Miracle-dz/UniFAR-FTUs huggingface dataset:
Critical evaluation on roles of macrophagic myofasciitis and aluminum adjuvants in HPV vaccine–induced adverse events

Cervical cancer is caused by human papillomavirus (HPV) infection, which is preventable by HPV vaccines. In Japan, the HPV vaccination rate has remained extremely low due to the concerns for alleged neuropsychological symptoms or “diverse symptoms” following injections of two HPV vaccines, Cervarix and Gardasil, in HPV vaccine lawsuits. In the lawsuits, the attorneys' group has used several manuscripts proposing that aluminum (Al) adjuvant contained in HPV vaccines causes an immune‐mediated disease, called macrophagic myofasciitis (MMF), as well as pathology in the central nervous system (CNS). We scientifically evaluated these manuscripts describing the “Al adjuvant–induced pathologies,” particularly MMF. Although MMF patients have been reported to develop clinical symptoms/signs in various organs, including the CNS, muscle biopsy of the patients and animal experiments demonstrated that MMF pathology was localized only at the injected muscle. No muscle pathology which characterizes MMF was observed in any other muscles; thus, the systemic and neurological signs of MMF cases were irrelevant to localized MMF pathology. We evaluated that MMF‐like pathology was induced as a local inflammatory response following vaccinations; MMF pathology was not the cause of systemic inflammation or “diverse symptoms. ” Lastly, MMF cases have been reported after vaccinations with Al‐hydroxide–containing vaccines exclusively. As Al‐hydroxide is a component of Cervarix, but not Gardasil, “diverse symptoms” following two HPV vaccinations in Japan cannot be explained by MMF. Our evaluation would help readers understand the validity of the manuscripts on the role of Al adjuvants or MMF for the alleged “diverse symptoms. ”
Single‐molecule localization microscopy goes quantitative

In the last few years, single‐molecule localization (SMLM) techniques have been used to address biological questions in different research fields. More recently, super‐resolution has also been proposed as a quantitative tool for quantifying protein copy numbers at the nanoscale level. In this scenario, quantitative approaches, mainly based on stepwise photobleaching and quantitative SMLM assisted by calibration standards, offer an exquisite tool for investigating protein complexes. This primer focuses on the basic concepts behind quantitative super‐resolution microscopy, also providing strategies to overcome the technical hurdles that could limit their application.
Detecting changes in spectral shape of complex auditory signals: Profile analysis

This is a review of current theories and recent experimental data on how human listeners detect changes in the spectrum of a complex sound. The effects of parameters such as the number of components in the complex, their density, bandwidth, and whether the components are harmonic or equally spaced in logarithmic frequency will be described. Some new data on how signal duration affects the ability to detect spectral change will also be reviewed. It is believed that three distinct sets of cues mediate the detection of changes in the spectral shape depending on the total bandwidth of the complex. For wide bandwidths, the primary cue is a simultaneous comparison of level over different frequency regions. For spectra that are one or two critical bands in width, the primary cue is a change in pitch. For spectra less than one critical band, the primary cue is a change in the temporal fluctuation or roughness of the sound related to the power spectrum of the envelope.
Silver nanoparticles suppress forskolin-induced syncytialization in BeWo cells

Abstract Opportunities for the exposure of pregnant women to engineered nanoparticles have been increasing with the expanding use of these materials. Therefore, there are concerns that nanoparticles could have adverse effects on the establishment and maintenance of pregnancy. The effects of nanoparticles on the mother and fetus have been evaluated from this perspective, but there is still little knowledge about the effects on placentation and function acquisition, which are essential for the successful establishment and maintenance of pregnancy. Formation of the syncytiotrophoblast is indispensable for the acquisition of placental function, and impairment of syncytialization inevitably affects pregnancy outcomes. Here, we assessed the effect of nanoparticles on placental formation by using forskolin-treated BeWo cells, a typical in vitro model of trophoblast syncytialization. Immunofluorescence staining analysis revealed that silver nanoparticles with a diameter of 10 nm (nAg10) (at 0.156 µg/mL) significantly decreased the proportion of syncytialized BeWo cells, but gold nanoparticles with a diameter of 10 nm did not. Consistently, only nAg10 (at 0.156 µg/mL) significantly suppressed forskolin-induced elevation of CGB and SDC1 mRNA expression levels and human chorionic gonadotropin β production in a dose-dependent manner; these molecules are all markers of syncytialization. Besides, nAg10 significantly decreased the expression of ERVFRD-1, which encodes proteins associated with cell fusion. Moreover, nAg10 tended to suppress the expression of sFlt-1 e15a, a placental angiogenesis marker. Collectively, our data suggest that nAg10 could suppress formation of the syncytiotrophoblast and that induce placental dysfunction and the following poor pregnancy outcomes.
Exiting Patients’ Rooms and Ending Relationships: Questions and Challenges Faced by Hospital Chaplains

These data, the first to explore chaplains' challenges in ending visits/relationships with patients/families, has critical implications for practice, education, and research. Questions arise about the scope/boundaries of chaplains' relationships with patients/families. Interviews were conducted with 23 chaplains who face questions/challenges regarding how to end visits and interactions, including individual conversations and ongoing relationships with patients/families. Chaplains confront uncertainties and rely on verbal- and non-verbal cues to gauge how long to stay with each patient/family, and they are sometimes unsure. These data have critical implications for practice, education, and research.
Reconstruction of the chaotic set from classical cross section data

We study a paradigm of a chaotic scattering system with one open and one closed degree of freedom. We show how the development scenario of the chaotic invariant set is reflected in the changes of the rainbow singularities in the classical cross section. This allows us to reconstruct the actual development stage of the chaotic set from the knowledge of the cross section. We do this by following the rainbow structure of the cross section along a curve in parameter space which connects the case we are interested in with a known case, for example, the case of a complete horseshoe. We conclude with a discussion about the generality of our procedure and of its application to various systems.
Wavelet transcoding in the block discrete cosine transform space

Transcoding in the transform domain avoids inverse transform and re-transform computations. In this paper, discrete cosine transform, the authors propose a new technique for transcoding wavelet coefficients to block discrete cosine transform (DCT) coefficients in the transform domain. In the first step, wavelet coefficients are transformed into upsampled DCT blocks. Subsequently, these transformed blocks are synthesised by filtering in the block DCT space. To reduce the cost of transcoding, the authors perform upsampling and filtering operations in a single combined step. The proposed technique achieves the quality of reconstruction (except rounding errors in processing) as same as the spatial domain technique with reduced complexity for a given wavelet synthesis filter. The proposed technique is based on simple linear operations like matrix multiplication. This makes the algorithm more convenient for efficient hardware implementations. The technique can be used by the DCT-based services when the input data are available as wavelet coefficients.
Behavioral status modulates CA2 influence on hippocampal network dynamics

Dynamic interactions between the subregions of the hippocampus are required for the encoding and consolidation of memory. While the interplay and contributions of the CA1 and CA3 regions are well understood, we continue to learn more about how CA2 differentially contributes to the organization of network function. For example, CA2 place cells have been reported to be less spatially tuned during exploration, but uniquely capable of coding place while an animal stops. Here we applied chemogenetics to transiently silence CA2 pyramidal cells and found that CA2 influences hippocampal dynamics in a state‐dependent manner. We find that during rest, CA2 inhibition reduces synchronization across regions (CA1, CA2, CA3) and frequency bands (low‐gamma‐ and ripple‐band). Moreover, during new learning CA1 place field formation is slower in the absence of CA2 transmission and during pausing, CA1 pyramidal cells are less excitable without CA2 drive. On the network level, a novel convolutional neural network (SpikeDecoder) was employed to show subregion and state‐dependent changes in spatial coding that agree with our observations on the single cell level. Together these data suggest additional novel roles for CA2 in governing and differentiating hippocampal dynamics under discrete behavioral states.
The Functors K -i and Pseudo-Isotopies of Polyhedra

map 9P(X) QWh(X) which is highly connected; and that, in general, there exists a homotopy equivalence 9P(X x Q) -- QWh(X) where Q denotes the Hilbert cube. The latter equivalence depends partly on results of T.A. Chapman [5]. In this paper we study 9P(X) when X is an arbitrary polyhedron. Our
The Self-Concept and Identity Measure in Patients with Personality Disorders: A Psychometric Evaluation and Associations With Identity Processes, Core Domains of Self-Functioning, and Personality Disorder Symptoms

As developmental and clinical research on identity has largely developed in disconnect, scholars recommend adopting a developmental psychopathology perspective on identity, which considers adaptive and pathological identity functioning. Such a perspective has also been introduced in the Diagnostic and Statistical Manual of Mental Disorders (5th ed.; DSM-5) Alternative Model for Personality Disorders (AMPD), which suggests that all personality disorders (PDs) are marked by moderate to extreme deficits in self-functioning (i.e., identity and self-direction). The present study aims to validate the Dutch Self-Concept and Identity Measure (SCIM), a 27-item self-report questionnaire that assesses consolidated identity, disturbed identity, and lack of identity, in 153 psychiatric inpatients with PDs (75.2% female; Mage = 31.73). We investigated the factor structure and reliability of the SCIM, and examined associations of SCIM scales with typical identity processes, AMPD domains of self-functioning, and symptoms of all PDs. Results indicated that a 23-item Dutch SCIM produced valid and reliable scores among patients with PDs. Furthermore, SCIM scales were significantly and differentially related to identity commitment processes, ruminative identity exploration, domains of self-functioning, and symptoms of all PDs. Moreover, findings indicated that PDs varied regarding the severity of identity impairment.
Development of excitation system for a large-area high-pressure CO2-amplifier

Abstract The paper discusses the problem of developing superatmospheric pressure CO2-amplifiers intended to amplify picosecond light pulses. The advantages of the systems for active medium excitation by a soft X-ray preionized self-sustained discharge are demonstrated. The characteristics of the CO2-amplifier with a 5 cm interelectrode gap and a gaseous medium pressure up to 5 atm are presented.
Evaluation of Alfalfa Fields and Pastures as Sources of Spissistilus festinus (Hemiptera: Membracidae): Quantification of Reproductive and Nutritional Parameters

Abstract The threecornered alfalfa hopper (Spissistilus festinus) is a pest of grapevine, with damage caused by transmission of grapevine red blotch virus. Because grapevine is not a preferred host of the threecornered alfalfa hopper, abundance in vineyards depends on proximity to source habitats and presence of preferred hosts in vineyard understories. The potential for alfalfa fields and pastures in the Central Valley of California to serve as sources of threecornered alfalfa hopper was evaluated by quantifying parameters associated with threecornered alfalfa hopper reproductive and nutritional status. Laboratory studies determined that the threecornered alfalfa hopper is synovigenic, emerging as an adult prior to initiation of oogenesis and that females have multiple rounds of egg production. Alfalfa fields, irrigated pastures, and vineyards were sampled monthly. Adults were observed year-round in alfalfa fields and pastures, with populations peaking in fall. Gravid females were observed from February through November. While rare, adult threecornered alfalfa hoppers were collected from 2 of 4 sampled vineyards. In spring, adults were observed in samples collected from vineyard ground cover. In fall, adults were observed in samples collected from vineyard ground cover and foliage samples. Samples collected from pastures and vineyards were male biased, whereas equal numbers of males and females were observed in alfalfa fields. Adults collected from alfalfa fields were larger, heavier, and had greater estimated energetic reserves than adults collected from pastures. Adults collected from vineyards were of above average size and had relatively high estimated energetic reserves. Results suggest that alfalfa fields are more likely to serve as sources of threecornered alfalfa hoppers than irrigated pastures and that differences in male and female behavior may affect rates of pathogen transmission.
The evolution of the elements

Abstract We now believe that only the lightest elements, hydrogen and helium, were created during the ‘Big Bang’ origin of the Universe and that all heavier elements were synthesized by nuclear reactions in stars, the interstellar medium and possibly in ‘little bangs’ in the nuclei of galaxies. The composition of the interstellar medium has evolved through enrichment by processed material shed by evolving stars and the composition of the Solar System reflects that of the interstellar medium at the time of its formation. Differentiation processes during the evolution of the Solar System and individual planets account for the different compositions of the Sun and planets. The measurement of the abundance distribution of the elements has become a very powerful tool in the elucidation of the evolution of the Solar System, stars and the Galaxy. This review attempts to trace the formation of the elements in stars and their subsequent evolution.
Identification of potent COVID-19 main protease inhibitors by loading of favipiravir on Mg12O12 and Zn12O12 nanoclusters: an in silico strategy for COVID-19 treatment

Abstract Pandemic new severe acute respiratory syndrome coronavirus (SARS-CoV-2) virus has increased throughout the world. There is no effective treatment against this virus until now. Since its appearance in Wuhan, China in December 2019, SARS-CoV-2 becomes the largest challenge the world is opposite today, including the discovery of an antiviral drug for this virus. Several viral proteins have been prioritized as SARS-CoV-2 antiviral drug targets, among them the papain-like protease (PLpro) and the main protease (Mpro). Inhibition of these proteases would target viral replication, viral maturation and suppression of host innate immune responses. Potential candidates have been identified to show inhibitory effects against Mpro, both in biochemical assays and viral replication in cells. There are different molecules such as lopinavir and favipiravir considerably inhibit the activity of Mpro in vitro. Different studies have shown that structurally improved favipiravir and other similar compounds can inhibit SARS-CoV-2 main protease. In this work, we study the interactions between favipiravir with Mg12O12 and Zn12O12 nanoclusters by density functional theory (DFT) and quantum mechanics atoms in molecules (QMAIM) methods to summarize the ability to load favipiravir onto Mg12O12 and Zn12O12 nanoclusters. Favipiravir-Mg12O12 and favipiravir-Zn12O12 lowest structures complexes were chosen to dock inside the SARS-CoV-2 main protease by molecular docking study. The molecular docking analysis revealed that the binding affinity of Mg12O12 and Zn12O12 nanoclusters inside the Mpro receptor is larger than that of favipiravir. Also, the loading of favipiravir on the surface of Mg12O12 and Zn12O12 nanoclusters increased the binding affinity against the Mpro receptor. Subsequently, 100 ns molecular dynamics simulation of the favipiravir-Mg12O12, and favipiravir-Zn12O12 docked inside the Mpro complexes established that favipiravir-Mg12O12, forms the most stable complex with the Mpro. Further molecular mechanics Poisson Boltzmann surface area (MMPBSA) analyses using the MD trajectories also demonstrated the higher binding affinity of favipiravir-Mg12O12 inside the Mpro. In summary, this study demonstrates a new way to characterize leads for novel anti-viral drugs against SARS-CoV-2, by improving the drug ability of favipiravir via loading it on Mg12O12 and Zn12O12 nanoclusters. Communicated by Ramaswamy H. Sarma
A parameterization for computing grid-averaged solar fluxes for inhomogeneous marine boundary layer

Abstract A method of computing grid-averaged solar radiative fluxes for horizontally inhomogeneous marine boundary layer cloud fields is presented. Its underlying assumptions are as follows: i) the independent pixel approximation (IPA) is applicable and ii) for regions the size of general circulation model (GCM) grid cells, frequency distributions of cloud optical depth τ can be approximated by gamma distribution functions. Equations are furnished for albedo and transmittance that, when applied to judiciously chosen spectral bands, require about three to four times as much CPU time as plane-parallel, homogeneous (PPH) two-stream approximations, which are ubiquitous to GCMs. This is not a hindrance, as two-stream solutions command typically less than 1% of a GCM's CPU consumption. This method, referred to as the gamma IPA, requires estimates of the mean and variance of τ for each applicable grid cell. Biases associated with PPH models are assessed assuming that cloud properties in GCMs are tuned to yield a.
Reconstruction for 7T high‐resolution whole‐brain diffusion MRI using two‐stage N/2 ghost correction and L1‐SPIRiT without single‐band reference

To combine a new two‐stage N/2 ghost correction and an adapted L1‐SPIRiT method for reconstruction of 7T highly accelerated whole‐brain diffusion MRI (dMRI) using only autocalibration scans (ACS) without the need of additional single‐band reference (SBref) scans.
Targeted bacterial conjugation mediated by synthetic cell-to-cell adhesions

Abstract Genetic interventions on microbiomes, for clinical or biotechnological purposes, remain challenging. Conjugation-based delivery of genetic cargo is still unspecific and limited by low conjugation rates. Here we report an approach to overcome these problems, based on a synthetic bacterial adhesion system. Mating assemblers consist on a synthetic adhesion formed by the expression on the surface of donor and target cells of specific nanobodies (Nb) and their cognate antigen (Ag). The Nb–Ag bridge increased 1–3 logs transfer of a variety of plasmids, especially in liquid media, confirming that cell-cell docking is a main determinant limiting mating efficiency. Synthetic cell-to-cell adhesion allows efficient conjugation to targeted recipients, enhancing delivery of desired genes to a predefined subset of prey species, or even specific pathogenic strains such as enterohemorrhagic Escherichia coli (EHEC), within a bacterial community. The synthetic conjugation enhancer presented here optimizes plasmid delivery by selecting the target hosts with high selectivity.
Black-Scholes Option Pricing Model Modified to Admit a Miniscule Drift Can Reproduce the Volatility Smile

This paper develops a closed-form solution to an extended Black-Scholes (EBS) pricing formula which admits an implied drift parameter alongside the standard implied volatility. The market volatility smiles for vanilla call options on the S&P 500 index are recreated fitting the best volatility-drift combination in this new EBS. Using a likelihood ratio test, the implied drift parameter is seen to be quite significant in explaining volatility smiles. The implied drift parameter is sufficiently small to be undetectable via historical pricing analysis, suggesting that drift is best considered as an implied parameter rather than a historically-fit one. An overview of option-pricing models is provided as background.
A systems biology approach identifies the role of dysregulated PRDM6 in the development of hypertension

Genetic variants in the third intron of the PRDM6 gene have been associated with BP traits in multiple GWAS. By combining fine mapping, massively parallel reporter assays, and gene editing, we identified super enhancers that drive the expression of PRDM6 and are partly regulated by STAT1 as the causal variants for hypertension. The heterozygous disruption of Prdm6 in mice expressing Cre recombinase under the control of mouse smooth muscle cell protein 22-α promoter (Prdm6fl/+ SM22-Cre) exhibited a markedly higher number of renin-producing cells in the kidneys at E18.5 compared with WT littermates and developed salt-induced systemic hypertension that was completely responsive to the renin inhibitor aliskiren. Strikingly, RNA-Seq analysis of the mouse aortas identified a network of PRDM6-regulated genes that are located in GWAS-associated loci for blood pressure, most notably Sox6, which modulates renin expression in the kidney. Accordingly, the smooth muscle cell–specific disruption of Sox6 in Prdm6fl/+ SM22-Cre mice resulted in a dramatic reduction of renin. Fate mapping and histological studies also showed increased numbers of neural crest–derived cells accompanied by increased collagen deposition in the kidneys of Prdm6fl/+ Wnt1Cre-ZsGreen1Cre mice compared with WT mice. These findings establish the role of PRDM6 as a regulator of renin-producing cell differentiation into smooth muscle cells and as an attractive target for the development of antihypertensive drugs.
Ten quick tips for computational analysis of medical images

Medical imaging is a great asset for modern medicine, since it allows physicians to spatially interrogate a disease site, resulting in precise intervention for diagnosis and treatment, and to observe particular aspect of patients’ conditions that otherwise would not be noticeable. Computational analysis of medical images, moreover, can allow the discovery of disease patterns and correlations among cohorts of patients with the same disease, thus suggesting common causes or providing useful information for better therapies and cures. Machine learning and deep learning applied to medical images, in particular, have produced new, unprecedented results that can pave the way to advanced frontiers of medical discoveries. While computational analysis of medical images has become easier, however, the possibility to make mistakes or generate inflated or misleading results has become easier, too, hindering reproducibility and deployment. In this article, we provide ten quick tips to perform computational analysis of medical images avoiding common mistakes and pitfalls that we noticed in multiple studies in the past. We believe our ten guidelines, if taken into practice, can help the computational–medical imaging community to perform better scientific research that eventually can have a positive impact on the lives of patients worldwide.