Miracle-dz/UniFAR-FTUs huggingface dataset:
Noncommutative dispersion relation and mass-radius relation of white dwarfs

The equation of state of the electron degenerate gas in a white dwarf is usually treated by employing the ideal dispersion relation. However, the effect of quantum gravity is expected to be inevitably present and when this effect is considered through a non-commutative formulation, the dispersion relation undergoes a substantial modification. In this paper, we take such a modified dispersion relation and find the corresponding equation of state for the degenerate electron gas in white dwarfs. Hence we solve the equation of hydrostatic equilibrium and find that this leads to the possibility of the existence of excessively high values of masses exceeding the Chandrasekhar limit, although the quantum gravity effect is taken to be very small. It is only when we impose the additional effect of neutronization that we obtain white dwarfs with masses close to the Chandrasekhar limit with nonzero radii at the neutronization threshold. We demonstrate these results by giving numerical estimates for the masses and radii of helium, carbon and oxygen white dwarfs.
Regularized Ultrasound Phantom-Free Local Attenuation Coefficient Slope (ACS) Imaging in Homogeneous and Heterogeneous Tissues

Attenuation maps or measurements based on the local attenuation coefficient slope (ACS) in quantitative ultrasound (QUS) have shown potential for the diagnosis of liver steatosis. In liver cancers, tissue abnormalities and tumors detected using ACS are also of interest to provide new image contrast to clinicians. Current phantom-based approaches have the limitation of assuming a comparable speed of sound between the reference phantom and insonified tissues. Moreover, these methods present the inconvenience for operators to acquire data on phantoms and patients. The main goal was to alleviate these drawbacks by proposing a methodology for constructing phantom-free regularized (PF-R) local ACS maps and investigate the performance in both homogeneous and heterogeneous media. The proposed method was tested on two tissue-mimicking media with different ACS constructed as homogeneous phantoms, side-by-side and top-to-bottom phantoms, and inclusion phantoms with different attenuations. Moreover, an in vivo proof-of-concept was performed on healthy, steatotic, and cancerous human liver datasets. Modifications brought to previous works include: 1) a linear interpolation of the power spectrum in the log scale; 2) the relaxation of the underlying hypothesis on the diffraction factor; 3) a generalization to nonhomogeneous local ACS; and 4) an adaptive restriction of frequencies to a more reliable range than the usable frequency range. Regularization was formulated as a generalized least absolute shrinkage and selection operator (LASSO), and a variant of the Bayesian information criterion (BIC) was applied to estimate the Lagrangian multiplier on the LASSO constraint. In addition, we evaluated the proposed algorithm when applying median filtering before and after regularization. Tests conducted showed that the PF-R yielded robust results in all tested conditions, suggesting potential for additional validation as a diagnosis method.
Network pharmacology and molecular docking analysis on the mechanism of Baihe Zhimu decoction in the treatment of postpartum depression

Baihe Zhimu decoction (BZD) has significant antidepressant properties and is widely used to treat mental diseases. However, the multitarget mechanism of BZD in postpartum depression (PPD) remains to be elucidated. Therefore, the aim of this study was to explore the molecular mechanisms of BDZ in treating PPD using network pharmacology and molecular docking. Active components and their target proteins were screened from the traditional Chinese Medicine Systems Pharmacology Database and Analysis Platform (TCMSP). The PPD-related targets were obtained from the OMIM, CTD, and GeneCards databases. After overlap, the targets of BZD against PPD were collected. Protein–protein interaction (PPI) network and core target analyses were conducted using the STRING network platform and Cytoscape software. Moreover, molecular docking methods were used to confirm the high affinity between BZD and targets. Finally, the DAVID online tool was used to perform gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis of overlapping targets. The TCMSP database showed that BZD contained 23 active ingredients in PPD. KEGG analysis showed that overlapping genes were mainly enriched in HIF-1, dopaminergic synapses, estrogen, and serotonergic synaptic signalling pathways. Combining the PPI network and KEGG enrichment analysis, we found that ESR1, MAOA, NR3C1, VEGFA, and mTOR were the key targets of PPD. In addition, molecular docking confirmed the high affinity between BZD and the PPD target. Verified by a network pharmacology approach based on data mining and molecular docking methods, the multi-target drug BZD may serve as a promising therapeutic candidate for PPD, but further in vivo/in vitro experiments are needed.
Primary hepatocyte urea assessment in the sodium-alginate patterned hydrogel by electrochemical procedure containing umbilical cord conditioned media

Limitations in liver transplantation and advances in cell therapy methods motivated us to study primary hepatocytes. The main challenge in using primary hepatocytes for liver regeneration is that they lose their functionalities. We aimed to develop a controlled-shape hydrogel and apply the conditioned-media of mesenchymal stromal cells (CM-MSCs) to improve in vitro hepatocyte functions. In this experimental study, following rat hepatocyte isolation by collagenase perfusion and collection of human umbilical cord CM-MSCs, a simple and precise system called electrodeposition was used to produce the patterned alginate hydrogel. To reduce the cytopathic effects, we used an indirect electrodeposition method. For characterizing this structure, mechanical properties, Fourier-transform infrared spectroscopy (FTIR), water uptake, in-vitro degradation, and hydrogel stability were studied. Urea synthesis as a basic function of hepatocytes was assessed in five different groups. Scanning electron microscope (SEM) was utilized to evaluate the primary hepatocyte morphology and their dispersion in the fabricated structure. We observed a significant increase in urea synthesis in the presence of CM-MSCs in patterned hydrogel alginate compared to 2D culture on day 3 (p<0.05). However, there was no significant difference in simple and patterned hydrogel on day 2. We found that the electrodeposition method is appropriate for the rapid fabricating of hydrogel structures with arbitrary patterns for 3D cell culture.
North American House Sparrows Are Competent for Usutu Virus Transmission

Usutu virus (USUV) is a zoonotic mosquito-borne virus that can cause neuroinvasive disease, including meningitis and encephalitis, in humans and has resulted in hundreds of thousands of deaths in wild birds. The perpetuation of USUV in nature is dependent on transmission between Culex spp. mosquitoes and various avian species. ABSTRACT Usutu virus (USUV, Flaviviridae) is an emerging mosquito-borne virus that has been implicated in neuroinvasive disease in humans and epizootic deaths in wild birds. USUV is maintained in an enzootic cycle between ornithophilic mosquitoes, primarily Culex spp. , and wild birds, predominantly passerine species. However, limited experimental data exist on the species competent for USUV transmission. Here, we demonstrate that house sparrows are susceptible to multiple USUV strains. Our study also revealed that Culex quinquefasciatus mosquitoes are susceptible to USUV, with a significantly higher infection rate for the Netherlands 2016 USUV strain compared to the Uganda 2012 USUV strain at 50% and 19%, respectively. To assess transmission between avian host and mosquito vector, we allowed mosquitoes to feed on either juvenile chickens or house sparrows inoculated with USUV. Both bird models transmitted USUV to C. quinquefasciatus mosquitoes. Linear regression analyses indicated that C. quinquefasciatus infection rates were positively correlated with avian viremia levels, with 3 to 4 log10 PFU/mL representing the minimum avian viremia threshold for transmission to mosquitoes. Based on the viremia required for transmission, house sparrows were estimated to more readily transmit the Netherlands 2016 strain compared to the Uganda 2012 strain. These studies provide insights on a competent reservoir host of USUV. IMPORTANCE Usutu virus (USUV) is a zoonotic mosquito-borne virus that can cause neuroinvasive disease, including meningitis and encephalitis, in humans and has resulted in hundreds of thousands of deaths in wild birds. The perpetuation of USUV in nature is dependent on transmission between Culex spp. mosquitoes and various avian species. To date, few experimental data exist for determining which bird species are important for the maintenance of USUV. Our studies showed that house sparrows can transmit infectious Usutu virus, indicating their role as a competent host species. By identifying reservoir species of USUV, we can predict areas of USUV emergence and mitigate its impacts on global human and wildlife health.
Is a top-heavy initial mass function needed to reproduce the submillimetre galaxy number counts?

Matching the number counts and redshift distribution of submillimeter galaxies (SMGs) without invoking modifications to the initial mass function (IMF) has proved challenging for semi-analytic models (SAMs) of galaxy formation. We adopt a previously developed SAM that is constrained to match the z=0 galaxy stellar mass function and makes various predictions that agree well with observational constraints; we do not recalibrate the SAM for this work. We implement three prescriptions to predict the submillimeter flux densities of the model galaxies; two depend solely on star formation rate, whereas the other also depends on the dust mass. By comparing the predictions of the models, we find that taking into account the dust mass, which affects the dust temperature and thus influences the far-infrared spectral energy distribution, is crucial for matching the number counts and redshift distribution of SMGs. Moreover, despite using a standard IMF, our model can match the observed SMG number counts and redshift distribution reasonably well, which contradicts the conclusions of some previous studies that a top-heavy IMF, in addition to taking into account the effect of dust mass, is needed to match these observations. Although we have not identified the key ingredient that is responsible for our model matching the observed SMG number counts and redshift distribution without IMF variation- which is challenging given the different prescriptions for physical processes employed in the SAMs of interest-our results demonstrate that in SAMs, IMF variation is degenerate with other physical processes, such as stellar feedback.
Countering Narrative Misinformation: Investigating the Effects of Narrative Corrections and Character Trust on Story-Related Knowledge of HPV

ABSTRACT Guided by the entertainment overcoming resistance model (EORM), participants (N = 334) were exposed to narrative correction strategies designed to reduce reliance on a character that portrayed misinformation about HPV within a narrative. In a 2 × 2 experiment, participants were randomly assigned to either read a warning about an untrustworthy character or a description of the show and to view a post-show video where hosts discussed the motives and actions of that character or a control clip. Both narrative correction strategies reduced individuals’ trust of the protagonist and, in turn, increased the number of correct answers on an HPV knowledge test. Identification moderated the indirect relationship between exposure to the post-show discussion and HPV knowledge. For those who reported greater identification with the protagonist, the post-show discussion reduced character trust whereas those who reported low identification were not impacted by this narrative correction strategy. The effect of the pre-show warning did not depend on level of identification. The results build on previous studies concerning narrative correction strategies as well as extend the EORM to narrative correction outcomes.
GenomicKB: a knowledge graph for the human genome

Abstract Genomic Knowledgebase (GenomicKB) is a graph database for researchers to explore and investigate human genome, epigenome, transcriptome, and 4D nucleome with simple and efficient queries. The database uses a knowledge graph to consolidate genomic datasets and annotations from over 30 consortia and portals, including 347 million genomic entities, 1.36 billion relations, and 3.9 billion entity and relation properties. GenomicKB is equipped with a web-based query system (https://gkb.dcmb.med.umich.edu/) which allows users to query the knowledge graph with customized graph patterns and specific constraints on entities and relations. Compared with traditional tabular-structured data stored in separate data portals, GenomicKB emphasizes the relations among genomic entities, intuitively connects isolated data matrices, and supports efficient queries for scientific discoveries. GenomicKB transforms complicated analysis among multiple genomic entities and relations into coding-free queries, and facilitates data-driven genomic discoveries in the future.
Microstructural and heavy metal analysis of gallstones prevalent in Jharkhand and its implications in the treatment

ABSTRACT Objectives In the present study the structural and compositional analysis of gallstones was carried out by various characterization techniques. Also, the utility of the study was evaluated on how the findings can enhance the treatment and dissolution therapies of gallstones? Methods Gallstones from the Jharkhand region were analyzed both structurally as well as chemically using Field emission scanning electron microscope (FESEM) and Energy-dispersive X-ray spectroscopy, inductively coupled optical emission spectrometry (ICP-OES), Carbon hydrogen and nitrogen analyzer (CHNS), Nuclear magnetic resonance (NMR), Thermal gravimetric analysis (TGA) and Differential Thermal Analysis (DTA) and other instruments. The content of heavy metal was represented statistically as a mean with standard deviation. Results FESEM analysis unveiled the crystal and globular structure of cholesterol and pigment gallstones respectively. Through ICP-OES analysis metals such as Fe, Mn, Cu, Pb, Cr, Zn etc. were detected in gallstones. FTIR and XRD analysis confirmed the presence of cholesterol and calcium carbonate and other compounds in mixed stones and calcium bilirubinate and bilirubin in pigment gallstones. NMR analysis revealed the presence of monohydrate cholesterol (Crystalline) in Cholesterol and mixed gallstones. Mixed gallstones were found to be predominant in this region in contrast to pigmented stones that were prevalent earlier. Conclusion The present study uncovered the current composition and content of different heavy metals in gallstones of Jharkhand region which can be instrumental in enhancing the dissolution therapies for gallstone treatment. This can serve as a major tool for practitioners for gallstone treatment and change the way they are looked at. Graphical Abstract
Quasiparticle bound states and low-temperature peaks of the conductance of NIS junctions in d-wave superconductors

Contributions of quasiparticle states, bound to the boundary of anisotropically paired superconductors, to the density of states and to the conductance of normal-metal{endash}insulator{endash}superconduction (NIS) junctions are studied both analytically and numerically. For smooth surfaces and real order parameters, we find some general results for the bound-state energies. In particular, we show that under fairly general conditions quasiparticle states with nonzero energies exist for momentum directions within a narrow region around the surface normal. The energy dispersion of the bound states always has an extremum for the direction along the normal. Along with the zero-bias anomaly due to midgap states, we find, for quasi-two-dimensional materials, additional low-temperature peaks in the conductance of NIS junctions for voltages determined by the extrema of the bound-state energies. The influence of interface roughness on the conductance is investigated within the framework of Ovchinnikov{close_quote}s model. We show that nonzero-bias peaks at low temperatures may give information on the order parameter in the bulk, even though it is suppressed at the surface. {copyright} {ital 1997} {ital The American Physical Society}
Ocular findings and a comparative study of hair, skin and iris color in Chinese patients with albinism

ABSTRACT Background Oculocutaneous albinism (OCA) could be either non-syndromic or syndromic. There are significant challenges in clinically recognizing and differentiating Hermansky-Pudlak syndrome (HPS) from non-syndromic OCA. Materials and Methods In a prospective consecutive case series, 63 patients (less than 18 years old) with a molecular genetic diagnosis of albinism (except OCA1A), Ocular albinism (OA) and Hermansky-Pudlak syndrome seen over a 3-year period were evaluated and analyzed. Hair colour, iris colour was graded, compared and correlated with the degree of fundus pigmentation and foveal development. Results A total of 63 patients were evaluated. Forty-five patients had non-syndromic OCA (11 OCA1B, 24 OCA2, 9 OCA4, and 1 OCA6), 5 patients had OA and 13 patients had HPS. All 3 BLOC-related HPS categories were seen (1 with BLOC1, 7 with BLOC-2 and 5 with BLOC-3 related HPS). All patients with OA were hyperopic, had darker fundus pigmentation, but had poor foveal development. All HPS patients had lighter fundus pigmentation. The degree of fundus pigmentation correlated positively with the iris pigmentation and also with the foveal development only in OCA2. Conclusions Careful observation of the phenotype by comparison of the skin, hair, iris colour, with the degree of fundus pigmentation and foveal development may help clinically differentiate HPS from OCA patients of Chinese ethnicity even in the absence of any bleeding tendency.
Simultaneous multiple-stimulus auditory brain–computer interface with semi-supervised learning and prior probability distribution tuning

Objective. Auditory brain–computer interfaces (BCIs) enable users to select commands based on the brain activity elicited by auditory stimuli. However, existing auditory BCI paradigms cannot increase the number of available commands without decreasing the selection speed, because each stimulus needs to be presented independently and sequentially under the standard oddball paradigm. To solve this problem, we propose a double-stimulus paradigm that simultaneously presents multiple auditory stimuli. Approach. For addition to an existing auditory BCI paradigm, the best discriminable sound was chosen following a subjective assessment. The new sound was located on the right-hand side and presented simultaneously with an existing sound from the left-hand side. A total of six sounds were used for implementing the auditory BCI with a 6 × 6 letter matrix. We employ semi-supervised learning (SSL) and prior probability distribution tuning to improve the accuracy of the paradigm. The SSL method involved updating of the classifier weights, and their prior probability distributions were adjusted using the following three types of distributions: uniform, empirical, and extended empirical (e-empirical). The performance was evaluated based on the BCI accuracy and information transfer rate (ITR). Main results. The double-stimulus paradigm resulted in a BCI accuracy of 67.89 ± 11.46% and an ITR of 2.67 ± 1.09 bits min−1, in the absence of SSL and with uniform distribution. The proposed combination of SSL with e-empirical distribution improved the BCI accuracy and ITR to 74.59 ± 12.12% and 3.37 ± 1.27 bits min−1, respectively. The event-related potential analysis revealed that contralateral and right-hemispheric dominances contributed to the BCI performance improvement. Significance. Our study demonstrated that a BCI based on multiple simultaneous auditory stimuli, incorporating SSL and e-empirical prior distribution, can increase the number of commands without sacrificing typing speed beyond the acceptable level of accuracy.
An Adaptive Threshold Algorithm for Joint Sparse Recovery

This paper presents a new greedy algorithm for joint sparse recovery, called adaptive threshold simultaneous orthogonal matching pursuit (AT-SOMP). In this algorithm, an adaptive threshold is designed based on subspace decomposition to stop the iterative process, during which the support of target signal is identified iteratively just like the simultaneous orthogonal matching pursuit (S-OMP) algorithm. As the adaptive threshold can change with the noise power adaptively, the proposed algorithm is applied to the situation that both the sparsity and SNR of the target signal are unknown. Experiments validate that in this situation the proposed algorithm has a better recovery performance than those methods with a fixed threshold. Keywords-compressed sensing; joint sparse recovery; adaptive threshold; simultaneous orthogonal matching pursuit
Serine/threonine kinase activity associates with brain glucose metabolism changes in Alzheimer's Disease

Positron emission tomography (PET) imaging has greatly improved the diagnosis and monitoring of Alzheimer's disease (AD). The recently developed neuroinformatic field is expanding analytical and computational strategies to study multimodal neuroscience data. One approach is integrating PET imaging and omics to provide new insights into AD pathophysiology. Hippocampal and blood transcriptomic data of cognitively unimpaired (CU) and cognitively impaired (CI) individuals were obtained from Gene Expression Omnibus (GEO) databases and the Alzheimer's Disease Neuroimaging Initiative (ADNI). We used the differentially expressed genes (DEGs) from these datasets to implement a modular dimension reduction approach based on Gene Ontology (GO) and reverse engineering of transcriptional networks centered on transcription factors (TF). GO clusters and regulatory units of TF were selected to undergo integration with [18F]Fluorodeoxyglucose ([18F]FDG)-PET images using voxel-wise linear regression models adjusted for age, gender, years of education, and APOE{epsilon}4 status. The GO semantic similarity resulted in 16 GO clusters enriched with overlapping DEGs in blood and the brain. Voxel-wise analysis revealed a strong association between the cluster related to the regulation of protein serine/threonine kinase activity and the [18F]FDG-PET signal in the brain. The master regulator analysis showed 61 regulatory units of TF significantly enriched with DEGs. The voxel-wise analysis of these regulons showed that zinc-finger-related regulatory units had the closest association with brain glucose metabolism. We identified multiple biological processes and regulatory units of TF associated with [18F]FDG-PET metabolism in the brain of individuals across the aging and AD clinical spectrum. Furthermore, the prominent enrichment of protein serine/threonine kinase activity-related GO cluster and the zinc-finger-related regulatory units highlight the potential gene signatures associated with changes in glucose metabolism due to AD pathology.