Miracle-dz/UniFAR-FTUs huggingface dataset:
Constraints on Cosmological and Galaxy Parameters from Strong Gravitational Lensing Systems

Strong gravitational lensing along with the distance sum rule method can constrain both cosmological parameters as well as density profiles of galaxies without assuming any fiducial cosmological model. To constrain galaxy parameters and cosmic curvature, we use a newly compiled database of $161$ galactic scale strong lensing systems for distance ratio data. For the luminosity distance in the distance sum rule method, we use databases of supernovae type-Ia (Pantheon) and Gamma Ray Bursts (GRBs). We use a general lens model, namely the Extended Power-Law lens model. We consider three different parametrisations of mass density power-law index $(\gamma)$ to study the dependence of $\gamma$ on redshift. We find that parametrisations of $\gamma$ have a negligible impact on the best fit value of cosmic curvature parameter. Furthermore, measurement of time delay can provide a promising cosmographic probe via the "time delay distance" that includes the ratio of distances between the observer, lens and the source. We use the distance sum rule method with $12$ datapoints of time-delay distance data to put constraints on the Cosmic Distance Duality Relation (CDDR) and the cosmic curvature parameter. For this we consider three different parametrisations of distance duality parameter $(\eta)$. Our results indicate that a flat universe can be accommodated within $95\%$ confidence level for all the parametrisations of $\eta$. Further, we find that within 95\% confidence level, there is no violation of CDDR if $\eta$ is assumed to be redshift dependent but CDDR is violated if $\eta$ is considered redshift independent. Hence, we need a larger sample of strong gravitational lensing systems in order to improve the constraints on the cosmic curvature and distance duality parameter.
Disorder and magnetoconductivity in tilted Weyl semimetals

Gapless Weyl semimetals (WSMs) are a novel class of topological materials that host massless Weyl fermions as their low-energy excitations. When the Weyl cone is tilted, the Lorentz invariance is broken and the Lifshitz transition drives the system from type-I WSMs into type-II WSMs. Here, based on the lattice model, we perform a systematic numerical study of the effect of on-site disorder on the diagonal magnetoconductivity in tilted WSMs. We use the self-consistent Born approximation to calculate the disorder-induced self-energy and then apply the Kubo-Streda formula to calculate the diagonal magnetoconductivity. For the transverse magnetoconductivity ${\ensuremath{\sigma}}_{xx}$, the disorder is found to exhibit distinct effects in the quantum limit regime and in the quantum oscillation regime of type-I WSMs, which could be understood from Einstein's relationship. With strong disorder, ${\ensuremath{\sigma}}_{xx}$ shows a linear relation with the inverse magnetic field $\frac{1}{B}$, which exhibits certain robustness to both the Fermi energy and the Weyl cone tilting. For the longitudinal magnetoconductivity ${\ensuremath{\sigma}}_{zz}$, the strong disorder can break the positive magnetoconductivity as well as the Shubnikov--de Haas oscillations. By analyzing the spectral function, we find that the chiral anomaly is still preserved at strong disorder even when the Weyl cone is overtilted, as there is no gap opening around the Weyl nodes. The implications of our results for experiments are discussed.
Fast Fair Regression via Efficient Approximations of Mutual Information

Most work in algorithmic fairness to date has focused on discrete outcomes, such as deciding whether to grant someone a loan or not. In these classification settings, group fairness criteria such as independence, separation and sufficiency can be measured directly by comparing rates of outcomes between subpopulations. Many important problems however require the prediction of a real-valued outcome, such as a risk score or insurance premium. In such regression settings, measuring group fairness criteria is computationally challenging, as it requires estimating information-theoretic divergences between conditional probability density functions. This paper introduces fast approximations of the independence, separation and sufficiency group fairness criteria for regression models from their (conditional) mutual information definitions, and uses such approximations as regularisers to enforce fairness within a regularised risk minimisation framework. Experiments in real-world datasets indicate that in spite of its superior computational efficiency our algorithm still displays state-of-the-art accuracy/fairness tradeoffs.
Unraveling nanotopography of cell surface receptors

Cells communicate with their environment via surface receptors, but nanoscopic receptor organization with respect to complex cell surface morphology remains unclear. This is mainly due to a lack of accessible, robust and high-resolution methods. Here, we present an approach for mapping the topography of receptors at the cell surface with nanometer precision. The method involves coating glass coverslips with glycine, which preserves the fine membrane morphology while allowing immobilized cells to be positioned close to the optical surface. We developed an advanced and simplified algorithm for the analysis of single-molecule localization data acquired in a biplane detection scheme. These advancements enable direct and quantitative mapping of protein distribution on ruffled plasma membranes with near isotropic 3D nanometer resolution. As demonstrated successfully for CD4 and CD45 receptors, the described workflow is a straightforward quantitative technique to study molecules and their interactions at the complex surface nanomorphology of differentiated metazoan cells.
Combined Silicon-Phosphorus Fertilization Affects the Biomass and Phytolith Stock of Rice Plants

Phytoliths are silica bodies formed in living plant tissues. Once deposited in soils through plant debris, they can readily dissolve and then increase the fluxes of silicon (Si) toward plants and/or watersheds. These fluxes enhance Si ecological services in agricultural and marine ecosystems through their impact on plant health and carbon fixation by diatoms, respectively. Fertilization increases crop biomass through the supply of plant nutrients, and thus may enhance Si accumulation in plant biomass. Si and phosphorus (P) fertilization enhance rice crop biomass, but their combined impact on Si accumulation in plants is poorly known. Here, we study the impact of combined Si-P fertilization on the production of phytoliths in rice plants. The combination of the respective supplies of 0.52 g Si kg–1 and 0.20 g P kg−1 generated the largest increase in plant shoot biomass (leaf, flag leaf, stem, and sheath), resulting in a 1.3-fold increase compared the control group. Applying combined Si-P fertilizer did not affect the content of organic carbon (OC) in phytoliths. However, it increased plant available Si in soil, plant phytolith content and its total stock (mg phytolith pot−1) in dry plant matter, leading to the increase of the total amount of OC within plants. In addition, P supply increased rice biomass and grain yield. Through these positive effects, combined Si-P fertilization may thus address agronomic (e.g., sustainable ecosystem development) and environmental (e.g., climate change) issues through the increase in crop yield and phytolith production as well as the promotion of Si ecological services and OC accumulation within phytoliths.
Brain Resting-State Network Alterations Associated With Crohn's Disease

Inflammatory bowel disease (IBD) is a chronic disease that is associated with aspects of brain anatomy and activity. In this preliminary MRI study, we investigated differences in brain structure and in functional connectivity (FC) of brain regions in 35 participants with Crohn's disease (CD) and 21 healthy controls (HC). Voxel-based morphometry (VBM) analysis was performed to contrast CD and HC structural images. Region of interest (ROI) analyses were run to assess FC for resting-state network nodes. Independent component analysis (ICA) identified whole brain differences in FC associated with resting-state networks. Though no structural differences were found, ROI analyses showed increased FC between the frontoparietal (FP) network and salience network (SN), and decreased FC between nodes of the default mode network (DMN). ICA results revealed changes involving cerebellar (CER), visual (VIS), and SN components. Differences in FC associated with sex were observed for both ROI analysis and ICA. Taken together, these changes are consistent with an influence of CD on the brain and serve to direct future research hypotheses.
Intracellular Recording of Human Cardiac Action Potentials on Market-Available Multielectrode Array Platforms

High quality attenuated intracellular action potentials from large cell networks can be recorded on multi-electrode arrays by means of 3D vertical nanopillars using electrical pulses. However, most of the techniques require complex 3D nanostructures that prevent the straightforward translation into marketable products and the wide adoption in the scientific community. Moreover, 3D nanostructures are often delicate objects that cannot sustain several harsh use/cleaning cycles. On the contrary, laser optoacoustic poration allows the recording of action potentials on planar nanoporous electrodes made of noble metals. However, these constraints of the electrode material and morphology may also hinder the full exploitation of this methodology. Here, we show that optoacoustic poration is also very effective for porating cells on a large family of MEA electrode configurations, including robust electrodes made of nanoporous titanium nitride or disordered fractal-like gold nanostructures. This enables the recording of high quality cardiac action potentials in combination with optoacoustic poration, providing thus attenuated intracellular recordings on various already commercial devices used by a significant part of the research and industrial communities.
Monanchocidin A From Subarctic Sponges of the Genus Monanchora and Their Promising Selectivity Against Melanoma in vitro

Marine sources have long been known for their potential to produce unique skeletons and various biological activities. Fractionation of the ethanol extracts of an undescribed species of Monanchora Carter, 1883 and a specimen closely comparable to Monanchora pulchra (Lambe, 1894/1895) (Class Demospongiae, Order Poecilosclerida, Family Crambeidae), yielded a known compound, monanchocidin A. Monanchocidin A, a secondary metabolite, showed very modest antibacterial, antifungal, and antiprotozoal activities with IC50 values ranging between 255.75 and 7288.92 μM. Monanchocidin A also exhibited potent selective activity for the melanoma panel in the NCI cancer cell screening panel.
The Cytochrome P450 Monooxygenase Inventory of Grapevine (Vitis vinifera L.): Genome-Wide Identification, Evolutionary Characterization and Expression Analysis

The cytochrome P450 (CYP) monooxygenase superfamily, belonging to heme-thiolate protein products, plays a vital role in metabolizing physiologically valuable compounds in plants. To date, CYP superfamily genes have not yet been characterized in grapevine (V. vinifera L.), and their functions remain unclear. In this study, a sum of 236 VvCYPs, divided into 46 families and clustered into nine clans, have been identified based on bioinformatics analyses in grapevine genome. The characteristics of both exon–intron organizations and motif structures further supported the close evolutionary relationships of VvCYP superfamily as well as the reliability of phylogenetic analysis. The gene number-based hierarchical cluster of CYP subfamilies of different plants demonstrated that the loss of CYP families seems to be limited to single species or single taxa. Promoter analysis elucidated various cis-regulatory elements related to phytohormone signaling, plant growth and development, as well as abiotic/biotic stress responses. The tandem duplication mainly contributed to the expansion of the VvCYP superfamily, followed by singleton duplication in grapevine. Global RNA-sequencing data of grapevine showed functional divergence of VvCYPs as diverse expression patterns of VvCYPs in various organs, tissues, and developmental phases, which were confirmed by quantitative real-time reverse transcription PCR (qRT-PCR). Taken together, our results provided valuable inventory for understanding the classification and biological functions of the VvCYPs and paved the way for further functional verification of these VvCYPs and are helpful to grapevine molecular breeding.
Host and Microbial Tryptophan Metabolic Profiling in Multiple Sclerosis

Multiple sclerosis (MS) is an autoimmune disease of the central nervous system (CNS) that is associated with demyelination and neuronal loss. Over recent years, the immunological and neuronal effects of tryptophan (Trp) metabolites have been largely investigated, leading to the hypothesis that these compounds and the related enzymes are possibly involved in the pathophysiology of MS. Specifically, the kynurenine pathway of Trp metabolism is responsible for the synthesis of intermediate products with potential immunological and neuronal effects. More recently, Trp metabolites, originating also from the host microbiome, have been identified in MS, and it has been shown that they are differently regulated in MS patients. Here, we sought to discuss whether, in MS patients, a specific urinary signature of host/microbiome Trp metabolism can be potentially identified so as to select novel biomarkers and guide toward the identification of specific metabolic pathways as drug targets in MS.
Acoustic Change Responses to Amplitude Modulation in Cochlear Implant Users: Relationships to Speech Perception

Objectives The ability to understand speech is highly variable in people with cochlear implants (CIs) and to date, there are no objective measures that identify the root of this discrepancy. However, behavioral measures of temporal processing such as the temporal modulation transfer function (TMTF) has previously found to be related to vowel and consonant identification in CI users. The acoustic change complex (ACC) is a cortical auditory-evoked potential response that can be elicited by a “change” in an ongoing stimulus. In this study, the ACC elicited by amplitude modulation (AM) change was related to measures of speech perception as well as the amplitude detection threshold in CI users. Methods Ten CI users (mean age: 50 years old) participated in this study. All subjects participated in behavioral tests that included both speech and amplitude modulation detection to obtain a TMTF. CI users were categorized as “good” (n = 6) or “poor” (n = 4) based on their speech-in noise score (<50%). 64-channel electroencephalographic recordings were conducted while CI users passively listened to AM change sounds that were presented in a free field setting. The AM change stimulus was white noise with four different AM rates (4, 40, 100, and 300 Hz). Results Behavioral results show that AM detection thresholds in CI users were higher compared to the normal-hearing (NH) group for all AM rates. The electrophysiological data suggest that N1 responses were significantly decreased in amplitude and their latencies were increased in CI users compared to NH controls. In addition, the N1 latencies for the poor CI performers were delayed compared to the good CI performers. The N1 latency for 40 Hz AM was correlated with various speech perception measures. Conclusion Our data suggest that the ACC to AM change provides an objective index of speech perception abilities that can be used to explain some of the variation in speech perception observed among CI users.
Sequential Surgical Procedures in Vascular Surgery Patients Are Associated With Perioperative Adverse Cardiac Events

Patients at elevated cardiovascular risk are prone to perioperative cardiovascular complications, like myocardial injury after non-cardiac surgery (MINS). We have demonstrated in a mouse model of atherosclerosis that perioperative stress leads to an increase in plaque volume and higher plaque vulnerability. Regulatory T cells (Tregs) play a pivotal role in development and destabilization of atherosclerotic plaques. For this exploratory post-hoc analysis we identified 40 patients recruited into a prospective perioperative biomarker study, who within the inclusion period underwent sequential open vascular surgery. On the basis of protein markers measured in the biomarker study, we evaluated the perioperative inflammatory response in patients' plasma before and after index surgery as well as before and after a second surgical procedure. We also analyzed available immunohistochemistry samples to describe plaque vulnerability in patients who underwent bilateral carotid endarterectomy (CEA) in two subsequent surgical procedures. Finally, we assessed if MINS was associated with sequential surgery. The inflammatory response of both surgeries was characterized by postoperative increases of interleukin-6,−10, Pentraxin 3 and C-reactive protein with no clear-cut difference between the two time points of surgery. Plaques from CEA extracted during the second surgery contained less Tregs, as measured by Foxp3 staining, than plaques from the first intervention. The 2nd surgical procedure was associated with MINS. In conclusion, we provide descriptive evidence that sequential surgical procedures involve repeat inflammation, and we hypothesize that elevated rates of cardiovascular complications after the second procedure could be related to reduced levels of intraplaque Tregs, a finding that deserves confirmatory testing and mechanistic exploration in future populations.
Antiangiogeneic Strategies in Mesothelioma

There is a strong rationale for inhibiting angiogenesis in mesothelioma. Vascular endothelial growth factor (VEGF) is an autocrine growth factor in mesothelioma and a potent mitogen for mesothelial cells. Further, the abnormal tumor vasculature promotes raised interstitial pressure and hypoxia, which may be detrimental to both penetration and efficacy of anticancer agents. Antiangiogenic agents have been trialed in mesothelioma for close to two decades, with early phase clinical trials testing vascular targeting agents, the VEGF-A targeting monoclonal antibody bevacizumab, and numerous tyrosine kinase inhibitors, many with multiple targets. None of these have shown efficacy which has warranted further development as single agents in any line of therapy. Whilst a randomized phase II trial combining the multitargeted tyrosine kinase inhibitor nintedanib with platinum/pemetrexed chemotherapy was positive, these results were not confirmed in a subsequent phase III study. The combination of cisplatin and pemetrexed with bevacizumab, in appropriately selected patients, remains the only anti-angiogenic combination showing efficacy in mesothelioma. Extensive efforts to identify biomarkers of response have not yet been successful.
Strategies to Dissect Host-Microbial Immune Interactions That Determine Mucosal Homeostasis vs. Intestinal Inflammation in Gnotobiotic Mice

When identifying the key immunologic-microbial interactions leading to either mucosal homeostasis in normal hosts or intestinal inflammatory responses in genetically susceptible individuals, it is important to not only identify microbial community correlations but to also define the functional pathways involved. Gnotobiotic rodents are a very effective tool for this purpose as they provide a highly controlled environment in which to identify the function of complex intestinal microbiota, their individual components, and metabolic products. Herein we review specific strategies using gnotobiotic mice to functionally evaluate the role of various intestinal microbiota in host responses. These studies include basic comparisons between host responses in germ-free (GF), specific-pathogen-free or conventionally raised wild-type mice or those with underlying genetic susceptibilities to intestinal inflammation. We also discuss what can be learned from studies in which GF mice are colonized with single wild-type or genetically-modified microbial isolates to examine the functions of individual bacteria and their targeted bacterial genes, or colonized by multiple defined isolates to determine interactions between members of defined consortia. Additionally, we discuss studies to identify functions of complex microbial communities from healthy or diseased human or murine hosts via fecal transplant into GF mice. Finally, we conclude by suggesting ways to improve studies of immune-microbial interactions using gnotobiotic mice.
LINC00346 Acts as a Competing Endogenous RNA Regulating Development of Hepatocellular Carcinoma via Modulating CDK1/CCNB1 Axis

Hepatocellular carcinoma (HCC) is one of the important types of liver cancer. LncRNA is an important regulatory factor that regulates many biological processes such as tumor cells during tumorigenesis and metastasis. LINC00346 has been associated with various types of liver cancer, but its role and regulatory mechanism in HCC remain unclear. In our study, we found the LINC00356-miR-199a-3p-CDK1/CCNB1 axis through bioinformatics analysis. The expressions of LINC00356, miR-199a-3p, CDK1, and CCNB1 in HCC and normal hepatocytes were determined by qRT-PCR and WB. The results showed that LINC00356, CDK1 and CCNB1 were highly expressed in HCC, while miR-199a-3p was lowly expressed. Dual luciferase reporter gene assay, RIP and RNA-pull down assays demonstrated the targeted binding relationship of LINC00346-miR-199a-3p-CDK1/CCNB1. Overexpressing LINC00460 and silencing miR-199a-3p promoted cell invasion, inhibited apoptosis of HCC, and arrested the cell cycle in S phase while opposite results were obtained when silencing LINC00346, CDK1, and CCNB1. LINC00346 indirectly affects liver cancer by promoting the expression of CDK1/CCNB1 through competitive adsorption of miR-199a-3p. In addition, the study also demonstrated that overexpression of LINC00346 indirectly inhibited the expression of p53 and p21 proteins by promoting CDK1/CCNB1 expressions, thereby blocking the p53 signaling pathway. These results proved that LINC00346 could regulate the expression of CDK1/CCNB1 through the competitive adsorption of miR-199a-3p, thereby affecting the p53 signaling pathway and finally regulating the apoptosis, invasion and cell cycle of HCC cells. In conclusion, LINC00346 can be used as a tumor promoter and potential therapeutic target for HCC metastasis and prognosis.
Syndecans in Inflammation at a Glance

Syndecans are transmembrane proteoglycans with heparan and chondroitin sulfate chains attached to their extracellular domain. Like many proteoglycans, they interact with a large number of ligands, such as growth factors, adhesion receptors, soluble small molecules, proteinases, and other extracellular matrix proteins to initiate downstream signaling pathways. Syndecans play a major role in inflammation, mainly by regulating leukocyte extravasation and cytokine function. At the same time, syndecans can undergo cytokine mediated changes in their expression levels during inflammation. The function of syndecans during inflammation appears to depend on the stage of inflammation, sulfation of heparan/chondroitin sulfate chains, the rate of ectodomain shedding and the solubility of the ectodomains. From the current literature, it is clear that syndecans are not only involved in the initial recruitment of pro-inflammatory molecules but also in establishing a balanced progression of inflammation. This review will summarize how cell surface and soluble syndecans regulate multiple aspects of inflammation.