julilili42/papers huggingface dataset:
Case report: A vertebral bone spur as an etiology for spinal cord herniation: case presentation, surgical technique, and review of the literature
2023-08-08

Objective The pathophysiology of idiopathic spinal cord herniation remains unknown. However, several different factors have been postulated, such as congenital causes (ventral dura mater duplication, preexisting pseudomeningocele, or other congenital dural defects), inflammation, remote spinal trauma, or thoracic disc herniation. Herein, the diagnosis and surgical treatment of a patient with spinal cord herniation caused by an intraspinal bone spur is presented along with a relevant literature review. Case presentation A 56-year-old male patient presented with a non-traumatic Brown-Sequard syndrome persisting for over 1 year. A magnetic resonance imaging of the spinal axis revealed a ventral spinal cord displacement in the level of T 6/7. A supplementary thin-sliced computed tomography of the spine revealed a bone spur at the same level. For neurosurgical intervention, T 6 and T 7 laminectomy was performed. The cranial and caudal end of the right paramedian ventral dural defect was visualized and enlarged. Following extradural spinal cord mobilization by denticulate ligament transection, the spinal cord was finally released. The spinal cord was rotated and the ventral closure of the dural defect was performed by continuous suture. The patient recovered from surgery without additional deficits. The patient’s postoperative gait, sensory, and motor function deficits improved, and further neurological deterioration was prevented. Conclusion Since the first description of spinal cord herniation by Wortzman et al. in 1974, approximately 260 cases have been reported in the literature. In addition to other causes, intraspinal bone spur is a possible cause of spinal cord herniation.
Hypercubes and Hamilton cycles of display sets of rooted phylogenetic networks
2023-08-08

In the context of reconstructing phylogenetic networks from a collection of phylogenetic trees, several characterisations and subsequently algorithms have been established to reconstruct a phylogenetic network that collectively embeds all trees in the input in some minimum way. For many instances however, the resulting network also embeds additional phylogenetic trees that are not part of the input. However, little is known about these inferred trees. In this paper, we explore the relationships among all phylogenetic trees that are embedded in a given phylogenetic network. First, we investigate some combinatorial properties of the collection P of all rooted binary phylogenetic trees that are embedded in a rooted binary phylogenetic network N. To this end, we associated a particular graph G, which we call rSPR graph, with the elements in P and show that, if |P|=2k, where k is the number of vertices with in-degree two in N, then G has a Hamilton cycle. Second, by exploiting rSPR graphs and properties of hypercubes, we turn to the well-studied class of rooted binary level-1 networks and give necessary and sufficient conditions for when a set of rooted binary phylogenetic trees can be embedded in a level-1 network without inferring any additional trees. Lastly, we show how these conditions translate into a polynomial-time algorithm to reconstruct such a network if it exists.
Computations and neural dynamics of audiovisual causal and perceptual inference in schizophrenia
2023-08-08

Abstract Hallucinations and perceptual abnormalities in psychosis are thought to arise from imbalanced integration of prior information and sensory inputs during perceptual inference. In this study, we combined psychophysics, Bayesian modelling and electroencephalography (EEG) to investigate potential changes in perceptual and causal inference in medicated individuals with schizophrenia when exposed to audiovisual sequences with varying numbers of flashes and beeps from either common or independent sources. Our findings reveal that individuals with schizophrenia, like their healthy controls, balance sensory integration and segregation in line with Bayesian causal inference rather than resorting to simpler heuristics. Both groups showed comparable weighting of prior information regarding the signals’ causal structure, with the schizophrenia group slightly overweighting prior information about the number of flashes or beeps. At the neural level, both groups computed Bayesian causal inference through dynamic encoding of perceptual estimates that segregate and flexibly combine audiovisual inputs. In conclusion, our results demonstrate that the computational and neural mechanisms of multisensory perceptual and causal inference remain remarkably intact in medicated individuals with schizophrenia during flash-beep scenarios.
The cycling mechanism of manganese-oxide cathodes in zinc batteries: A theory-based approach
2023-08-08

Zinc-based batteries offer good volumetric energy densities and are compatible with environmentally friendly aqueous electrolytes. Zinc-ion batteries (ZIBs) rely on a lithium-ion-like Zn -shuttle, which enables higher roundtrip efficiencies and better cycle life than zinc-air batteries. Manganese-oxide cathodes in near-neutral zinc sulfate electrolytes are the most prominent candidates for ZIBs. Zn -insertion, H -insertion, and Mn -dissolution are proposed to contribute to the charge-storage mechanism. During discharge and charge, two distinct phases are observed. Notably, the pH-driven precipitation of zinc-sulfate-hydroxide is detected during the second discharge phase. However, a complete and consistent understanding of the two-phase mechanism of these ZIBs is still missing. This paper presents a continuum full cell model supported by DFT calculations to investigate the implications of these observations. We integrate the complex-formation reactions of near-neutral aqueous electrolytes into the battery model and, in combination with the DFT calculations, draw a consistent picture of the cycling mechanism. We investigate the interplay between electrolyte pH and reaction mechanisms at the manganese-oxide cathodes and identify the dominant charge-storage mechanism. Our model is validated with electrochemical cycling data, cyclic voltammograms, and in-situ pH measurments. This allows us to analyse the influence of cell design and electrolyte composition on cycling and optimize the battery performance.
Identifying potential circulating miRNA biomarkers for the diagnosis and prediction of ovarian cancer using machine-learning approach: application of Boruta
2023-08-09

Introduction In gynecologic oncology, ovarian cancer is a great clinical challenge. Because of the lack of typical symptoms and effective biomarkers for noninvasive screening, most patients develop advanced-stage ovarian cancer by the time of diagnosis. MicroRNAs (miRNAs) are a type of non-coding RNA molecule that has been linked to human cancers. Specifying diagnostic biomarkers to determine non-cancer and cancer samples is difficult. Methods By using Boruta, a novel random forest-based feature selection in the machine-learning techniques, we aimed to identify biomarkers associated with ovarian cancer using cancerous and non-cancer samples from the Gene Expression Omnibus (GEO) database: GSE106817. In this study, we used two independent GEO data sets as external validation, including GSE113486 and GSE113740. We utilized five state-of-the-art machine-learning algorithms for classification: logistic regression, random forest, decision trees, artificial neural networks, and XGBoost. Results Four models discovered in GSE113486 had an AUC of 100%, three in GSE113740 with AUC of over 94%, and four in GSE113486 with AUC of over 94%. We identified 10 miRNAs to distinguish ovarian cancer cases from normal controls: hsa-miR-1290, hsa-miR-1233-5p, hsa-miR-1914-5p, hsa-miR-1469, hsa-miR-4675, hsa-miR-1228-5p, hsa-miR-3184-5p, hsa-miR-6784-5p, hsa-miR-6800-5p, and hsa-miR-5100. Our findings suggest that miRNAs could be used as possible biomarkers for ovarian cancer screening, for possible intervention.
Enlarged Numerical Attractors for Lattice Systems with Porous Media Degeneracies
2023-08-09

.A positively invariant ball and a global attractor for the porous media lattice system are obtained. By the implicit Euler scheme, the continuous-time model is discretized as a discrete-time porous media lattice system, which generates a discrete semigroup on the positively invariant ball for sufficiently small step sizes. It is shown that the discrete semigroup has a numerical attractor, which converges upper semicontinuously to the global attractor as the step size tends to zero. A new subject on enlarged attractors for lattice systems is investigated, which includes unique existence and convergence of attractors as well as solutions on the larger initial space. The second-order Taylor expansion and discretization error on the enlarged regular space are established to prove the upper semicontinuity of the enlarged numerical attractors with respect to the step size, while an upper bound of the enlarged attractors is provided to establish the lower semicontinuity in special cases.Keywordsporous media degeneracieslattice dynamical systems systemnumerical attractorsenlarged regularityMSC codes35B4037L6065L20
Sol–Gel-Controlled Size and Morphology of Mesoporous Silica Microspheres Using Hard Templates
2023-08-09

Mesoporous silica microspheres (MPSMs) represent a promising material as a stationary phase for HPLC separations. The use of hard templates provides a preparation strategy for producing such monodisperse silica microspheres. Here, 15 MPSMs were systematically synthesized by varying the sol-gel reaction parameters of water-to-precursor ratio and ammonia concentration in the presence of a porous <i>p</i>(GMA-<i>co</i>-EDMA) polymeric hard template. Changing the sol-gel process factors resulted in a wide range of MPSMs with varying particle sizes from smaller than one to several micrometers. The application of response surface methodology allowed to derive quantitative predictive models based on the process factor effects on particle size, pore size, pore volume, and specific surface area of the MPSMs. A narrow size distribution of the silica particles was maintained over the entire experimental space. Two larger-scale batches of MPSMs were prepared, and the particles were functionalized with trimethoxy(octadecyl) silane for the application as stationary phase in reversed-phases liquid chromatography. The separation of proteins and amino acids was successfully accomplished, and the effect of the pore properties of the silica particles on separation was demonstrated.
Genetic Diversity of Hepatitis B and C Viruses Revealed by Continuous Surveillance from 2015 to 2021 in Gabon, Central Africa
2023-08-09

Viral hepatitis remains one of the largest public health concerns worldwide. Especially in Central Africa, information on hepatitis virus infections has been limited, although the prevalence in this region has been reported to be higher than the global average. To reveal the current status of hepatitis B and C virus (HBV and HCV) infections and the genetic diversity of the viruses, we conducted longitudinal surveillance in Gabon. We detected 22 HBV and 9 HCV infections in 2047 patients with febrile illness. Genetic analyses of HBV identified subgenotype A1 for the first time in Gabon and an insertion generating a frameshift to create an X-preC/C fusion protein. We also revealed that most of the detected HCVs belonged to the “Gabon-specific” HCV subtype 4e (HCV-4e), and the entire nucleotide sequence of the HCV-4e polyprotein was determined to establish the first reference sequence. The HCV-4e strains possessed resistance-associated substitutions similar to those of other HCV-4 strains, indicating that the use of direct-acting antiviral therapy may be complex. These results provide a better understanding of the current situation of hepatitis B and C virus infections in Central Africa and will help public health organizations develop effective countermeasures to eliminate chronic viral hepatitis in this region.
PARP Inhibitors Effectively Reduce MAPK Inhibitor Resistant Melanoma Cell Growth and Synergize with MAPK Inhibitors through a Synthetic Lethal Interaction In Vitro and In Vivo
2023-08-09

The efficacy of targeting the MAPK signaling pathway in patients with melanoma is limited by the rapid development of resistance mechanisms that result in disease relapse. In this article, we focus on targeting the DNA repair pathway as an antimelanoma therapy, especially in MAPK inhibitor resistant melanoma cells using PARP inhibitors. We found that MAPK inhibitor resistant melanoma cells are particularly sensitive to PARP inhibitor treatment due to a lower basal expression of the DNA damage sensor ataxia-telangiectasia mutated (ATM). As a consequence, MAPK inhibitor resistant melanoma cells have decreased homologous recombination repair activity leading to a reduced repair of double-strand breaks caused by the PARP inhibitors. We validated the clinical relevance of our findings by ATM expression analysis in biopsies from patients with melanoma before and after development of resistance to MAPK inhibitors. Furthermore, we show that inhibition of the MAPK pathway induces a homologous recombination repair deficient phenotype in melanoma cells irrespective of their MAPK inhibitor sensitivity status. MAPK inhibition results in a synthetic lethal interaction of a combinatorial treatment with PARP inhibitors, which significantly reduces melanoma cell growth in vitro and in vivo. In conclusion, this study shows that PARP inhibitor treatment is a valuable therapy option for patients with melanoma, either as a single treatment or as a combination with MAPK inhibitors depending on ATM expression. Significance: We show that MAPK inhibitor resistant melanoma cells exhibit low ATM expression increasing their sensitivity toward PARP inhibitors and that a combination of MAPK/PARP inhibitors act synthetically lethal in melanoma cells. Our study shows that PARP inhibitor treatment is a valuable therapy option for patients with melanoma, either as a single treatment or as a combination with MAPK inhibitors depending on ATM expression, which could serve as a novel biomarker for treatment response.
Defective airway intraflagellar transport underlies a combined motile and primary ciliopathy syndrome caused byIFT74mutations
2023-08-09

Abstract Ciliopathies are inherited disorders caused by defective cilia. Mutations affecting motile cilia usually cause the chronic muco-obstructive sinopulmonary disease primary ciliary dyskinesia (PCD) and are associated with laterality defects, while a broad spectrum of early developmental as well as degenerative syndromes arise from mutations affecting signalling of primary (non-motile) cilia. Cilia assembly and functioning requires intraflagellar transport (IFT) of cargos assisted by IFT-B and IFT-A adaptor complexes. Within IFT-B, the N-termini of partner proteins IFT74 and IFT81 govern tubulin transport to build the ciliary microtubular cytoskeleton. We detected a homozygous 3-kb intragenic IFT74 deletion removing the exon 2 initiation codon and 40 N-terminal amino acids in two affected siblings. Both had clinical features of PCD with bronchiectasis, but no laterality defects. They also had retinal dysplasia and abnormal bone growth, with a narrowed thorax and short ribs, shortened long bones and digits, and abnormal skull shape. This resembles short-rib thoracic dysplasia, a skeletal ciliopathy previously linked to IFT defects in primary cilia, not motile cilia. Ciliated nasal epithelial cells collected from affected individuals had reduced numbers of shortened motile cilia with disarranged microtubules, some misorientation of the basal feet, and disrupted cilia structural and IFT protein distributions. No full-length IFT74 was expressed, only truncated forms that were consistent with N-terminal deletion and inframe translation from downstream initiation codons. In affinity purification mass spectrometry, exon 2-deleted IFT74 initiated from the nearest inframe downstream methionine 41 still interacts as part of the IFT-B complex, but only with reduced interaction levels and not with all its usual IFT-B partners. We propose that this is a hypomorphic mutation with some residual protein function retained, which gives rise to a primary skeletal ciliopathy combined with defective motile cilia and PCD.
In vitro and in vivo comparative analysis of antibacterial activity of green‐synthesized silver nanoparticles
2023-08-09

Abstract This study aims to compare antibacterial effects of green‐synthesized silver nanoparticles (AgNPs) with silver nitrate (AgNO 3 ). AgNPs were successfully synthesized using Eucalyptus camaldulensis leaf extract as a reducing and stabilizing agent. Minimum inhibitory concentrations (MIC) of AgNPs and AgNO 3 against Staphylococcus aureus and Pseudomonas aeruginosa ranged between 4.8 and 6.75 μg mL −1 . Growth curves demonstrated that inhibition of P. aeruginosa occurred right after AgNPs were added and throughout the period of the study (72 h). Antibacterial effects of both AgNPs and AgNO 3 could be abrogated by cysteine and 2‐mercaptoethanol, thiol‐containing compounds. Galleria mellonella model revealed relatively low toxic effects of both AgNPs and AgNO 3 . At 20MIC of AgNPs (≈137.8 mg kg −1 ), more than 80% survival of G. mellonella was observed. Unexpectedly, silver‐containing agents could not rescue larvae after S. aureus infection. Further ex vivo experiments in the presence of coelomic larval fluid demonstrated the reduction of antibacterial activity of both AgNPs and AgNO 3 . It was speculated that anionic molecules present in the coelomic fluid might neutralize the action of Ag ions. Binding of AgNPs or AgNO 3 to albumin, a major protein in human blood which transport several endogenous compounds was not detected, indicating that the silver‐containing agents could be applied as an antimicrobial agent.
Mural Serum Response Factor (SRF) Deficiency Provides Insights into Retinal Vascular Functionality and Development
2023-08-09

Serum response factor (SRF) controls the expression of muscle contraction and motility genes in mural cells (MCs) of the vasculature. In the retina, MC-SRF is important for correct angiogenesis during development and the continuing maintenance of the vascular tone. The purpose of this study was to provide further insights into the effects of MC SRF deficiency on the vasculature and function of the mature retina in SrfiMCKO mice that carry a MC-specific deletion of Srf. Retinal morphology and vascular integrity were analyzed in vivo via scanning laser ophthalmoscopy (SLO), angiography, and optical coherence tomography (OCT). Retinal function was evaluated with full-field electroretinography (ERG). We found that retinal blood vessels of these mutants exhibited different degrees of morphological and functional alterations. With increasing severity, we found vascular bulging, the formation of arteriovenous (AV) anastomoses, and ultimately, a retinal detachment (RD). The associated irregular retinal blood pressure and flow distribution eventually induced hypoxia, indicated by a negative ERG waveform shape. Further, the high frequency of interocular differences in the phenotype of individual SrfiMCKO mice points to a secondary nature of these developments far downstream of the genetic defect and rather dependent on the local retinal context.
Group coordination catalyzes individual and cultural intelligence
2023-08-09

A large program of research has aimed to ground large-scale cultural phenomena in processes taking place within individual minds. For example, investigating whether individual agents equipped with the right social learning strategies can enable cumulative cultural evolution given long enough time horizons. However, this approach often omits the critical group-level processes that mediate between individual agents and multi-generational societies. Here, we argue that interacting groups are a necessary and explanatory level of analysis, linking individual and collective intelligence through two characteristic feedback loops. In the first loop, more sophisticated individual-level social learning mechanisms based on Theory of Mind facilitate group-level complementarity, allowing distributed knowledge to be compositionally recombined in groups; these group-level innovations, in turn, ease the cognitive load on individuals. In the second loop, societal-level processes of cumulative culture provide groups with new cognitive technologies, including shared language and conceptual abstractions, which set in motion new group-level processes to further coordinate, recombine, and innovate. Taken together, these cycles establish group-level interaction as a dual engine of intelligence, catalyzing both individual cognition and cumulative culture.
Measuring the Numerical Viscosity in Simulations of Protoplanetary Disks in Cartesian Grids -- The Viscously Spreading Ring Revisited
2023-08-09

Hydrodynamical simulations solve the governing equations on a discrete grid of space and time. This discretization causes numerical diffusion similar to a physical viscous diffusion, whose magnitude is often unknown or poorly constrained. With the current trend of simulating accretion disks with no or very low prescribed physical viscosity, it becomes essential to understand and quantify this inherent numerical diffusion, in the form of a numerical viscosity. We study the behavior of the viscous spreading ring and the spiral instability that develops in it. We then use this setup to quantify the numerical viscosity in Cartesian grids and study its properties. We simulate the viscous spreading ring and the related instability on a two-dimensional polar grid using PLUTO as well as FARGO, and ensure convergence of our results with a resolution study. We then repeat our models on a Cartesian grid and measure the numerical viscosity by comparing results to the known analytical solution, using PLUTO and Athena++. We find that the numerical viscosity in a Cartesian grid scales with resolution as approximately and is equivalent to an effective for a common numerical setup. We also show that the spiral instability manifests as a single leading spiral throughout the whole domain on polar grids. This is contrary to previous results and indicates that sufficient resolution is necessary in order to correctly resolve the instability. Our results are relevant in the context of models where the origin should be included in the computational domain, or when polar grids cannot be used. Examples of such cases include models of disk accretion onto a central binary and inherently Cartesian codes.