julilili42/papers huggingface dataset:
Prevalence and Severity of Corneal Guttata After Descemet Membrane Endothelial Keratoplasty
2024-12-10

Purpose: The postoperative occurrence of corneal guttae (CG) in patients after Descemet membrane endothelial keratoplasty (DMEK) can lead to a significant reduction in visual acuity (VA) with the subsequent need for repeat DMEK. Therefore, the aim of this study was to analyze the prevalence and clinical significance of CG in transplanted corneas after DMEK. Methods: The prevalence and progression of CG after DMEK of 1657 patients were examined using endothelial specular microscopy images. The severity grade of CG was classified into 3 grades (G1 &lt;40%, G2 40-80%, G3 &gt;80%). Central corneal thickness, VA, and endothelial cell density (ECD) were examined during a postoperative follow-up time of 19.5 ± 17.6 months (range 6–84 months). Results: The prevalence of CG postoperatively was 1.3% (22/1657 eyes) after 4-6 weeks. We could classify 15/22 (68%) as G1, 5/22 (23%) as G2, and 2/22 (9%) as G3. In 12/22 (55%), either preparation and/or implantation was conspicuously difficult. None of the eyes showed an increase in CG during follow-up. 21/22 were stable in VA, central corneal thickness, and ECD during the entire follow-up. One patient with G3 required a repeat DMEK after 12 months (secondary graft failure). Conclusions: The prevalence of CG in our study population was notably lower than previously described and was mainly characterized by mild, low-grade findings without clinical significance and were stable during the follow-up. Preoperative overlook of CG in the tissue bank cannot be completely excluded, but the remarkable proportion of intraoperative complications in this group may have led to the occurrence of these CG.
Electrospun microfibers to enhance nutrient supply in bioinks and 3D-bioprinted tissue precursors
2024-12-11

Abstract 3D-bioprinting is a promising technique to mimic the complex anatomy of natural tissues, as it comprises a precise and gentle way of placing bioinks containing cells and hydrogel. Although hydrogels expose an ideal growth environment due to their extracellular matrix (ECM)-like properties, high water amount and tissue like microstructure, they lack mechanical strength and possess a diffusion limit of a couple of hundred micrometers. Integration of electrospun fibers could hereby benefit in multiple ways, for instance by controlling mechanical characteristics, cell orientation, direction of diffusion and anisotropic swelling behavior. The aim of this study was to create an advanced ECM-biomimicking scaffold material for tissue engineering, which offers enhanced diffusion properties. PCL bulk membranes were successfully electrospun and fragmented using a cryo cutting technique. Subsequently, these short single fibers (&lt;400 μ m in length and ∼5–10 μ m in diameter) were embedded in an agarose-based hydrogel after hydrophilization of the short single fibers by O 2 plasma treatment. Fiber-filled bioinks exhibit significantly improved biomolecule diffusion (&gt;500 μ m), swelling properties (20%–60% of control), and higher mechanical strength, while its viscosity (5–30 mPas*s) and gelation kinetics (28 °C) remained almost unaffected. The diffusion tests indicate a high level of size selectivity, which can be utilized for targeted biomolecule transport in the future. Finally, applying 3D-bioprinting technology (drop-on-demand vs. microextrusion) a print setting dependent post-dispensing orientation of the fibers could be induced, which ultimately paves way for the fabrication of metamaterials with anisotropic material properties. As expected, the fiber-filled bioink was found to be non-cytotoxic in cell culture trials using HUVECs and HepG2 (&gt;80% viability). In summary, microfiber integration holds great promise for 3D-bioprinting of tissue percursors with advanced metamaterial properties and thus offers high applicability in various fields of research, such as in-vitro tissue models, tissue engineered implants or cultivated meat.
Beyond Mere Algorithm Aversion: Are Judgments About Computer Agents More Variable?
2024-12-11

Several studies have reported algorithm aversion, reflected in harsher judgments about computers that commit errors, compared to humans who commit the same errors. Two online studies ( N = 67, N = 252) tested whether similar effects can be obtained with a referential communication task. Participants were tasked with identifying Japanese kanji characters based on written descriptions allegedly coming from a human or an AI source. Crucially, descriptions were either flawed (ambiguous) or not. Both concurrent measures during experimental trials and pre-post questionnaire data about the source were captured. Study 1 revealed patterns of algorithm aversion but also pointed at an opposite effect of “algorithm benefit”: ambiguous descriptions by an AI (vs. human) were evaluated more negatively, but non-ambiguous descriptions were evaluated more positively, suggesting the possibility that judgments about AI sources exhibit larger variability. Study 2 tested this prediction. While human and AI sources did not differ regarding concurrent measures, questionnaire data revealed several patterns that are consistent with the variability explanation.
A decision-theoretic model of multistability: perceptual switches as internal actions
2024-12-11

Abstract Perceptual multistability has been studied for centuries using a diverse collection of approaches. Insights derived from this phenomenon range from core principles of information processing, such as perceptual inference, to high-level concerns, such as visual awareness. The dominant computational explanations of perceptual multistability are based on the Helmholtzian view of perception as inverse inference. However, these approaches struggle to account for the crucial role played by value, e.g., with percepts paired with reward dominating for longer periods than unpaired ones. In this study, we formulate perceptual multistability in terms of dynamic, value-based, choice, employing the formalism of a partially observable Markov decision process (POMDP). We use binocular rivalry as an example, considering different explicit and implicit sources of reward (and punishment) for each percept. The resulting values are time-dependent and influenced by novelty as a form of exploration. The solution of the POMDP is the optimal perceptual policy, and we show that this can replicate and explain several characteristics of binocular rivalry, ranging from classic hallmarks such as apparently spontaneous random switches with approximately gamma-distributed dominance periods to more subtle aspects such as the rich temporal dynamics of perceptual switching rates. Overall, our decision-theoretic perspective on perceptual multistability not only accounts for a wealth of unexplained data, but also opens up modern conceptions of internal reinforcement learning in service of understanding perceptual phenomena, and sensory processing more generally.
Pyrazinyl-Substituted Aminoazoles as Covalent Inhibitors of Thrombin: Synthesis, Structure, and Anticoagulant Properties
2024-12-11

This study presents a novel series of <i>N</i>-acylated 1,2,4-triazol-5-amines and 1<i>H</i>-pyrazol-5-amines, featuring a pyrazin-2-yl moiety, developed as covalent inhibitors of thrombin. These compounds demonstrated potent inhibitory activity, with derivatives <b>13a</b> and <b>13b</b> achieving IC<sub>50</sub> values as low as 0.7 and 0.8 nM, respectively. Mass-shift assays confirmed that these inhibitors covalently bind to the catalytic Ser195 of thrombin, leading to temporary inhibition of its activity through specific acylation. The anticoagulant efficacy of these compounds was validated in plasma coagulation assays, with selected derivatives extending coagulation times in both an activated partial thromboplastin time (aPTT) and prothrombin time (PT) test. Thrombin generation assays further demonstrated that compounds of this series effectively reduced thrombin generation without substantially prolonging clotting times, suggesting a lower risk of bleeding. Selected compounds also strongly inhibited cancer cell- and thrombin-induced platelet aggregation. These results indicate that acylated aminoazoles hold a promise as new anticoagulants.
Sound amongst the din: primate strategies against noise
2024-12-11

Ambient noise disrupts vocal communication amongst animals. Recent studies show that some species, such as marmosets, can rapidly adjust the patterns of ongoing calls according to noisy environments. This substantial vocal flexibility reveals that non-human primates have more advanced cognitive control over when and what to vocalize than previously thought.
A novel method for recombinant mammalian‐expressed S‐HBsAg virus‐like particle production for assembly status analysis and improved anti‐HBs serology
2024-12-11

Abstract The Hepatitis B surface antigen (HBsAg) as the only lipid‐associated envelope protein of the Hepatitis B virus (HBV) acts as cellular attachment and entry mediator of HBV making it the main target of neutralizing antibodies to provide HBV immunity after infection or vaccination. Despite its central role in inducing protective immunity, there is however a surprising lack of comparative studies examining different HBsAgs and their ability to detect anti‐HBs antibodies. On the contrary, various time‐consuming complex HBsAg production protocols have been established, which result in structurally and functionally insufficiently characterized HBsAg. Here, we present an easy‐to‐perform, streamlined and robust method for recombinant S‐HBsAg virus‐like particle (VLP) production by transient expression in mammalian cells and purification from the cell lysate with the aim of displaying uniform antigenic epitopes on the surface to improve serological detection of anti‐HBs antibodies. We not only compare assembly status and particle composition by transmission electron microscopy and mass photometry of our S‐HBsAg and of commonly used HBsAg reference samples, but also assess their antigenic quality and functional suitability for anti‐HBs antibody detection to identify the best performing sample for serological screenings. While we found that serum‐isolated and recombinant HBsAg VLPs are assembled differently, our S‐HBsAg VLPs detected anti‐HBs antibodies with the highest sensitivity and specificity in multiplex serology when compared to yeast or serum HBsAg making it the most suitable antigen for analysis of HBV immunity through anti‐HBs serostatus.
Developing Gingerol-Based Analogs against Pseudomonas aeruginosa Infections
2024-12-11

<i>Pseudomonas aeruginosa</i> (<i>P. aeruginosa</i>), a Gram-negative opportunistic pathogen, produces virulent factors and forms biofilms through a quorum sensing (QS) mechanism. Modulating QS networks is considered an effective strategy for treating <i>P. aeruginosa</i> infections. Particularly, the <i>rhl</i> system, one of the QS networks, can be a potential target in treating patients with chronic infections. We previously discovered that gingerol acts as a RhlR antagonist of <i>P. aeruginosa</i>. Based on the chemical structure of gingerol, we have designed and synthesized gingerol derivatives by introducing various functional groups in the middle and tail regions. A comprehensive structure-activity relationship study showed that compound <b>5a</b> substituted with phenyl group in the tail region was the most potent in various biological assessments, such as RhlR binding affinity, <i>rhl</i> gene expression, and virulence factor production of <i>P. aeruginosa</i>. Furthermore, compound <b>5a</b> decreased the biofilm formation and pathogenicity of <i>P. aeruginosa</i>. Interestingly, compound <b>5a</b> also influenced <i>las</i> system in addition to the <i>rhl</i> system. Taken together, compound <b>5a</b> can be utilized as a potent compound for controlling <i>P. aeruginosa</i> infection.
Brain morphometry and psychomotor development in children with PCH2A
2024-12-11

Abstract Introduction Pontocerebellar hypoplasia type 2A (PCH2A) is a rare neurogenetic disease causing severe cognitive and motor impairment. We report on brain morphometry and psychomotor development of affected children. Materials and Methods We analyzed 78 cerebral MRI datasets of 57 patients with genetically proven PCH2A. Volumetry and in-plane measurements were performed in cerebellum, neocortex and pons. Supratentorial width and width of the anterior horns of the lateral ventricles was used to calculate the Evans index. Caregivers of 65 patients with PCH2A (7 months to 33 years) filled in a survey assessing motor and cognitive development. Developmental status was compared to MRI measurements. Results In children with PCH2A, cerebellar volume was markedly smaller than in healthy children at birth, with slower increase and stagnation at around 12 months. No cerebellar growth was observed in the cranio-caudal axis. Long-term data did not show a decrease in cerebellar volume or in-plane measurements. Supratentorial measurements showed progressive microcephaly and a continuous increase of the Evans index, indicating progressive cerebral atrophy. Patients showed severely impaired cognitive and motor development. Developmental regression was reported only for a minority. No statistical relationship between brain measurements and cognitive or motor development was observed. Conclusion MRI of patients with PCH2A shows limited cerebellar growth during infancy, especially restricted along the cranio-caudal axis. After infancy, cerebellar volume remains relatively stable. Supratentorial measurements indicate slowly progressive atrophy. Psychomotor development is severely impaired, but regression is rare. Highlights - MRI (57 patients) and developmental data (65 patients) of children with PCH2A - Cerebellar growth is affected in a spatial manner, resulting in the dragonfly sign - Ongoing supratentorial atrophy, potentially secondary to cerebellar pathology - Psychomotor development is delayed, but takes place and regression is rare - No relation between brain measurements and developmental trajectories
Toxicity and Biodegradation of Two Different Hydrothermal Liquefaction Process Waters to Anaerobic Digestion and the Effect of Microaeration
2024-12-11

Abstract Hydrothermal liquefaction (HTL) can convert a considerable portion of the carbon in complex feedstocks into renewable bio-oil, but it also generates a liquid byproduct ( i.e. , HTL process water) that retains 15 – 55% of the carbon from the HTL feedstock. Feeding HTL process water to anaerobic digestion (AD) is a promising approach for maximizing resource recovery, enabling the conversion of the retained carbon into biogas. However, various toxic and poorly biodegradable compounds in HTL process water make its treatment with AD challenging. Presently, the underlying mechanisms remain often unclear. We investigated the impact of HTL process water from two different feedstocks – a food-waste proxy ( i.e. , dog food, rich in proteins) and wheat straw (rich in lignocellulose) – on the different trophic groups in the food web of AD. We found that methanogens rather than acidogens were inhibited by HTL process water. Comparative toxicity and biodegradability analyses showed that wheat-straw process water had a higher biodegradability regardless of its higher toxicity to acetoclastic methanogens than food-waste process water, due to its higher content in toxic but easily degradable aromatic compounds. Microaeration enhanced the biodegradation and methane yields of food-waste process water, particularly under anoxic conditions. However, microaeration was ineffective for wheat-straw process water. These findings highlight the importance of feedstock-specific strategies to optimize AD for biogas production from HTL process water.
Arabidopsis WALL-ASSOCIATED KINASES are not required for oligogalacturonide-induced signaling and immunity
2024-12-12

Abstract Carbohydrate-based cell wall signaling impacts plant growth, development, and stress responses; however, how cell wall signals are perceived and transduced remains poorly understood. Several cell wall breakdown products have been described as typical damage-associated molecular patterns that activate plant immunity, including pectin-derived oligogalacturonides (OGs). Receptor kinases of the WALL-ASSOCIATED KINASE (WAK) family bind pectin and OGs and were previously proposed as OG receptors. However, unambiguous genetic evidence for the role of WAKs in OG responses is lacking. Here, we investigated the role of Arabidopsis (Arabidopsis thaliana) WAKs in OG perception using a clustered regularly interspaced short palindromic repeats mutant in which all 5 WAK genes were deleted. Using a combination of immune assays for early and late pattern-triggered immunity, we show that WAKs are dispensable for OG-induced signaling and immunity, indicating that they are not bona fide OG receptors.
Earliest modern human genomes constrain timing of Neanderthal admixture
2024-12-12

Abstract Modern humans arrived in Europe more than 45,000 years ago, overlapping at least 5,000 years with Neanderthals 1–4 . Limited genomic data from these early modern humans have shown that at least two genetically distinct groups inhabited Europe, represented by Zlatý kůň, Czechia 3 and Bacho Kiro, Bulgaria 2 . Here we deepen our understanding of early modern humans by analysing one high-coverage genome and five low-coverage genomes from approximately 45,000-year-old remains from Ilsenhöhle in Ranis, Germany 4 , and a further high-coverage genome from Zlatý kůň. We show that distant familial relationships link the Ranis and Zlatý kůň individuals and that they were part of the same small, isolated population that represents the deepest known split from the Out-of-Africa lineage. Ranis genomes harbour Neanderthal segments that originate from a single admixture event shared with all non-Africans that we date to approximately 45,000–49,000 years ago. This implies that ancestors of all non-Africans sequenced so far resided in a common population at this time, and further suggests that modern human remains older than 50,000 years from outside Africa represent different non-African populations.
Illusory traits: Wrong but sometimes useful.
2024-12-12

Psychological measures frequently show trait-like properties, and the ontological status of stable psychological traits has been discussed for decades. We argue that these properties can emerge from causal dynamics of time-varying processes, which are <i>omitted</i> from the analysis model, potentially leading to the estimation of traits that are, at least in part, illusory. Theories positing the importance of a large set of dynamic psychological causes across development are consistent with the existence of illusory traits. We show via simulation that even a linear system with many processes can generate a covariance matrix with trait-like properties. We then attempt to examine how illusory traits affect our conclusions drawn from a common statistical model, which assumes stable traits to analyze longitudinal panel data-a random-intercept cross-lagged panel model (RI-CLPM). We find that the RI-CLPM sometimes falsely detects the existence of traits in the presence of omitted processes, even when the data-generating model does not include any traits. However, in this scenario, the RI-CLPM estimates less causally biased autoregressive and cross-lagged effects than an analysis model, which does not assume traits (i.e., the cross-lagged panel model). The results indicate that the detection of trait variance should not be inferred as strong evidence for the existence of time-invariant trait causes. On the other hand, even when traits are illusory, statistical models assuming stable traits may sometimes be useful for causal inference. (PsycInfo Database Record (c) 2025 APA, all rights reserved).
Deep phosphoproteomics of Klebsiella pneumoniae reveals HipA-mediated tolerance to ciprofloxacin
2024-12-12

Klebsiella pneumoniae belongs to the group of bacterial pathogens causing the majority of antibiotic-resistant nosocomial infections worldwide; however, the molecular mechanisms underlying post-translational regulation of its physiology are poorly understood. Here we perform a comprehensive analysis of Klebsiella phosphoproteome, focusing on HipA, a Ser/Thr kinase involved in antibiotic tolerance in Escherichia coli . We show that overproduced K . pneumoniae HipA (HipA kp ) is toxic to both E . coli and K . pneumoniae and its toxicity can be rescued by overproduction of the antitoxin HipB kp . Importantly, HipA kp overproduction leads to increased tolerance against ciprofloxacin, a commonly used antibiotic in the treatment of K . pneumoniae infections. Proteome and phosphoproteome analyses in the absence and presence of ciprofloxacin confirm that HipA kp has Ser/Thr kinase activity, auto-phosphorylates at S150, and shares multiple substrates with HipA ec , thereby providing a valuable resource to clarify the molecular basis of tolerance and the role of Ser/Thr phosphorylation in this human pathogen.
Typical Macroscopic Long-Time Behavior for Random Hamiltonians
2024-12-12

Abstract We consider a closed macroscopic quantum system in a pure state <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"> <mml:msub> <mml:mi>ψ</mml:mi> <mml:mi>t</mml:mi> </mml:msub> </mml:math> evolving unitarily and take for granted that different macro states correspond to mutually orthogonal subspaces <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"> <mml:msub> <mml:mi>H</mml:mi> <mml:mi>ν</mml:mi> </mml:msub> </mml:math> (macro spaces) of Hilbert space, each of which has large dimension. We extend previous work on the question what the evolution of <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"> <mml:msub> <mml:mi>ψ</mml:mi> <mml:mi>t</mml:mi> </mml:msub> </mml:math> looks like macroscopically, specifically on how much of <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"> <mml:msub> <mml:mi>ψ</mml:mi> <mml:mi>t</mml:mi> </mml:msub> </mml:math> lies in each <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"> <mml:msub> <mml:mi>H</mml:mi> <mml:mi>ν</mml:mi> </mml:msub> </mml:math> . Previous bounds concerned the absolute error for typical <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"> <mml:msub> <mml:mi>ψ</mml:mi> <mml:mn>0</mml:mn> </mml:msub> </mml:math> and/or t and are valid for arbitrary Hamiltonians H ; now, we provide bounds on the relative error, which means much tighter bounds, with probability close to 1 by modeling H as a random matrix, more precisely as a random band matrix (i.e., where only entries near the main diagonal are significantly nonzero) in a basis aligned with the macro spaces. We exploit particularly that the eigenvectors of H are delocalized in this basis. Our main mathematical results confirm the two phenomena of generalized normal typicality (a type of long-time behavior) and dynamical typicality (a type of similarity within the ensemble of <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"> <mml:msub> <mml:mi>ψ</mml:mi> <mml:mn>0</mml:mn> </mml:msub> </mml:math> from an initial macro space). They are based on an extension we prove of a no-gaps delocalization result for random matrices by Rudelson and Vershynin (Geom Funct Anal 26:1716–1776, 2016).