bluuebunny/crossref_metadata_2025_split huggingface dataset:
Using a DNA mini-barcode within the ITS region to identify toxic Amanita in mushroom poisoning cases
Authors: Xing Ran-Ran , Bai Wen-Ming , Hu Di , Deng Ting-Ting , Zhang Jiu-Kai , Chen Ying 
Published: June 2024

Abstract
Mushroom poisoning contributes significantly to global foodborne diseases and related fatalities. Amanita mushrooms frequently cause such poisonings; however, identifying these toxic species is challenging due to the unavailability of fresh and intact samples. It is often necessary to analyze residues, vomitus, or stomach extracts to obtain DNA sequences for the identification of species responsible for causing food poisoning. This usually proves challenging to obtain usable DNA sequences that can be analyzed using conventional molecular biology techniques. Therefore, this study aimed to develop a DNA mini-barcoding method for the identification of Amanita species. Following the evaluation and optimization of universal primers for DNA mini-barcoding in Amanita mushrooms, we found that the internal transcribed spacer (ITS) gene sequence primer ITS-a was the most suitable DNA barcode primer for identifying Amanita species. Forty-three Amanita samples were subsequently amplified and sequenced. The sequences obtained were analyzed for intra- and inter-species genetic distances, and a phylogenetic tree was constructed. The findings indicated that the designed primers had strong universality among the Amanita samples and could accurately identify the target gene fragment with a length of 290 bp. Notably, the DNA mini-barcode accurately identified the 43 Amanita samples, demonstrating high consistency with the conventional DNA barcode. Furthermore, it effectively identified DNA from digested samples. In summary, this DNA mini-barcode is a promising tool for detecting accidental ingestion of toxic Amanita mushrooms. It may be used as an optimal barcode for species identification and traceability in events of Amanita-induced mushroom poisoning.

Key points
• Development of a DNA mini-barcoding method for Amanita species identification without fresh samples.
• The ITS-a primer set was optimized for robust universality in Amanita samples.
• The mini-barcode is suitable for screening toxic mushroom species in mushroom poisoning cases.

Graphical Abstract
Connectivity based on glucose dynamics reveals exaggerated sensorimotor network coupling on subject-level in Parkinson’s disease
Authors: Ruppert-Junck Marina C. , Heinecke Vanessa , Librizzi Damiano , Steidel Kenan , Beckersjürgen Maya , Verburg Frederik A. , Schurrat Tino , Luster Markus , Müller Hans-Helge , Timmermann Lars , Eggers Carsten , Pedrosa David 
Published: June 2024

Abstract
Purpose
While fMRI provides information on the temporal changes in blood oxygenation, 2- [18F]fluoro-2-deoxy-D-glucose ([18F]FDG)-PET has traditionally offered a static snapshot of brain glucose consumption. As a result, studies investigating metabolic brain networks as potential biomarkers for neurodegeneration have primarily been conducted at the group level. However, recent pioneering studies introduced time-resolved [18F]FDG-PET with constant infusion, which enables metabolic connectivity studies at the individual level.

Methods
In the current study, this technique was employed to explore Parkinson’s disease (PD)-related alterations in individual metabolic connectivity, in comparison to inter-subject measures and hemodynamic connectivity. Fifteen PD patients and 14 healthy controls with comparable cognition underwent sequential resting-state dynamic PET with constant infusion and functional MRI. Intrinsic networks were identified by independent component analysis and interregional connectivity calculated for summed static PET images, PET time series and functional MRI.

Results
Our findings revealed an intrinsic sensorimotor network in PD patients that has not been previously observed to this extent. In PD, a significantly higher number of connections in cortical motor areas was observed compared to elderly control subjects, as indicated by both static PET and functional MRI (pBonferroni−Holm = 0.027), as well as constant infusion PET and functional MRI connectomes (pBonferroni−Holm = 0.012). This intensified coupling was associated with disease severity (ρ = 0.56, p = 0.036).

Conclusion
Metabolic connectivity, as revealed by both static and dynamic PET, provides unique information on metabolic network activity. Subject-level metabolic connectivity based on constant infusion PET may serve as a potential marker for the metabolic network signature in neurodegeneration.
Population and clonal structure of Acropora cf. hyacinthus to inform coral restoration practices on the Great Barrier Reef
Authors: Howlett Lorna , Camp Emma F. , Locatelli Nicolas S. , Baums Iliana B. , Strudwick Paige , Rassmussen Sage , Suggett David J. 
Published: June 2024

AbstractA key goal of coral restoration is to re-establish self-sustaining coral populations and ensure resilience to future stressors, which requires that genetic diversity is maximised. However, coral genetic and genotypic (clonal) diversity is variable across reef sites via success of sexual recruitment, and cryptic species diversity can complicate breeding efforts. Assessing genotypic and genetic diversity of colonies to be used in restoration is therefore critical to avoid founder, inbreeding or outbreeding effects. Considering recent efforts to upscale coral propagation on the Great Barrier Reef (GBR), we examined species, population and clonal structure of a commonly out-planted tabular Acropora species—Acropora hyacinthus (Dana, 1864). A total of 189 colonies were sampled from six reef systems throughout the northern-central GBR and genotyped using an Acropora-specific Affymetrix microarray, which resulted in 1387 variant sites that passed quality control. Cryptic species were readily resolved and all sampled A. hyacinthus colonies represented unique genotypes within sites at three reefs. At reefs that contained multi-ramet genets (clonal genotypes), the mean and maximum between-ramet distances were 0.68 and 1.99 m, respectively. Therefore, sampling colonies > 2 m apart increases the likelihood these colonies represent distinct genets. Such a sampling design therefore maximises genotypic diversity when sourcing colonies for propagation and out-planting. Based on these variant sites, we found no between-reef genetic divergence based on locality. Furthermore, through unintentional sampling of non-target tabular Acroporid species, we show how this genotyping method may be used for resolving taxonomic uncertainty as well as population dynamics.
Visual analysis of fitness landscapes in architectural design optimization
Authors: Abdelaal Moataz , Galuschka Marcel , Zorn Max , Kannenberg Fabian , Menges Achim , Wortmann Thomas , Weiskopf Daniel , Kurzhals Kuno 
Published: June 2024

AbstractIn architectural design optimization, fitness landscapes are used to visualize design space parameters in relation to one or more objective functions for which they are being optimized. In our design study with domain experts, we developed a visual analytics framework for exploring and analyzing fitness landscapes spanning data, projection, and visualization layers. Within the data layer, we employ two surrogate models and three sampling strategies to efficiently generate a wide array of landscapes. On the projection layer, we use star coordinates and UMAP as two alternative methods for obtaining a 2D embedding of the design space. Our interactive user interface can visualize fitness landscapes as a continuous density map or a discrete glyph-based map. We investigate the influence of surrogate models and sampling strategies on the resulting fitness landscapes in a parameter study. Additionally, we present findings from a user study (N= 12), revealing how experts’ preferences regarding projection methods and visual representations may be influenced by their level of expertise, characteristics of the techniques, and the specific task at hand. Furthermore, we demonstrate the usability and usefulness of our framework by a case study from the architecture domain, involving one domain expert.
New online dynamic nomograms to predict recurrence-free and overall survival after resection of endometrial cancer: a single-institution retrospective cohort study
Authors: Hu Zhen , Li Junying , Du Junqiang 
Published: June 2024

Abstract
Purpose
The significant global burden of endometrial cancer (EC) and the challenges associated with predicting EC recurrence indicate the need for a dynamic prediction model. This study aimed to propose nomograms based on clinicopathological variables to predict recurrence-free survival (RFS) and overall survival (OS) after surgical resection for EC.

Methods
This single-institution retrospective cohort study included patients who underwent surgical resection for EC. Web-based nomograms were developed to predict RFS and OS following resection for EC, and their discriminative and calibration abilities were assessed.

Results
This study included 289 patients (median age, 56 years). At a median follow-up of 51.1 (range, 4.1–128.3) months, 13.5% (39/289) of patients showed relapse or died, and 10.7% (31/289) had non-endometrioid tumors (median size: 2.8 cm). Positive peritoneal cytology result (hazard ratio [HR], 35.06; 95% confidence interval [CI], 1.12–1095.64; P = 0.0428), age-adjusted Charlson comorbidity index (AACCI) (HR, 52.08; 95% CI, 12.35–219.61; P < 0.001), and FIGO (Federation of Gynecology and Obstetrics) stage IV (HR, 138.33; 95% CI, 17.38–1101.05; P < 0.001) were predictors of RFS. Similarly, depth of myometrial invasion ≥ 1/2 (HR, 1; 95% CI, 0.46–2.19; P = 0.995), AACCI (HR, 93.63; 95% CI, 14.87–589.44; P < 0.001), and FIGO stage IV (HR, 608.26; 95% CI, 73.41–5039.66; P < 0.001) were predictors of OS. The nomograms showed good predictive capability, positive discriminative ability, and calibration (RFS: 0.895 and OS: 0.891).

Conclusion
The nomograms performed well in internal validation when patients were stratified into prognostic groups, offering a personalized approach for risk stratification and treatment decision-making.
Variations in orientation relationships between rutile inclusions and garnet host relate to magmatic growth zoning
Authors: Kohn Victoria , Griffiths Thomas A. , Alifirova Taisia , Daneu Nina , Ageeva Olga , Abart Rainer , Habler Gerlinde 
Published: June 2024

AbstractRutile inclusions in almandine-spessartine garnet from a peraluminous pegmatoid from the Moldanubian zone (Bohemian Massif, AT) show distinct changes in aspect ratio, shape preferred orientations (SPO) and crystallographic orientation relationships (COR) along the transition between microstructurally different growth zones in the garnet core and rim. For identification of the COR characteristics we pool specific CORs based on their common axial relationship into three COR groups: Group 103R/111G, Group 001R/111G and Group 001R/100G. The rutile inclusions in the garnet core domains are elongated along the four Grt$$\langle$$
⟨
111$$\rangle$$
⟩
directions and are dominated by COR Group 103R/111G. The garnet rim zone additionally contains rutile needles elongated along Grt$$\langle$$
⟨
100$$\rangle$$
⟩
. Here, Group 001R/111G and 001R/100G are more abundant than in the garnet core. Needle-shaped rutile in the rim shows a systematic correlation between SPOs and CORs as needles elongated parallel to Grt$$\langle$$
⟨
111$$\rangle$$
⟩
are dominated by Group 103R/111G and 001R/111G, whereas those needles elongated parallel to Grt$$\langle$$
⟨
100$$\rangle$$
⟩
exclusively pertain to CORs of 001R/100G. Furthermore, the frequency of each particular SPO in the garnet rim clearly depends on the local growth direction of the particular Grt{112} sector. Facet-specific variations in rutile SPO frequencies in different sectors and growth zones of garnet were observed even between equivalent directions, indicating that the microstructures and textures of rutile inclusions reflect varying parameters of garnet growth. The characteristic differences in COR groups of different garnet growth zones are referred to compositional changes in the bulk melt or compositional boundary layer, associated with magmatic fractional crystallisation.
On the origin of alkali feldspar megacrysts in granitoids. Part 2: evidence for nucleation and growth under magmatic conditions from crystal size distributions of the Cathedral Peak Granodiorite, California, USA
Authors: Seitz Susanne , Gualda Guilherme A. R. , Harmon Lydia J. 
Published: June 2024

AbstractThe mechanisms whereby alkali feldspar megacrysts form have been debated for several decades; yet, we do not understand well the processes that lead to their formation. We take advantage of glacially polished outcrop surfaces from the Cathedral Peak Granodiorite in the Tuolumne Intrusive Complex, CA to quantitatively characterize alkali feldspar textures, to provide better insight into their origin. On the glacially polished surfaces, we traced alkali feldspar crystals > 10 mm in the field. From the same localities, we also collected large slabs and stained them to reveal feldspar textures for crystals < 20 mm in size. We scaned the resulting field tracings and rock slabs to quantify CSDs using image processing techniques with the software ImageJ. The CSDs from glacially polished outcrop surfaces and complementary polished and stained rock slabs reveal two stages of crystallization. Crystals > 20 mm show log-linear CSDs with shallow slopes, suggesting magmatic nucleation and growth on timescales of thousands of years. Crystals < 20 mm define a second stage of crystallization, with much steeper slopes, suggesting a period of enhanced nucleation leading to formation of a groundmass during the final stages of solidification on timescales of decades to centuries. We do not find any evidence for CSDs affected by textural coarsening, or any effects of subsolidus processes. Our data suggest that these megacrysts form in large, slowly cooling magma, where low nucleation rates dominate. These crystals are not special in their magmatic formation—only in their size. A change in solidification conditions led to the formation of a groundmass, which warrants further study to better understand this crystallization stage in a plutonic environment.
COVID-19 and silent hypoxemia in a minimal closed-loop model of the respiratory rhythm generator
Authors: Diekman Casey O. , Thomas Peter J. , Wilson Christopher G. 
Published: June 2024

AbstractSilent hypoxemia, or “happy hypoxia,” is a puzzling phenomenon in which patients who have contracted COVID-19 exhibit very low oxygen saturation ($$\text {SaO}_2$$

SaO
2

< 80%) but do not experience discomfort in breathing. The mechanism by which this blunted response to hypoxia occurs is unknown. We have previously shown that a computational model of the respiratory neural network (Diekman et al. in J Neurophysiol 118(4):2194–2215, 2017) can be used to test hypotheses focused on changes in chemosensory inputs to the central pattern generator (CPG). We hypothesize that altered chemosensory function at the level of the carotid bodies and/or the nucleus tractus solitarii are responsible for the blunted response to hypoxia. Here, we use our model to explore this hypothesis by altering the properties of the gain function representing oxygen sensing inputs to the CPG. We then vary other parameters in the model and show that oxygen carrying capacity is the most salient factor for producing silent hypoxemia. We call for clinicians to measure hematocrit as a clinical index of altered physiology in response to COVID-19 infection.
Hepatic infarction occurred after 125I particle stent treatment for hepatocellular carcinoma with portal vein tumor thrombus: A case report
Authors: Yang Jiemin , Qin Yang , Lv Zhongyuan , Xiao Qingqing , Miao Ying , Huang Huiping , Wei Bing , Mao Jingsong 
Published: June 2024

Abstract
Background
Hepatic infarction is a rare liver condition. The purpose of this study is to report a case of hepatic infarction caused by thrombus formation following portal vein stent implantation in a patient with hepatocellular carcinoma and portal vein tumor thrombus, and to explore the underlying causes.

Case report
The patient in this study was a 52-year-old male admitted with diffuse hepatocellular carcinoma involving the right lobe and portal vein tumor thrombus. After undergoing portal vein stent implantation and 125I particle strand implantation treatment, the portal vein was patent, and the pressure decreased. However, multiple instances of hepatic artery chemoembolization combined with targeted immunotherapy resulted in gradual reduction in the diameter of the hepatic artery and affecting hepatic arterial blood flow. Two months post-stent implantation, thrombus formation within the stent was noted, and the patient’s condition did not improve with anticoagulant therapy, as evidenced by follow-up CT scans showing an increase in thrombi. Six months later, the patient suffered from gastrointestinal bleeding and, despite emergency esophagogastric variceal ligation and hemostatic treatment, developed hepatic parenchymal infarction and liver function failure.

Conclusions
We reveal the underlying cause is that (1) thrombus formation within the portal vein stent, leading to portal vein embolism and obstructed blood flow due to exacerbate portal hypertension after various treatments; and (2) the effect of hepatic artery chemoembolization, immunotherapy, and targeted therapy on tumor angiogenesis, causing reduced hepatic artery diameter and impaired arterial blood flow. These factors disrupt the liver’s dual blood supply system, ultimately contributing to hepatic infarction. To our knowledge, this is the first report of hepatic infarction as a complication following portal vein stent implantation for hepatocellular carcinoma with portal vein tumor thrombus, and it holds significant reference value for guiding the treatment of hepatocellular carcinoma with concurrent portal vein tumor thrombus in a clinical setting.
Did steam boost the height and growth rate of the giant Hunga eruption plume?
Authors: Mastin Larry G. , Van Eaton Alexa R. , Cronin Shane J. 
Published: June 2024

AbstractThe eruption of Hunga volcano on 15 January 2022 produced a higher plume and faster-growing umbrella cloud than has ever been previously recorded. The plume height exceeded 58 km, and the umbrella grew to 450 km in diameter within 50 min. Assuming an umbrella thickness of 10 km, this growth rate implied an average volume injection rate into the umbrella of 330–500 km3 s−1. Conventional relationships between plume height, umbrella-growth rate, and mass eruption rate suggest that this period of activity should have injected a few to several cubic kilometers of rock particles (tephra) into the plume. Yet tephra fall deposits on neighboring islands are only a few centimeters thick and can be reproduced using ash transport simulations with only 0.1–0.2 km3 erupted volume (dense-rock equivalent). How could such a powerful eruption contain so little tephra? Here, we propose that seawater mixing at the vent boosted the plume height and umbrella growth rate. Using the one-dimensional (1-D) steady plume model Plumeria, we find that a plume fed by ~90% water vapor at a temperature of 100 °C (referred to here as steam) could have exceeded 50 km height while keeping the injection rate of solids low enough to be consistent with Hunga’s modest tephra-fall deposit volume. Steam is envisaged to rise from intense phreatomagmatic jets or pyroclastic density currents entering the ocean. Overall, the height and expansion rate of Hunga’s giant plume is consistent with the total mass of fall deposits plus underwater density current deposits, even though most of the erupted mass decoupled from the high plume. This example represents a class of high (> 10 km), ash-poor, steam-driven plumes, that also includes Kīlauea (2020) and Fukutoku-oka-no-ba (2021). Their height is driven by heat flux following well-established relations; however, most of the heat is contained in steam rather than particles. As a result, the heights of these water-rich plumes do not follow well-known relations with the mass eruption rate of tephra.
Performant almost-latch-free data structures using epoch protection in more depth
Authors: Li Tianyu , Chandramouli Badrish , Madden Samuel 
Published: June 2024

AbstractMulti-core scalability presents a major implementation challenge for data system designers today. Traditional methods such as latching no longer scale in today’s highly parallel architectures. While the designer can make use of techniques such as latch-free programming to painstakingly design specialized, highly-performant solutions, such solutions are often intricate to build and difficult to reason about. Of particular interest to data system designers is a class of data structures we call almost-latch-free; such data structures can be made scalable in the common case, but have rare complications (e.g., dynamic resizing) that prevent full latch-free implementations. In this work, we present a new programming framework called Epoch-Protected Version Scheme (EPVS) to make it easy to build such data structures. EPVS makes use of epoch protection to preserve performance in the common case of latch-free operations, while allowing users to specify critical sections that execute under mutual exclusion for the rare, non-latch-free operations. We showcase the use of EPVS-based concurrency primitives in a few practical systems to demonstrate its competitive performance and intuitive guarantees. EPVS is available in open source as part of Microsoft’s FASTER project (Epoch Protected Version Scheme (source code) 2022; Microsoft FASTER 2022).
High-energy emulsification of Allium sativum essential oil boosts insecticidal activity against Planococcus citri with no risk to honeybees
Authors: Modafferi Antonino , Giunti Giulia , Urbaneja Alberto , Laudani Francesca , Latella Ilaria , Pérez-Hedo Meritxell , Ricupero Michele , Palmeri Vincenzo , Campolo Orlando 
Published: June 2024

AbstractThe ecotoxicological consequences of synthetic pesticides have encouraged stakeholders to search for eco-friendly pest control tools, like essential oils (EOs). Nano-delivery systems (nanoparticles and nano-emulsions) seem ideal for developing EO-based biopesticides, although production processes should be standardized and implemented. In this study, nano-emulsions loaded with a high amount of Allium sativum L. EO (15%) were developed using different mixed bottom-up/top-down processes. Garlic EO was chemically analyzed by gas chromatography-mass spectrometry (GC-MS) and formulations were physically characterized using Dynamic Light Scattering (DLS) apparatus. The insecticidal activity against Planococcus citri Risso (Hemiptera: Pseudococcidae) and selectivity toward Apis mellifera L. (Hymenoptera: Apidae) worker bees was evaluated. Garlic EO was mainly composed of sulphur components (96.3%), with diallyl disulphide and diallyl trisulphide as the most abundant compounds (37.26% and 28.15%, respectively). Top-down processes could produce stable nano-emulsions with droplet size in the nanometric range (< 200nm) and good polydispersity index (PDI < 0.2). In contrast, the bottom-up emulsion was unstable, and its droplet size was around 500nm after 24 hours. High-energy emulsification processes significantly increased the residual toxicity of garlic EO against 3rd instar P. citri nymphs, whereas the developed formulations were harmless to A. mellifera workers in topical application. This study confirmed that the production process significantly affected the physical properties and efficacy against target pests. The lack of adverse impact on honeybees denotated the potential of these formulations as bioinsecticides in organic and/or IPM programs, although further extended ecotoxicological studies are necessary.