangement of some tRNAs in the mitogenomes of B. nipponicum and C. villosum differs from that found in all other acanthocephalans, except Polymorphus minutus. Phylogenetic results based on concatenated amino acid (AA) sequences of the 12 protein-coding genes (PCGs) strongly supported that the family Polymorphidae is a sister to the Centrorhynchidae rather than the Plagiorhynchidae, and also confirmed the sister relationship of the genera Bolbosoma and Corynosoma in the Polymorphidae based on the mitogenomic data for the first time. Our present findings further clarified the phylogenetic relationships of the 3 families Plagiorhynchidae, Centrorhynchidae and Polymorphidae, enriched the mitogenome data of the phylum Acanthocephala (especially the order Polymorphida), and provided the resource of genetic data for diagnosing these 2 pathogenic parasites of human acanthocephaliasis.
The design and kinematic representation of a soft robot in a simulation environment
Authors: Emet Hazal , Gür Berke , Dede Mehmet İsmet Can 
Published: November 2023

AbstractThe increase of human presence in the subsea and seabed environments necessitates the development of more capable and highly dexterous, innovative underwater manipulators. Biomimetic soft-robot arms represent a promising candidate for such manipulation systems. However, the well-known modeling techniques and control theories of traditional rigid robots do not apply to soft robots. The challenges of kinematic and dynamic modeling of soft robots with infinite degrees of freedom require the development of dedicated modeling methods. A novel procedure for representing soft-robotic arms and their motion in a rigid-body simulation environment is proposed in this paper. The proposed procedure relies on the piecewise constant curvature approach to simplify the very complex model of hyper-redundant soft-robotic arms, making it suitable for real-time applications. The proposed method is implemented and verified to be used in model-mediated teleoperation of the soft arms of a biomimetic robotic squid designed for underwater manipulation as a case study.
Prevalence and incidence of emergency department presentations and hospital separations with injecting-related infections in a longitudinal cohort of people who inject drugs
Authors: Curtis Stephanie J. , Colledge-Frisby Samantha , Stewardson Andrew J. , Doyle Joseph S. , Higgs Peter , Maher Lisa , Hickman Matthew , Stoové Mark A. , Dietze Paul M. 
Published: November 2023

Abstract
People who inject drugs are at risk of acute bacterial and fungal injecting-related infections. There is evidence that incidence of hospitalizations for injecting-related infections are increasing in several countries, but little is known at an individual level. We aimed to examine injecting-related infections in a linked longitudinal cohort of people who inject drugs in Melbourne, Australia. A retrospective descriptive analysis was conducted to estimate the prevalence and incidence of injecting-related infections using administrative emergency department and hospital separation datasets linked to the SuperMIX cohort, from 2008 to 2018. Over the study period, 33% (95%CI: 31–36%) of participants presented to emergency department with any injecting-related infections and 27% (95%CI: 25–30%) were admitted to hospital. Of 1,044 emergency department presentations and 740 hospital separations, skin and soft tissue infections were most common, 88% and 76%, respectively. From 2008 to 2018, there was a substantial increase in emergency department presentations and hospital separations with any injecting-related infections, 48 to 135 per 1,000 person-years, and 18 to 102 per 1,000 person-years, respectively. The results emphasize that injecting-related infections are increasing, and that new models of care are needed to help prevent and facilitate early detection of superficial infection to avoid potentially life-threatening severe infections.
The nutrient profile and cost of specialty dietary patterns: a hypothetical case study
Authors: Lenferna De La Motte Kayla-Anne , Zinn Caryn 
Published: November 2023

AbstractObjective:Ketogenic and vegan diets have become increasingly popular. The rising popularity of these dietary trends has been met in kind by the food industry producing a variety of specialty ultra-processed foods (UPF). Despite increasing popularity, the cost and nutrient profile of vegan and ketogenic diets (KD) that rely on UPF specialty products is poorly understood. We aimed to assess the cost and nutrient profile of vegan and KD that relied primarily on UPF and compare this to those that relied primarily on whole foods.Design:We designed and calculated the cost of four 1-d meal plans for a hypothetical weight-stable adult female. Two meal plans were created for the vegan-style and ketogenic-style diets, respectively, with one of each being predominantly whole food based and the other constituting primarily of UPF. Carbohydrates were limited to ≤50 g, protein was set at 15–20 % and fat ≥75 % for the ketogenic meal plans. Carbohydrates were set between 45 and 65 %, protein 15 and 25 % and fat 20 and 35 % for the vegan meal plans. FoodWorks dietary analysis software was used to assess data against the national Australian/New Zealand nutrient reference value for adult females and cost was calculated using Countdown online shopping (a local New Zealand supermarket).Setting:New Zealand.Participants:None.Results:The whole food-based meal plans met a greater proportion of the macro and micronutrient thresholds and were less costly when compared with the specialty-based meal plans.Conclusions:This study demonstrates that well-planned, predominantly whole food diets (regardless of dietary trend) are nutritionally superior and more cost-effective than those that rely on UPF.
Pain in patients with motor neuron disease: Variation of pain and association with disease severity, health-related quality of life and depression – A longitudinal study
Authors: Spörndly-Nees Sören , Jakobsson Larsson Birgitta , Zetterberg Lena , Åkerblom Ylva , Nyholm Dag , Åsenlöf Pernilla 
Published: November 2023

AbstractObjectivesTo describe levels of pain over time during disease progression in individual patients and for a total sample of patients with motor neuron disease (MND), respectively, and to examine associations between pain, disease severity, health-related quality of life (HRQOL), and depression.MethodsA prospective cohort study was conducted on 68 patients with MND, including data collected on five occasions over a period of 2 years. Pain was assessed using the Brief Pain Inventory – Short Form. Depression was assessed using the Amyotrophic Lateral Sclerosis (ALS)-Depression-Inventory (ADI-12). Disability progression was measured using the Amyotrophic Lateral Sclerosis Functional Rating Scale – Revised Version (ALSFRS-R). HRQOL was assessed using the Amyotrophic Lateral Sclerosis Assessment Questionnaire (ALSAQ-5).ResultsParticipants reported great individual variation over time. The median level of pain was 4 (min 0 and max 10). Higher levels of pain during the last 24 h were associated with higher depression scores (ADI-12), poorer quality of life (ALSAQ-5), and lower reporting of fine and gross motor skills (ALSFRS-R). Baseline pain levels did not predict future values of depression and function. Individuals reporting average pain >3 experienced more hopelessness toward the future and reported higher depression scores compared with participants reporting average pain <3.Significance of resultsGreat within-individual variation of pain intensity was reported. Pain intensity was associated with depression, function and HRQOL cross-sectionally, but it did not have a strong prognostic value for future depression, function, or HRQOL. Patients with MND should be offered frequent assessment of pain and depressive symptoms in person-centered care, allowing for individualization of treatment.
A generative model to simulate spatiotemporal dynamics of biomolecules in cells
Authors: Balsollier Lisa , Lavancier Frédéric , Salamero Jean , Kervrann Charles 
Published: November 2023

Abstract
Generators of space-time dynamics in bioimaging have become essential to build ground truth datasets for image processing algorithm evaluation such as biomolecule detectors and trackers, as well as to generate training datasets for deep learning algorithms. In this contribution, we leverage a stochastic model, called birth-death-move (BDM) point process, in order to generate joint dynamics of biomolecules in cells. This particle-based stochastic simulation method is very flexible and can be seen as a generalization of well-established standard particle-based generators. In comparison, our approach allows us: (1) to model a system of particles in motion, possibly in interaction, that can each possibly switch from a motion regime (e.g., Brownian) to another (e.g., a directed motion); (2) to take into account finely the appearance over time of new trajectories and their disappearance, these events possibly depending on the cell regions but also on the current spatial configuration of all existing particles. This flexibility enables to generate more realistic dynamics than standard particle-based simulation procedures, by for example accounting for the colocalization phenomena often observed between intracellular vesicles. We explain how to specify all characteristics of a BDM model, with many practical examples that are relevant for bioimaging applications. As an illustration, based on real fluorescence microscopy datasets, we finally calibrate our model to mimic the joint dynamics of Langerin and Rab11 proteins near the plasma membrane, including the well-known colocalization occurrence between these two types of vesicles. We show that the resulting synthetic sequences exhibit comparable features as those observed in real microscopy image sequences.
VistoSeg: Processing utilities for high-resolution images for spatially resolved transcriptomics data
Authors: Tippani Madhavi , Divecha Heena R. , Catallini Joseph L. , Kwon Sang H. , Weber Lukas M. , Spangler Abby , Jaffe Andrew E. , Hyde Thomas M. , Kleinman Joel E. , Hicks Stephanie C. , Martinowich Keri , Collado-Torres Leonardo , Page Stephanie C. , Maynard Kristen R. 
Published: November 2023

Abstract
Spatially resolved transcriptomics (SRT) is a growing field that links gene expression to anatomical context. SRT approaches that use next-generation sequencing (NGS) combine RNA sequencing with histological or fluorescent imaging to generate spatial maps of gene expression in intact tissue sections. These technologies directly couple gene expression measurements with high-resolution histological or immunofluorescent images that contain rich morphological information about the tissue under study. While broad access to NGS-based spatial transcriptomic technology is now commercially available through the Visium platform from the vendor 10× Genomics, computational tools for extracting image-derived metrics for integration with gene expression data remain limited. We developed VistoSeg as a MATLAB pipeline to process, analyze and interactively visualize the high-resolution images generated in the Visium platform. VistoSeg outputs can be easily integrated with accompanying transcriptomic data to facilitate downstream analyses in common programing languages including R and Python. VistoSeg provides user-friendly tools for integrating image-derived metrics from histological and immunofluorescent images with spatially resolved gene expression data. Integration of this data enhances the ability to understand the transcriptional landscape within tissue architecture. VistoSeg is freely available at http://research.libd.org/VistoSeg/.
A spatial statistical framework for the parametric study of fiber networks: Application to fibronectin deposition by normal and activated fibroblasts
Authors: Grapa Anca-Ioana , Efthymiou Georgios , Van Obberghen-Schilling Ellen , Blanc-Féraud Laure , Descombes Xavier 
Published: November 2023

Abstract
Due to the complex architectural diversity of biological networks, there is an increasing need to complement statistical analyses with a qualitative and local description of their spatial properties. One such network is the extracellular matrix (ECM), a biological scaffold for which changes in its spatial organization significantly impact tissue functions in health and disease. Quantifying variations in the fibrillar architecture of major ECM proteins should considerably advance our understanding of the link between tissue structure and function. Inspired by the analysis of functional magnetic resonance imaging (fMRI) images, we propose a novel statistical analysis approach embedded into a machine learning paradigm, to measure and detect local variations of meaningful ECM parameters. We show that parametric maps representing fiber length and pore directionality can be analyzed within the proposed framework to differentiate among various tissue states. The parametric maps are derived from graph-based representations that reflect the network architecture of fibronectin (FN) fibers in a normal, or disease-mimicking in vitro setting. Such tools can potentially lead to a better characterization of dynamic matrix networks within fibrotic tumor microenvironments and contribute to the development of better imaging modalities for monitoring their remodeling and normalization following therapeutic intervention.
Physical and Chemical Stability of Nanoparticles in Ferrofluid Before and After Impregnation: Implications for Magnetic Pore Fabric Studies
Authors: Biedermann Andrea R. , Mazurek Martin , Schröder Johanna , Arenz Matthias 
Published: November 2023

AbstractMagnetic pore fabrics (MPFs) are a promising approach to explore the 3D pore space of rocks. There exist empirical relationships between the orientation, degree, and shape of MPF with pore space geometry and permeability anisotropy. Nevertheless, the precise nature of these relationships remains elusive. A common assumption in MPF studies is that ferrofluid uniformly fills the pore space, establishing a constant nanoparticle density and magnetic properties in space and time. However, this assumption is challenged by observations of particle sedimentation and time‐dependent magnetic properties, which render the quantitative interpretation of MPFs challenging. This study explores the physical and chemical stability of ferrofluid, mobility of particles after impregnation, and the magnetic properties of impregnated rocks over time. Water‐based ferrofluids are physically more stable than oil‐based ferrofluids, though with higher magnetic variability. In impregnated rock, magnetic nanoparticles display a certain degree of mobility, resulting in changes in MPF degree and shape. When ferrofluid is mixed with epoxy, particles are less mobile, though some changes were observed both during polymerization and aging. The susceptibility of ferrofluid‐epoxy mixtures is lower than for ferrofluid and carrier liquid at the same concentration. Interestingly, the susceptibility of impregnated rock increases over time, regardless of the ferrofluid used for the impregnation. Understanding and controlling these processes will enhance the reliability of MPF interpretations and increase the applicability of the method.
Mapping Plague Risk Using Super Species Distribution Models and Forecasts for Rodents in the Zhambyl Region, Kazakhstan
Authors: Rametov N. M. , Steiner M. , Bizhanova N. A. , Abdel Z. Zh. , Yessimseit D. T. , Abdeliyev B. Z. , Mussagalieva R. S. 
Published: November 2023

AbstractOne of the most extensive natural plague centers, or foci, is located in Central Asia, in particular, the Zhambyl region in Southern Kazakhstan. Here, we conducted plague surveillance from 2000 to 2020 in the Zhambyl region in Kazakhstan and confirmed 3,072 cases of infected wild animals. We used Species Distribution Modeling by employing MaxEnt, and identified that the natural plague foci are primarily located in the Moiynqum, Betpaqdala, and Tauqum Deserts. The Zhambyl region's central part, including the Moiynqum and Sarysu districts, has a high potential risk of plague outbreak for the rural towns and villages. Since the phenomenon of climate change has been identified as a determinant that affects the rodent populations, thereby elevating the likelihood of an outbreak of plague, we investigated the potential dissemination routes of the disease under the changing climate conditions, thus creating Species Distribution Forecasts for the rodent species in southern part of Kazakhstan for the year 2100. By 2100, in case of increasing temperatures, the range of host species is likely to expand, leading to a higher risk of plague outbreaks. The highest risk of disease transmission can be expected at the outer limits of the modeled total distribution range, where infection rates are high, but antibody presence is low, making many species susceptible to the pathogen. To mitigate the risk of a potential plague outbreak, it is necessary to implement appropriate sanitary‐epidemiological measures and climate mitigation policies.
Time‐Dependent Weakening of Granite at Hydrothermal Conditions
Authors: Jeppson T. N. , Lockner D. A. , Beeler N. M. , Moore D. E. 
Published: November 2023

AbstractThe evolution of a fault's frictional strength during the interseismic period is a critical component of the earthquake cycle, yet there have been relatively few studies that examine the time‐dependent evolution of strength at conditions representative of seismogenic depths. Using a simulated fault in Westerly granite, we examined how frictional strength evolves under hydrothermal conditions up to 250°C during slide‐hold‐slide experiments. At temperatures ≤100°C, frictional strength generally increases with hold duration but, at 200 and 250°C, an initial increase in strength transitions to rapid time‐dependent weakening for holds longer than 14 hr. Forward modeling of long hold periods at 250°C using the rate and state friction constitutive equations requires a second, strongly negative, state variable with a long evolution distance. This implies that significant hydrothermal alteration is occurring at 250°C, consistent with microstructural observations of dissolution and secondary mineral precipitation.
Omphacite Melting and the Destruction of Early High‐Pressure Rock Records
Authors: Liu Shuaiqi , Zhang Guibin , Zhang Lifei , Webb A. Alexander G. 
Published: November 2023

AbstractThe presence of eclogite marks high‐pressure metamorphism and deep, cold burial of crust, and is therefore a widely accepted indicator for the onset of modern‐style plate tectonics. However, eclogite is rarely preserved in many heavily granulite‐overprinted orogens, which are particularly common across ancient metamorphic terranes (i.e., Archean and Paleoproterozoic terranes). Here, we show that eclogite melting processes may be principally responsible for the poor preservation of high‐pressure records. We demonstrate eclogite melting via detailed petrological, geochronological, and geochemical analyses on eclogites and separated centimetric leucosomes from the central Himalaya. The central Himalayan eclogites were overprinted by strong granulite‐facies metamorphism, such that omphacite is only sparsely preserved. Thermodynamic modeling results indicate the eclogite experienced two types of anatectic reactions: phengite dehydration melting at high‐pressure in the presence of omphacite, and subsequent omphacite dominated melting during exhumation. Diagnostic features for these melting reactions include (a) the occurrence of Kfs‐Pl‐Qz multiphase solid inclusions and Cpx‐Pl‐Qz polymineralic inclusions; (b) the high Na2O/K2O melts and Na‐rich plagioclase in leucosomes; (c) the consistent trace elements patterns between omphacite and leucosomes; and (d) obvious Na2O zonation in clinopyroxene. Omphacite dominated melting is characterized by the jadeite breakdown, releasing Na and Al into the melts. This melting mechanism subsequently forms a less sodic clinopyroxene and high Na2O/K2O melts. These Himalayan findings appear relevant to early Earth explorations because of the high thermal gradients and intense granulite‐facies overprints, implying that partial melting of eclogite dominated by omphacite breakdown could have erased early high‐pressure records of modern‐style plate tectonics.