julilili42/papers huggingface dataset:
Biofunctionalization of ADA‐GEL Hydrogels Based on the Degree of Cross‐Linking and Polymer Concentration Improves Angiogenesis
2025-03-17

Abstract The creation of bioartificial tissues is a promising option for the reconstruction of large‐volume defects. The vascularization of tissue engineering constructs, as well as the material properties of the carrier matrix, are important factors for successful clinical application. In this regard, hydrogels are promising biomaterials, providing an extracellular matrix‐like milieu that enables the possibility of cell transplantation and de novo tissue formation. Furthermore, biofunctionalization allows for a certain fine‐tuning of angiogenic properties. This study aims to investigate vascularization and tissue formation of highly cross‐linked alginate dialdehyde (ADA) and gelatin (GEL). This highly cross‐linked network is created using a dural cross‐linking mechanism combining ionic (Ca 2+ ions) and enzymatic (human transglutaminase (hTG)) cross‐linking, resulting in reduced swelling and moderate degradation rates. Vascularization of the ADA‐GEL‐hTG constructs is induced surgically using arteriovenous (AV) loops. Biocompatibility, tissue formation, and vascularization are analyzed by histology and X‐ray microscopy. After only 2 weeks, vascularization of the ADA‐GEL‐hTG constructs is already present. After 4 weeks, both de novo tissue formation and vascularization of the ADA‐GEL‐hTG matrix increase. In conclusion, ADA‐GEL‐hTG‐based hydrogels are shown to be promising scaffold materials for tissue engineering applications.
Evaluation of Thiobacillus denitrificans’ sustainability in nitrate-reducing Fe(II) oxidation and the potential significance of Fe(II) as a growth-supporting reductant
2025-03-17

Abstract The betaproteobacterium Thiobacillus denitrificans (ATCC 25259) oxidizes Fe(II) while reducing nitrate, yet its capacity for autotrophic growth as a nitrate-reducing Fe(II)-oxidizer remains uncertain. This study explored this capacity through cultivation experiments across multiple transfers, using growth medium with Fe(II) and nitrate as sole electron donor and acceptor, respectively. This setup necessitated nitrate reduction coupled to Fe(II) oxidation as the primary energy-yielding mechanism and Fe(II) as the exclusive electron donor for CO2 fixation and biomass production. Thiosulfate/nitrate pregrown T. denitrificans oxidized 42% of 10 mM Fe(II), reduced 54% of 3.5 mM nitrate, and accumulated 1.6 mM nitrite, but showed no cell growth. Subsequent transfers from this Fe(II)/nitrate culture to fresh medium with Fe(II) and nitrate showed no nitrate-reducing Fe(II) oxidation or population growth. While bacterial activity [Fe(II) oxidation, nitrate reduction] occurred in the first transfer from thiosulfate/nitrate to Fe(II)/nitrate, nitrite was produced, further reacting with Fe(II) abiotically (chemodenitrification). A kinetic model assessed enzymatic versus abiotic Fe(II) oxidation, revealing enzymatic oxidation accounted for twice as much (ca. 70%) as abiotic denitrification (ca. 30%) within 22 days. These findings suggest T. denitrificans performs the first step of denitrification with Fe(II) as an electron donor but does not achieve autotrophic growth under these conditions.
Fractionation of nanosecond pulsed electric fields lowers lethal dose by enhancing cardiomyocyte membrane permeability
2025-03-17

Fractionated nsPEF improves cardiac ablation efficiency by enhancing membrane permeability and cell-killing effect. These findings suggest that fractionated delivery could optimize nsPEF therapies, offering a more effective approach for cardiac ablation.
Balancing the role of the ventral posterior thalamus in pain and temperature
2025-03-17

Funding Agencies|Shanghai Municipal Science and Technology Major Project [2019SHZDZX02]; National Natural Science Foundation of China Mianshang Project [32271049]; Fonds Wetenschappelijk Onderzoek-Vlaanderen (FWO-Flanders) [G0E0520N]; Max Planck Society
Quantifying spatial uncertainty to improve soil predictions in data-sparse regions
2025-03-17

Abstract. Artificial Neural Networks (ANNs) are valuable tools for predicting soil properties using large datasets. However, a common challenge in soil sciences is the uneven distribution of soil samples, which often results from past sampling projects that heavily sample certain areas while leaving similar yet geographically distant regions under-sampled. One potential solution to this problem is to transfer an already trained model to other similar regions. Robust spatial uncertainty quantification is crucial for this purpose, yet often overlooked in current research. We address this issue by using a Bayesian deep learning technique, Laplace Approximations, to quantify spatial uncertainty. This produces a probability measure encoding where the model’s prediction is deemed reliable, and where a lack of data should lead to a high uncertainty. We train such an ANN on a soil landscape dataset from a specific region in southern Germany and then transfer the trained model to another unseen but to some extend similar region, without any further model training. The model effectively generalized alluvial patterns, demonstrating its ability to recognize repetitive features of river systems. However, the model showed a tendency to favor overrepresented soil units, underscoring the importance of balancing training datasets to reduce overconfidence in dominant classes. Quantifying uncertainty in this way allows stakeholders to better identify regions and settings in need of further data collection, enhancing decision-making and prioritizing efforts in data collection. Our approach is computationally lightweight and can be added post-hoc to existing deep learning solutions for soil prediction, thus offering a practical tool to improve soil property predictions in under-sampled areas, as well as optimizing future sampling strategies, ensuring resources are allocated efficiently for maximum data coverage and accuracy.
Facing the taxonomic impediment — a reassessment of Merulanella Verhoeff, 1926 (Oniscidea, Armadillidae) through historical specimens
2025-03-18

The taxonomic impediment has been identified as a problem for conservation biology since 1988. Although several measures have been developed to overcome it, major non-specialized scientific publishers have not fully addressed it. One of the more challenging solutions relies on the identification of taxonomic needs and priorities hampered by the scarcity and inaccessibility of resources. Currently, publishers often consider taxonomy on its own not worth publishing unless supplementary to additional work, such as genetic analyses, pushing publication to a restricted space in specialized journals. A revision of the terrestrial isopod genus Merulanella , through the literature and historical specimens, shows that taxonomies outlined before the development of certain key concepts in evolutionary biology need to be urgently revisited before new studies are done on them. Furthermore, some species in this genus are considered endangered due to the pet trade, albeit they are not included on the IUCN Red List. The taxonomy of the genus Merulanella was developed before and during the development of zoogeography and before the modern concept of vicariance, explaining the wide distribution of this genus with seven species spanning over three biogeographic realms: M. carinata , M. wahrbergi , M. dollfusi (Australasia), M. bicolorata , M. gibbera , M. lattissima (Indomalay), and M. peltata (Afrotropics). After revising the literature, the context of the produced taxonomy, and assessing the type material, first-hand and through photographs, the morphological dissimilarity justifies restricting Merulanella to the species from New Caledonia (Australasian realm), namely M. carinata , M. wahrbergi , and M. dollfusi . A new genus is proposed for the species from Flores, Indonesia, erecting Floresiodillo gibberum gen. et comb. nov. , and F. latissimus gen. et. comb. nov. , a new genus is erected for the species in Myanmar, Ardentiella bicolarata , gen. et comb. nov. and A. caerulea gen. et comb. nov. (both in the Indomalayan realm), and a new genus is erected for the species in Seychelles, Acutodillo peltatus gen. et comb. nov. (Afrotropical realm). Further studies will be needed to determine the phylogenetic relationships between these new genera and the history of their distribution. Still, this new framework better captures the diversity of the family Armadillidae for its conservation.
Decreased dihydroartemisinin-piperaquine protection against recurrent malaria associated with Plasmodium falciparum plasmepsin 3 copy number variation in Africa
2025-03-18

Abstract Dihydroartemisinin-piperaquine (DHA-PPQ) is being recommended in Africa for the management of uncomplicated Plasmodium falciparum malaria and for chemoprevention strategies, based on the ability of piperaquine to delay re-infections. Although therapeutic resistance to piperaquine has been linked to increased copy number in plasmepsin-coding parasite genes ( pfpm ), their effect on the duration of the post-treatment prophylactic period remains unclear. Here, we retrospectively analyzed data from a randomized clinical trial, where patients received either DHA-PPQ or artesunate-amodiaquine for recurrent malaria episodes over two years. We observed an increase in the relative risk of re-infection among patients receiving DHA-PPQ compared to artesunate-amodiaquine after the first malaria season. This was driven by shorter average times to reinfection and coincided with an increased frequency of infections comprising pfpm3 multi-copy parasites. The decline in post-treatment protection of DHA-PPQ upon repeated use in a high transmission setting raises concerns for its wider use for chemopreventive strategies in Africa.
Deep learning reconstruction for accelerated 3-D magnetic resonance cholangiopancreatography
2025-03-18

Abstract Purpose This study aimed to compare a conventional three-dimensional (3-D) magnetic resonance cholangiopancreatography (MRCP) sequence with a deep learning (DL)-accelerated MRCP sequence (hereafter, MRCP DL ) regarding acquisition time and image quality. Materials and methods We conducted a prospective study of consecutive patients referred for MRCP between November 2023 and April 2024 at a single tertiary center. Each participant underwent 1.5T 3-D T2-weighted turbo spin echo MRCP using both a conventional sequence (threefold acceleration) and MRCP DL (eightfold acceleration). Three blinded readers independently evaluated image quality, including background signal suppression, bile and pancreatic duct visibility, artifact level, and diagnostic confidence on an ordinal four-point scale. Acquisition times were compared using a paired t-test. Image quality parameters were assessed with repeated measures ANOVA. Interreader agreement was analyzed using Fleiss' κ. Results Out of 419 consecutive patients, 30 participants were evaluated (mean age, 63 ± 15 years; 16 men, 14 women). The mean acquisition time was 10:30 ± 03:04 min for conventional MRCP and 3:57 ± 01:13 min for MRCP DL , P &lt; 0.001. MRCP DL reduced acquisition time by 62.4%. Artifact levels were rated at 3.17 ± 0.77 for conventional MRCP and 3.56 ± 0.66 for MRCP DL ( P = 0.041). Background signal suppression, bile duct visibility, pancreatic duct visibility, and diagnostic confidence did not differ significantly ( P &gt; 0.05). Interreader agreement was substantial to almost perfect (κ: 0.64–87). Conclusions Deep learning-accelerated 3-D MRCP reduced acquisition time by 62%, minimized artifacts, and preserved bile and pancreatic duct visibility, supporting its adoption in routine clinical practice.
Cryptic iron cycling influenced by organic carbon availability in a seasonally stratified lake
2025-03-18

Abstract Iron cycling including phototrophic Fe(II) oxidation has been observed in multiple permanently stratified meromictic lakes, yet less focus has been on dimictic lakes, which seasonally overturn and are vastly more common. Here, we investigated iron cycling in a dimictic lake, Großes Heiliges Meer in northwest Germany, using 16S rRNA amplicon sequencing, as well as in-situ and lab-based experiments. Bacterial community composition in the lake follows geochemical gradients and differs markedly between oxic and anoxic conditions. Potential iron-metabolizing bacteria were found mostly in anoxic conditions at 7 and 8 m depth and were comprised of taxa from the genera Chlorobium, Thiodictyon, Sideroxydans, Geobacter, and Rhodoferrax. We were able to recreate active iron cycling (1) with an ex-situ microbial community from 8 m depth and (2) with a successful microbial enrichment culture from 7 m depth. Varying the light and organic carbon availability in lab-based experiments showed that Fe(III) reduction overshadows Fe(II) oxidation leading to a cryptic iron cycle. Overall, we could demonstrate that microbial iron cycling can be a key biogeochemical process in dimictic lakes despite regular disturbance, and that complex environmental factors such as organic substrates control the balance between Fe(II) oxidation and Fe(III) reduction.
First insights into the safety and effectiveness of additional courses with cladribine tablets under real-world conditions
2025-03-18

Administering additional cladribine courses is an effective option to maintain disease control and did not trigger any serious adverse events attributable to the therapy. Patients with elevated serum transaminase levels should be regularly monitored.
The human microbiome-derived antimicrobial lugdunin self-regulates its biosynthesis by a feed-forward mechanism
2025-03-18

ABSTRACT Many human microbiome members inhibit bacterial competitors by production of antimicrobial compounds whose expression needs to be tightly controlled to balance the costs and benefits of compound biosynthesis. The nasal commensal Staphylococcus lugdunensis outcompetes Staphylococcus aureus using the antimicrobial lugdunin. The lugdunin biosynthetic gene cluster (BGC) encodes two potential regulators whose roles have remained unknown. Deletion of the regulator genes lugR or lugJ led to increased lugdunin production and/or immunity. While LugR was found to repress the transcription of the biosynthetic lugRABCTDZ operon, LugJ repressed the lugIEFGH export and immunity genes. Both regulators bound to different inverted repeats in the controlled promoter regions. Notably, both repressors were released from cognate promoters to allow transcription upon addition of exogenous lugdunin. Even minor structural changes disabled lugdunin derivatives to induce expression of its BGC, which is consistent with inferior binding to the predicted LugR and LugJ binding pockets. Thus, lugdunin controls its own biosynthesis through a feed-forward mechanism probably to avoid futile production. IMPORTANCE Biosynthetic gene clusters (BGCs) are usually tightly controlled to avoid production of costly goods at inappropriate time points or unfavorable conditions. However, in most cases, the regulatory signals of these clusters have remained unknown. Frequently, quorum sensing or two-component regulatory systems are involved in BGC expression control. This study elucidates the sophisticated regulation of lugdunin biosynthesis and secretion via two independent regulators, LugR and LugJ. Although belonging to different families of repressors, both directly interact with the antimicrobial lugdunin and thereby enhance biosynthesis and secretion in a feed forward-like mechanism.
About the Meaning of Φάντασμα in Aristotle
2025-03-18

Abstract I argue that Aristotle’s concept of φάντασμα should neither be equated with the notion of “mental image” nor understood as referring primarily to physiological processes. What Aristotle means by φάντασμα should be understood in the light of a pre-philosophical linguistic background in which the term refers to apparitions of objects that are suspected of not being real, such as ghosts. A φάντασμα in Aristotle is a content of which one is aware by a process that, although quasi-perceptual in nature, is known by the subject or by a third party to differ from perception.
Angular integrals with three denominators via IBP, mass reduction, dimensional shift, and differential equations
2025-03-19

A bstract Angular integrals arise in a wide range of perturbative quantum field theory calculations. In this work we investigate angular integrals with three denominators in d = 4 – 2 ε dimensions. We derive integration-by-parts relations for this class of integrals, leading to explicit recursion relations and a reduction to a small set of master integrals. Using a differential equation approach we establish results up to order ε for general integer exponents and masses. Here, reduction identities for the number of masses, known results for two-denominator integrals, and a general dimensional-shift identity for angular integrals considerably reduce the required amount of work. For the first time we find for angular integrals a term contributing proportional to a Euclidean Gram determinant in the ε -expansion. This coefficient is expressed as a sum of Clausen functions with intriguing connections to Euclidean, spherical, and hyperbolic geometry. The results of this manuscript are applicable to phase-space calculations with multiple observed final-state particles.
Bovine Meat and Milk Factor (BMMF) Protein Is Expressed in Macrophages Spread Widely over the Mucosa of Colorectal Cancer Patients
2025-03-19

Red meat consumption is considered a risk factor for colorectal cancer (CRC) development and stimulated isolation of plasmid-like DNA molecules from bovine serum and milk, termed bovine meat and milk factors (BMMFs). BMMFs encode a conserved replication protein (Rep). Increased populations of Rep-expressing macrophages have been identified in the peritumor of CRC patients and pre-cancerous tissues when compared to the tissues of healthy individuals. This supports the concept that BMMFs increase cancer risk by indirect carcinogenesis, upon induction of chronic inflammation. However, the spread of Rep+ immune cells in tissues at greater distances from primary tumors has not yet been assessed. Here, we immunohistologically analyzed the presence of Rep+ immune cells in sets of tumor, peritumor and, additionally, distant tissues of CRC patients (n = 13). We identified consistently high numbers of BMMF-positive macrophages in mucosal tissues at distances of as much as 25 cm away from the primary tumors, at levels comparable to peritumors and associated with M2-like macrophage polarization. The broad distribution of BMMFs suggests that BMMF+ macrophages might already exist at stages of pre-cancerous dysplasia or before. Quantification of BMMF tissue expression during colonoscopy might help to preventively stratify individuals at risk of developing polyps/CRC and recommend them for enhanced surveillance and/or changes in dietary lifestyle.
[18F]SiTATE Uptake in a Pancreatic Metastasis From a Renal Cell Carcinoma on a Long Axial Field of View PET/CT
2025-03-19

Here we present a 61-year-old woman with a history of renal cell carcinoma after nephrectomy and complete response to immunotherapy. Follow-up MRI revealed a contrast-enhanced lesion in the pancreatic tail, suspicious for a pancreatic neuroendocrine tumor. Subsequently, a SSTR-PET/CT with [ 18 F]SiTATE was conducted on a Biograph Vision Quadra. The pancreatic lesion showed intensive tracer uptake. Thus, a pancreatic tail resection was performed. Histopathologic results revealed no synaptophysin expression, but positivity for PAX8 and carboanhydrase 9. The final diagnosis was a solitary metastasis of the known renal cell carcinoma with SSTR2 expression in the intratumoral vascular network, explaining the [ 18 F]SiTATE uptake.
Sublethal systemic LPS in mice enables gut-luminal pathogens to bloom through oxygen species-mediated microbiota inhibition
2025-03-20

Abstract Endotoxin-driven systemic immune activation is a common hallmark across various clinical conditions. During acute critical illness, elevated plasma lipopolysaccharide triggers non-specific systemic immune activation. In addition, a compositional shift in the gut microbiota, including an increase in gut-luminal opportunistic pathogens, is observed. Whether a causal link exists between acute endotoxemia and abundance of gut-luminal opportunistic pathogens is incompletely understood. Here, we model acute, pathophysiological lipopolysaccharide concentrations in mice and show that systemic exposure promotes a 100–10’000-fold expansion of Klebsiella pneumoniae , Escherichia coli , Enterococcus faecium and Salmonella Typhimurium in the gut within one day, without overt enteropathy. Mechanistically, this is driven by a Toll-like receptor 4-dependent increase in gut-luminal oxygen species levels, which transiently halts microbiota fermentation and fuels growth of gut-luminal facultative anaerobic pathogens through oxidative respiration. Thus, systemic immune activation transiently perturbs microbiota homeostasis and favours opportunistic pathogens, potentially increasing the risk of infection in critically ill patients.
Photochromic Control in Hybrid Perovskite Photovoltaics
2025-03-20

Abstract The application of perovskite photovoltaics is hampered by issues related to the operational stability upon exposure to external stimuli, such as voltage bias and light. The dynamic control of the properties of perovskite materials in response to light could ensure the durability of perovskite solar cells, which is especially critical at the interface with charge‐extraction layers. We have applied a functionalized photochromic material based on spiro‐indoline naphthoxazine at the interface with hole‐transport layers in the corresponding perovskite solar cells with the aim of stabilizing them in response to voltage bias and light. We demonstrate photoinduced transformation by a combination of techniques, including transient absorption spectroscopy and Kelvin probe force microscopy. As a result, the application of the photochromic derivative offers improvements in photovoltaic performance and operational stability, highlighting the potential of dynamic photochromic strategies in perovskite photovoltaics.
Are text comprehension and calculation processes in word problem solving sequential or interactive? An eye-tracking study in children.
2025-03-20

The difficulty of a word problem is influenced by both linguistic and arithmetic processes. However, whether these processes are sequential or interactive is a matter of debate. Little is known about how eye-movement behaviour changes when faced with different linguistic and arithmetic task characteristics, both in relation to the entire problem and to specific components (i.e., numerical and textual elements). To address this gap, we conducted a study monitoring the eye movements of children aged 10-13 years during word problem solving. We manipulated linguistic and arithmetic task characteristics independently, focusing on the mathematical factor operation (addition/subtraction) and the linguistic factors consistency (consistent/inconsistent) and nominalization (verbalized/nominalized). The results revealed that eye movements generally increased as linguistic difficulty (e.g., nominalization) or arithmetic difficulty (e.g., operation) increased. Thereby, specific parts of the text were differentially affected based on the task characteristics. Increasing arithmetic difficulty led to a shift in eye movements towards numerical elements, while increasing linguistic difficulty resulted in a shift towards textual elements. Interestingly, the increase in arithmetic difficulty also influenced processing in the linguistic domain. For example, textual parts of the word problem received more fixations when the arithmetic difficulty increased, but not vice versa. This suggests that text comprehension and calculation processes in word problem solving are not separate and not strictly sequential; instead, they interact and/or do partially rely on shared cognitive resources. (PsycInfo Database Record (c) 2025 APA, all rights reserved).