bluuebunny/crossref_metadata_2025_split huggingface dataset:
Experimental validation of the free-energy principle with in vitro neural networks
Authors: Isomura Takuya , Kotani Kiyoshi , Jimbo Yasuhiko , Friston Karl J. 
Published: August 2023

AbstractEmpirical applications of the free-energy principle are not straightforward because they entail a commitment to a particular process theory, especially at the cellular and synaptic levels. Using a recently established reverse engineering technique, we confirm the quantitative predictions of the free-energy principle using in vitro networks of rat cortical neurons that perform causal inference. Upon receiving electrical stimuli—generated by mixing two hidden sources—neurons self-organised to selectively encode the two sources. Pharmacological up- and downregulation of network excitability disrupted the ensuing inference, consistent with changes in prior beliefs about hidden sources. As predicted, changes in effective synaptic connectivity reduced variational free energy, where the connection strengths encoded parameters of the generative model. In short, we show that variational free energy minimisation can quantitatively predict the self-organisation of neuronal networks, in terms of their responses and plasticity. These results demonstrate the applicability of the free-energy principle to in vitro neural networks and establish its predictive validity in this setting.
Metagenomic surveillance uncovers diverse and novel viral taxa in febrile patients from Nigeria
Authors: Oguzie Judith U. , Petros Brittany A. , Oluniyi Paul E. , Mehta Samar B. , Eromon Philomena E. , Nair Parvathy , Adewale-Fasoro Opeoluwa , Ifoga Peace Damilola , Odia Ikponmwosa , Pastusiak Andrzej , Gbemisola Otitoola Shobi , Aiyepada John Oke , Uyigue Eghosasere Anthonia , Edamhande Akhilomen Patience , Blessing Osiemi , Airende Michael , Tomkins-Tinch Christopher , Qu James , Stenson Liam , Schaffner Stephen F. , Oyejide Nicholas , Ajayi Nnenna A. , Ojide Kingsley , Ogah Onwe , Abejegah Chukwuyem , Adedosu Nelson , Ayodeji Oluwafemi , Liasu Ahmed A. , Okogbenin Sylvanus , Okokhere Peter O. , Park Daniel J. , Folarin Onikepe A. , Komolafe Isaac , Ihekweazu Chikwe , Frost Simon D. W. , Jackson Ethan K. , Siddle Katherine J. , Sabeti Pardis C. , Happi Christian T. 
Published: August 2023

AbstractEffective infectious disease surveillance in high-risk regions is critical for clinical care and pandemic preemption; however, few clinical diagnostics are available for the wide range of potential human pathogens. Here, we conduct unbiased metagenomic sequencing of 593 samples from febrile Nigerian patients collected in three settings: i) population-level surveillance of individuals presenting with symptoms consistent with Lassa Fever (LF); ii) real-time investigations of outbreaks with suspected infectious etiologies; and iii) undiagnosed clinically challenging cases. We identify 13 distinct viruses, including the second and third documented cases of human blood-associated dicistrovirus, and a highly divergent, unclassified dicistrovirus that we name human blood-associated dicistrovirus 2. We show that pegivirus C is a common co-infection in individuals with LF and is associated with lower Lassa viral loads and favorable outcomes. We help uncover the causes of three outbreaks as yellow fever virus, monkeypox virus, and a noninfectious cause, the latter ultimately determined to be pesticide poisoning. We demonstrate that a local, Nigerian-driven metagenomics response to complex public health scenarios generates accurate, real-time differential diagnoses, yielding insights that inform policy.
Myonectin protects against skeletal muscle dysfunction in male mice through activation of AMPK/PGC1α pathway
Authors: Ozaki Yuta , Ohashi Koji , Otaka Naoya , Kawanishi Hiroshi , Takikawa Tomonobu , Fang Lixin , Takahara Kunihiko , Tatsumi Minako , Ishihama Sohta , Takefuji Mikito , Kato Katsuhiro , Shimizu Yuuki , Bando Yasuko K. , Inoue Aiko , Kuzuya Masafumi , Miura Shinji , Murohara Toyoaki , Ouchi Noriyuki 
Published: August 2023

AbstractTo maintain and restore skeletal muscle mass and function is essential for healthy aging. We have found that myonectin acts as a cardioprotective myokine. Here, we investigate the effect of myonectin on skeletal muscle atrophy in various male mouse models of muscle dysfunction. Disruption of myonectin exacerbates skeletal muscle atrophy in age-associated, sciatic denervation-induced or dexamethasone (DEX)-induced muscle atrophy models. Myonectin deficiency also contributes to exacerbated mitochondrial dysfunction and reduces expression of mitochondrial biogenesis-associated genes including PGC1α in denervated muscle. Myonectin supplementation attenuates denervation-induced muscle atrophy via activation of AMPK. Myonectin also reverses DEX-induced atrophy of cultured myotubes through the AMPK/PGC1α signaling. Furthermore, myonectin treatment suppresses muscle atrophy in senescence-accelerated mouse prone (SAMP) 8 mouse model of accelerated aging or mdx mouse model of Duchenne muscular dystrophy. These data indicate that myonectin can ameliorate skeletal muscle dysfunction through AMPK/PGC1α-dependent mechanisms, suggesting that myonectin could represent a therapeutic target of muscle atrophy.
Combining gut microbiota modulation and chemotherapy by capecitabine-loaded prebiotic nanoparticle improves colorectal cancer therapy
Authors: Lang Tianqun , Zhu Runqi , Zhu Xiao , Yan Wenlu , Li Yu , Zhai Yihui , Wu Ting , Huang Xin , Yin Qi , Li Yaping 
Published: August 2023

AbstractColorectal cancer (CRC) therapy efficiency can be influenced by the microbiota in the gastrointestinal tract. Compared with traditional intervention, prebiotics delivery into the gut is a more controllable method for gut microbiota modulatory therapy. Capecitabine (Cap), the first-line chemotherapeutic agent for CRC, lacks a carrier that can prolong its half-life. Here, we construct a Cap-loaded nanoparticle using the prebiotic xylan-stearic acid conjugate (SCXN). The oral administration of SCXN delays the drug clearance in the blood and increases the intra-tumoral Cap concentration in the CRC mouse model. SCXN also facilitates the probiotic proliferation and short chain fatty acid production. Compared with free Cap, SCXN enhances the anti-tumor immunity and increases the tumor inhibition rate from 5.29 to 71.78%. SCXN exhibits good biocompatibility and prolongs the median survival time of CRC mice from 14 to 33.5 d. This prebiotics-based nanoparticle provides a promising CRC treatment by combining gut microbiota modulation and chemotherapy.
Backbone spiking sequence as a basis for preplay, replay, and default states in human cortex
Authors: Vaz Alex P. , Wittig John H. , Inati Sara K. , Zaghloul Kareem A. 
Published: August 2023

AbstractSequences of spiking activity have been heavily implicated as potential substrates of memory formation and retrieval across many species. A parallel line of recent evidence also asserts that sequential activity may arise from and be constrained by pre-existing network structure. Here we reconcile these two lines of research in the human brain by measuring single unit spiking sequences in the temporal lobe cortex as participants perform an episodic memory task. We find the presence of an average backbone spiking sequence identified during pre-task rest that is stable over time and different cognitive states. We further demonstrate that these backbone sequences are composed of both rigid and flexible sequence elements, and that flexible elements within these sequences serve to promote memory specificity when forming and retrieving new memories. These results support the hypothesis that pre-existing network dynamics serve as a scaffold for ongoing neural activity in the human cortex.
Saddles as rotational locks within shape-assisted self-assembled nanosheets
Authors: Woods Joseph F. , Gallego Lucía , Maisch Amira , Renggli Dominik , Cuocci Corrado , Blacque Olivier , Steinfeld Gunther , Kaech Andres , Spingler Bernhard , Vargas Jentzsch Andreas , Rickhaus Michel 
Published: August 2023

AbstractTwo-dimensional (2D) materials are a key target for many applications in the modern day. Self-assembly is one approach that can bring us closer to this goal, which usually relies upon strong, directional interactions instead of covalent bonds. Control over less directional forces is more challenging and usually does not result in as well-defined materials. Explicitly incorporating topography into the design as a guiding effect to enhance the interacting forces can help to form highly ordered structures. Herein, we show the process of shape-assisted self-assembly to be consistent across a range of derivatives that highlights the restriction of rotational motion and is verified using a diverse combination of solid state analyses. A molecular curvature governed angle distribution nurtures monomers into loose columns that then arrange to form 2D structures with long-range order observed in both crystalline and soft materials. These features strengthen the idea that shape becomes an important design principle leading towards precise molecular self-assembly and the inception of new materials.
Using orbital sensitivity analysis to pinpoint the role of orbital interactions in thermoelectric power factor
Authors: Zhang Wenhao , Halet Jean-François , Mori Takao 
Published: August 2023

AbstractThe modification of the electronic band structure is of critical importance for thermoelectric materials whose heat to electricity power generation is related to carrier effective mass and alignment of semiconductor band edges. One approach to optimize the electronic band structure is by modification of orbital interactions through doping or alloying. While the current ab-initio quantum chemical calculations can help us to investigate orbital components of electronic bands, they reveal little information on the relative tunability of electronic states and transport properties with respect to orbital interactions. In this work, we present a method, based on a symmetry-adapted tight-binding model and sensitivity analysis, that can pinpoint the role of orbital interactions in determining electronic band structure and transport properties. As an application, a systematic theoretical analysis is used to show how the power factor of PbTe can/cannot be improved by playing with interatomic orbital interactions. The orbital interaction sensitivity analysis introduced in this work can easily be applied to other compounds or properties.
Dynamic matrices with DNA-encoded viscoelasticity for cell and organoid culture
Authors: Peng Yu-Hsuan , Hsiao Syuan-Ku , Gupta Krishna , Ruland André , Auernhammer Günter K. , Maitz Manfred F. , Boye Susanne , Lattner Johanna , Gerri Claudia , Honigmann Alf , Werner Carsten , Krieg Elisha 
Published: August 2023

AbstractThree-dimensional cell and organoid cultures rely on the mechanical support of viscoelastic matrices. However, commonly used matrix materials lack control over key cell-instructive properties. Here we report on fully synthetic hydrogels based on DNA libraries that self-assemble with ultrahigh-molecular-weight polymers, forming a dynamic DNA-crosslinked matrix (DyNAtrix). DyNAtrix enables computationally predictable and systematic control over its viscoelasticity, thermodynamic and kinetic parameters by changing DNA sequence information. Adjustable heat activation allows homogeneous embedding of mammalian cells. Intriguingly, stress-relaxation times can be tuned over four orders of magnitude, recapitulating mechanical characteristics of living tissues. DyNAtrix is self-healing, printable, exhibits high stability, cyto- and haemocompatibility, and controllable degradation. DyNAtrix-based cultures of human mesenchymal stromal cells, pluripotent stem cells, canine kidney cysts and human trophoblast organoids show high viability, proliferation and morphogenesis. DyNAtrix thus represents a programmable and versatile precision matrix for advanced approaches to biomechanics, biophysics and tissue engineering.
Towards a circular economy: valorization of banana peels by developing bio-composites thermal insulators
Authors: Mohamed Gehad R. , Mahmoud Rehab K. , Shaban Mohamed , Fahim Irene S. , Abd El‑Salam H. M. , Mahmoud Hamada M. 
Published: August 2023

AbstractThe building construction materials are responsible for a large amount of energy and natural resource consumption. In light of the current challenges of resource scarcity and global climate change, the circular economy (CE) is a promising strategy to mitigate pressure on the environment, improve supplying of raw materials, and increase new market and employment opportunities. Developing eco-friendly thermal insulation materials based on agro-waste is a new waste management trend to achieve the sustainability of the resource and energy consumption in the construction sectors. In this work, banana-polystyrene composites were prepared by mixing the banana peels powder (BP) with polystyrene (PS) in different weight ratios (90:10, 80:20, 70:30, and 60:40). The physical and thermal properties such as thermal conductivity, electrical conductivity, Fourier Transform Infrared (FTIR), crystallographic structures of the fibers, X-Ray Diffraction (XRD), Thermogravimetric Analysis (TGA), and Differential Scanning Calorimetry (DSC) were carried out on BP and BP-PS1 that were prepared with ten wt.% and 20 wt.% of polystyrene powder (BP-PS2). The bio-composites results showed low thermal conductivity ranging from 0.028 to 0.030 W/m.K. The BP-PS2 exhibited a lower thermal conductivity of 0.027 W/m.K, while the pure peel powder demonstrated notable thermal stability, indicated by a total weight loss of 66.4% and a high crystallinity value of 56.1%. Furthermore, the thermal analysis (TGA) and X-Ray Diffraction (XRD) demonstrated that the pure banana peel has the highest thermal stability and crystallinity. These findings indicate that using banana peel-polystyrene composites represents an innovative solution for thermal insulation in buildings as an alternative to conventional materials to reduce energy and resource consumption.
Imaging-based study demonstrates how the DEK nanoscale distribution differentially correlates with epigenetic marks in a breast cancer model
Authors: Pierzynska-Mach Agnieszka , Cainero Isotta , Oneto Michele , Ferrando-May Elisa , Lanzanò Luca , Diaspro Alberto 
Published: August 2023

AbstractEpigenetic dysregulation of chromatin is one of the hallmarks of cancer development and progression, and it is continuously investigated as a potential general bio-marker of this complex disease. One of the nuclear factors involved in gene regulation is the unique DEK protein—a histone chaperon modulating chromatin topology. DEK expression levels increase significantly from normal to cancer cells, hence raising the possibility of using DEK as a tumor marker. Although DEK is known to be implicated in epigenetic and transcriptional regulation, the details of these interactions and their relevance in cancer development remain largely elusive. In this work, we investigated the spatial correlation between the nuclear distribution of DEK and chromatin patterns—alongside breast cancer progression—leveraging image cross-correlation spectroscopy (ICCS) coupled with Proximity Ligation Assay (PLA) analysis. We performed our study on the model based on three well-established human breast cell lines to consider this tumor's heterogeneity (MCF10A, MCF7, and MDA-MB-231 cells). Our results show that overexpression of DEK correlates with the overall higher level of spatial proximity between DEK and histone marks corresponding to gene promoters regions (H3K9ac, H3K4me3), although it does not correlate with spatial proximity between DEK and gene enhancers (H3K27ac). Additionally, we observed that colocalizing fractions of DEK and histone marks are lower for the non-invasive cell subtype than for the highly invasive cell line (MDA-MB-231). Thus, this study suggests that the role of DEK on transcriptionally active chromatin regions varies depending on the subtype of the breast cancer cell line.
Modified generalized Weibull distribution: theory and applications
Authors: Shama Mustafa S. , Alharthi Amirah Saeed , Almulhim Fatimah A. , Gemeay Ahmed M. , Meraou Mohammed Amine , Mustafa Manahil SidAhmed , Hussam Eslam , Aljohani Hassan M. 
Published: August 2023

AbstractThis article presents and investigates a modified version of the Weibull distribution that incorporates four parameters and can effectively represent a hazard rate function with a shape resembling a bathtub. Its significance in the fields of lifetime and reliability stems from its ability to model both increasing and decreasing failure rates. The proposed distribution encompasses several well-known models such as the Weibull, extreme value, exponentiated Weibull, generalized Rayleigh, and modified Weibull distributions. The paper derives key mathematical statistics of the proposed distribution, including the quantile function, moments, moment-generating function, and order statistics density. Various mathematical properties of the proposed model are established, and the unknown parameters of the distribution are estimated using different estimation techniques. Furthermore, the effectiveness of these estimators is assessed through numerical simulation studies. Finally, the paper applies the new model and compares it with various existing distributions by analyzing two real-life time data sets.
Management of perimesencephalic nonaneurysmal subarachnoid hemorrhage: a national survey
Authors: Wolfert Christina , Maurer Christoph J. , Sommer Björn , Steininger Kathrin , Motov Stefan , Bonk Maximilian-Niklas , Krauss Philipp , Berlis Ansgar , Shiban Ehab 
Published: August 2023

AbstractPerimesencephalic nonaneurysmal subarachnoid hemorrhage (NASAH) is a rare type of subarachnoid hemorrhage (SAH), usually associated with minor complications compared to aneurysmal SAH. Up to date, data is scarce and consensus on therapeutic management and follow-up diagnostics of NASAH is often missing. This survey aims to evaluate the clinical management among neurosurgical departments in Germany. 135 neurosurgical departments in Germany received a hardcopy questionnaire. Encompassing three case vignettes with minor, moderate and severe NASAH on CT-scans and questions including the in-hospital treatment with initial observation, blood pressure (BP) management, cerebral vasospasm (CV) prophylaxis and the need for digital subtraction angiography (DSA). 80 departments (59.2%) answered the questionnaire. Whereof, centers with a higher caseload state an elevated complication rate (Chi2 < 0.001). Initial observation on the intensive care unit is performed in 51.3%; 47.5%, 70.0% in minor, moderate and severe NASAH, respectively. Invasive BP monitoring is performed more often in severe NASAH (52.5%, 55.0%, 71.3% minor, moderate, severe). CV prophylaxis and transcranial doppler ultrasound (TCD) are performed in 41.3%, 45.0%, 63.8% in minor, moderate and severe NASAH, respectively. Indication for a second DSA is set in the majority of centers, whereas after two negative ones, a third DSA is less often indicated (2nd: 66.2%, 72.5%, 86.2%; 3rd: 3.8%, 3.8%, 13.8% minor, moderate, severe). This study confirms the influence of bleeding severity on treatment and follow-up of NASAH patients. Additionally, the existing inconsistency of treatment pathways throughout Germany is highlighted. Therefore, we suggest to conceive new treatment guidelines including this finding.
Combining atomic force microscopy and fluorescence-based techniques to explore mechanical properties of naive and ischemia-affected brain regions in mice
Authors: Fuhs Thomas , Flachmeyer Bianca , Krueger Martin , Blietz Alexandra , Härtig Wolfgang , Michalski Dominik 
Published: August 2023

AbstractKnowledge of the brain’s structure and function is essential for understanding processes in health and disease. Histochemical and fluorescence-based techniques have proven beneficial in characterizing brain regions and cellular compositions in pre-clinical research. Atomic force microscopy (AFM) has been introduced for mechanical tissue characterization, which may also help investigate pathophysiological aspects in disease-related models such as stroke. While combining AFM and fluorescence-based techniques, this study explored the mechanical properties of naive and ischemic brain regions in mice. Ischemia-affected regions were identified by the green signal of fluorescein isothiocyanate-conjugated albumin. A semi-automated protocol based on a brain atlas allowed regional allocations to the neocortex, striatum, thalamus, hypothalamus, hippocampus, and fiber tracts. Although AFM led to varying measurements, intra-individual analyses indicated a gradually increased tissue stiffness in the neocortex compared to subcortical areas, i.e., the striatum and fiber tracts. Regions affected by ischemia predominantly exhibited an increased tissue stiffness compared to those of the contra-lateral hemisphere, which might be related to cellular swelling. This study indicated intra-individual differences in mechanical properties among naive and ischemia-affected brain regions. The combination of AFM, semi-automated regional allocations, and fluorescence-based techniques thus qualifies for mechanical characterizations of the healthy and disease-affected brain in pre-clinical research.
Assessment of prokaryotic communities in Southwestern Atlantic deep-sea sediments reveals prevalent methanol-oxidising Methylomirabilales
Authors: Peres Francielli V. , Paula Fabiana S. , Bendia Amanda G. , Gontijo Júlia B. , de Mahiques Michel M. , Pellizari Vivian H. 
Published: August 2023

AbstractContinental slopes can play a significant contribution to marine productivity and carbon cycling. These regions can harbour distinct geological features, such as salt diapirs and pockmarks, in which their depressions may serve as natural sediment traps where different compounds can accumulate. We investigated the prokaryotic communities in surface (0–2 cm) and subsurface (18–20 or 22–24 cm) sediments from a salt diapir and pockmark field in Santos Basin, Southwest Atlantic Ocean. Metabarcoding of 16 samples revealed that surface sediments were dominated by the archaeal class Nitrososphaeria, while the bacterial class Dehalococcoidia was the most prevalent in subsurface samples. Sediment strata were found to be a significant factor explaining 27% of the variability in community composition. However, no significant difference was observed among geomorphological features. We also performed a metagenomic analysis of three surface samples and analysed the highest quality metagenome-assembled genome retrieved, which belonged to the family CSP1–5, phylum Methylomirabilota. This non-methanotrophic methylotroph contains genes encoding for methanol oxidation and Calvin Cycle pathways, along with diverse functions that may contribute to its adaptation to deep-sea habitats and to oscillating environmental conditions. By integrating metabarcoding and metagenomic approaches, we reported that CSP1–5 is prevalent in the sediment samples from Santos Basin slope, indicating the potential importance of methanol metabolism in this region. Finally, using a phylogenetic approach integrating 16S rRNA sequences assigned to Methylomirabilota in this study with those from a public database, we argued that CSP1–5 public sequences might be misclassified as Methylomirabilaceae (the methanotrophic clade) and, therefore, the role of these organisms and the methanol cycling could also be neglected in other environments.