Miracle-dz/UniFAR-FTUs huggingface dataset:
Life history traits of spotted lanternfly (Hemiptera: Fulgoridae) when feeding on grapevines and tree of heaven

The invasive planthopper, spotted lanternfly (SLF), Lycorma delicatula (White) (Hemiptera: Fulgoridae), feeds on a broad range of plants including species of economic importance such as grape. Although SLF feeds on wild and cultivated grape, the effect of grapevines on the insect’s life history traits is unknown. This study examined the effect of cultivated Concord grapevines (Vitis labrusca) and the insect’s preferred host tree of heaven (TOH), Ailanthus altissima, on SLF development, survival, reproduction, and body mass. Newly emerged nymphs were allowed to feed on either TOH, Concord grapevines or a mixed diet of Concord grapevines plus TOH through adulthood until death. Development, mortality, and oviposition of paired adults were tracked daily to calculate the SLF rate of development, survival, and reproduction among treatments. When feeding exclusively on Concord grapevines, SLF was able to develop and reproduce but had higher mortality, slower development, and produced fewer eggs. SLF fed on the mixed diet of grapevines plus TOH exhibited faster nymphal development, laid more eggs, and had higher body mass compared with those fed only on grape or TOH. SLF had greater survival when fed on either the mixed diet or on TOH alone. We conclude that Concord grapevines are a poor-quality host for SLF, but when combined with TOH, SLF fitness increases above that of feeding on TOH alone. This study supports the elimination of TOH as a part of SLF vineyard management practices.
Statistical rehabilitation of improper correlation matrices

The simplest way to describe the dependence for a set of financial assets is their correlation matrix. This correlation matrix can be improper when it is specified element-wise. We describe a new method for obtaining a positive definite correlation matrix starting from an improper one. The expert's opinion and trust in each pairwise correlation is described by a beta distribution. Then, by combining these individual distributions, a joint distribution over the space of positive definite correlation matrices is obtained using Cholesky factorization, and its mode constitutes the new proper correlation matrix. The optimization is complemented by a visual representation of the entries that were most affected by the legalization procedure. We also sketch a Bayesian approach to the same problem.
Global Trends and Research Progress of Photodynamic Therapy in Skin Cancer: A Bibliometric Analysis and Literature Review

Background Based on photochemical reactions through the combined use of light and photosensitizers, photodynamic therapy (PDT) is gaining popularity for the treatment of skin cancer. Various photosensitizers and treatment regimens are continuously being developed for enhancing the efficacy of PDT on skin cancer. Reviewing the development history of PDT on skin cancer, and summarizing its development direction and research status, is conducive to the further research. Methods To evaluate the research trends and map knowledge structure, all publications covering PDT on skin cancer were retrieved and extracted from Web of Science database. We applied VOSviewer and CiteSpace softwares to evaluate and visualize the countries, institutes, authors, keywords and research trends. Literature review was performed for the analysis of the research status of PDT on skin cancer. Results A total of 2662 publications were identified. The elements, mechanism, pros and cons, representative molecular photosensitizers, current challenges and research progress of PDT on skin cancer were reviewed and summarized. Conclusion This study provides a comprehensive display of the field of PDT on skin cancer, which will help researchers further explore the mechanism and application of PDT more effectively and intuitively.
Phylogeography of Ramalina farinacea (Lichenized Fungi, Ascomycota) in the Mediterranean Basin, Europe, and Macaronesia

Ramalina farinacea is an epiphytic lichen-forming fungus with a broad geographic distribution, especially in the Northern Hemisphere. In the eighties of the last century, it was hypothesized that R. farinacea had originated in the Macaronesian–Mediterranean region, with the Canary Islands as its probable southernmost limit, and thereafter it would have increased its distribution area. In order to explore the phylogeography of this emblematic lichen, we analyzed 120 thalli of R. farinacea collected in 38 localities distributed in temperate and boreal Europe, the Western Mediterranean Basin, and several Macaronesian archipelagos in the Atlantic Ocean. Data from two nuclear markers (nrITS and uid70) of the mycobiont were obtained to calculate genetic diversity indices to infer the phylogenies and haplotype networks and to investigate population structure. In addition, dating analysis was conducted to provide a valuable hypothesis of the timing of the origin and diversification of R. farinacea and its close allies. Our results highlight that phylogenetic species circumscription in the “Ramalina farinacea group” is complex and suggests that incomplete lineage sorting is at the base of conflicting phylogenetic signals. The existence of a high number of haplotypes restricted to the Macaronesian region, together with the diversification of R. farinacea in the Pleistocene, suggests that this species and its closest relatives originated during relatively recent geological times and then expanded its range to higher latitudes. However, our data cannot rule out whether the species originated from the Macaronesian archipelagos exclusively or also from the Mediterranean Basin. In conclusion, the present work provides a valuable biogeographical hypothesis for disentangling the evolution of this epiphytic lichen in space and time.
Interferometric redatuming of autofocused primaries and internal multiples

Recently, an iterative scheme has been introduced to retrieve the down- and upgoing Green's functions at an arbitrary level ? F inside an acoustic medium as if there were a source at the surface. This scheme requires as input the reflection response acquired at the surface and the direct arrival of the transmission response from the surface to level ? F. The source locations of these Green's functions can be effectively redatumed to level ? F by interferometric redatuming, which requires solving a multidimensional deconvolution problem, essentially being a Fredholm integral equation of the first kind. We show how this problem can be simplified by rewriting it as a Fredholm integral equation of the second kind that can be expanded as a Neumann series. Redatumed data can be used for multiplefree true-amplitude imaging at or in the vicinity of ? F. For imaging the closest reflector to ? F only, the Neumann series can be truncated at the first term without losing accuracy.
Diagnostic Performance of Two-Dimensional Ultrasound, Two-Dimensional Sonohysterography and Three-Dimensional Ultrasound in the Diagnosis of Septate Uterus—A Systematic Review and Meta-Analysis

Background: The septate uterus is the most common congenital uterine anomaly, and hysteroscopy is the gold standard for diagnosing it. The goal of this meta-analysis is to perform a pooled analysis of the diagnostic performance of two-dimensional transvaginal ultrasonography, two-dimensional transvaginal sonohysterography, three-dimensional transvaginal ultrasound, and three-dimensional transvaginal sonohysterography for the diagnosis of the septate uterus. Methods: Studies published between 1990 and 2022 were searched in PubMed, Scopus, and Web of Science. From 897 citations, we selected eighteen studies to include in this meta-analysis. Results: The mean prevalence of uterine septum in this meta-analysis was 27.8%. Pooled sensitivity and specificity were 83% and 99% for two-dimensional transvaginal ultrasonography (ten studies), 94% and 100% for two-dimensional transvaginal sonohysterography (eight studies), and 98% and 100% for three-dimensional transvaginal ultrasound (seven articles), respectively. The diagnostic accuracy of three-dimensional transvaginal sonohysterography was only described in two studies, and we did not calculate the pooled sensitivity and specificity for this method. Conclusion: Three-dimensional transvaginal ultrasound has the best performance capacity for the diagnosis of the septate uterus.
Image deblurring and near-real-time atmospheric seeing estimation through the employment of convergence of variance

Abstract A new image reconstruction algorithm is presented that will remove the effect of atmospheric turbulence on motion compensated frame average images. The primary focus of this research was to develop a blind deconvolution technique that could be employed in a tactical military environment where both time and computational power are limited. Additionally, this technique can be employed to measure atmospheric seeing conditions. In a blind deconvolution fashion, the algorithm simultaneously computes a high resolution image and an average model for the atmospheric blur parameterized by Fried’s seeing parameter. The difference in this approach is that it does not assume a prior distribution for the seeing parameter, rather it assesses the convergence of the image’s variance as the stopping criteria and identification of the proper seeing parameter from a range of candidate values. Experimental results show that the convergence of variance technique allows for estimation of the seeing parameter accurate to within 0.5 cm and often even better depending on the signal to noise ratio.
Techniques to determine the quiet day curve for a long period of subionospheric VLF observations

Very low frequency (VLF) transmissions propagating between the conducting Earth's surface and lower edge of the ionosphere have been used for decades to study the effect of space weather events on the upper atmosphere. The VLF response to these events can only be quantified by comparison of the observed signal to the estimated quiet time or undisturbed signal levels, known as the quiet day curve (QDC). A common QDC calculation approach for periods of investigation of up to several weeks is to use observations made on quiet days close to the days of interest. This approach is invalid when conditions are not quiet around the days of interest. Longer‐term QDCs have also been created from specifically identified quiet days within the period and knowledge of propagation characteristics. This approach is time consuming and can be subjective. We present three algorithmic techniques, which are based on either (1) a mean of previous days' observations, (2) principal component analysis, or (3) the fast Fourier transform (FFT), to calculate the QDC for a long‐period VLF data set without identification of specific quiet days as a basis. We demonstrate the effectiveness of the techniques at identifying the true QDCs of synthetic data sets created to mimic patterns seen in actual VLF data including responses to space weather events. We find that the most successful technique is to use a smoothing method, developed within the study, on the data set and then use the developed FFT algorithm. This technique is then applied to multiyear data sets of actual VLF observations.
Estimation of instantaneous parameters of speech signals with Teager-operator and Hilbert-Huang-transform

In digital speech processing the so-called quasi-stationary signal model is often used in solutions to a lot of practical problems. It means that it is possible to process the speech signal with the sequence of overlapped speech segments in order to complete the computations necessary for the algorithm in question. It is presumed that the parameters of the applied speech model do not vary during the segment under processing. According to the relevant literature, the suitable segment duration is 2.5 times longer than the fundamental period, and the sufficient overlap is 1.3 times of pitch period [1]. During the progress of digital speech processing a demand has arisen for analyzing methods suitable for investigating speech signal changes of lower duration than the pitch period itself. These types of speech signal changes constitute the fine structure of speech. The phenomenon of the small fluctuation of the fundamental period during nonlinear vocal chord vibration – among many others – is an example which calls for methods necessary to represent the fine structure of speech. These methods ought to derive physically meaningful parameters from few speech samples only. Consequently, for these purposes the speech processing methods based on the quasi-stationary assumption are not appropriate [2]. Summing up succinctly the essence of the problem, it could be said that it is not possible to increase the time-resolution of the analysis, while keeping the detailed frequency-domain representation because of the uncertainty-relation of Dennis Gabor. Nowadays, the wavelet-transform is widely used in applications requiring increased time-resolution. However, the time-resolution of the wavelet-method is also limited by the timescale uncertainty relation, which replaces the time-frequency uncertainty mentioned above [2,3]. A possible method, suitable for analyzing the fine structure of speech, is the Teager-operator-based Energy Separation (ES) algorithm. The wavelet-based analysis and the Teager-operator have recently led to successful applications [4]. Another possibility in determining the instantaneous parameters is the application of the Hilbert-Huang-transform [5]. Because we have not found published results in the relevant literature available to us on the comparison of the Teager-operatorbased methods and HHT-based ones, their comparison has been chosen as the subject of this article.
Pseudo super-resolution for improved calcification characterization for cone beam breast CT (CBBCT)

Cone Beam Breast CT imaging (CBBCT) is a promising tool for diagnosis of breast tumors and calcifications. However, as the sizes of calcifications in early stages are very small, it is not easy to distinguish them from background tissues because of the relatively high noise level. Therefore, it is necessary to enhance the visualization of calcifications for accurate detection. In this work, the Papoulis-Gerchberg (PG) method was introduced and modified to improve calcification characterization. PG method is an iterative algorithm of signal extrapolation and has been demonstrated to be very effective in image restoration like super-resolution (SR) and inpainting. The projection images were zoomed by bicubic interpolation method, then the modified PG method were applied to improve the image quality. The reconstruction from processed projection images showed that this approach can effectively improve the image quality by improving the Modulation Transfer Function (MTF) with a limited increase in noise level. As a result, the detectability of calcifications was improved in CBBCT images.
Using the Jurkat reporter T cell line for evaluating the functionality of novel chimeric antigen receptors

Background: T cells that are genetically modified with chimeric antigen receptor (CAR) hold promise for immunotherapy of cancer. Currently, there are intense efforts to improve the safety and efficacy of CAR T cell therapies against liquid and solid tumors. Earlier we designed a novel CAR backbone (FiCAR) where the spacer is derived from immunoglobulin (Ig) -like domains of the signal-regulatory protein alpha (SIRPα). However, the analysis of novel CAR using primary T cells is slow and laborious. Methods: To explore the versatility of the CAR backbone, we designed a set of variant FiCARs with different spacer lengths and targeting antigens. To expedite the analysis of the novel CARs, we transduced the FiCAR genes using lentiviruses into Jurkat reporter T cells carrying fluorescent reporter genes. The expression of fluorescent markers in response to FiCAR engagement with targets was analyzed by flow cytometry, and cytotoxicity was evaluated using killing assays. Furthermore, the killing mechanisms that are employed by FiCAR-equipped Jurkat T cells were investigated by flow cytometry, and the intracellular pathways involved in signaling by FiCAR were analyzed by phosphoproteomic analysis using mass spectrometry. Results: Seven different CARs were designed and transduced into Jurkat reporter cells. We show that the SIRPα derived FiCARs can be detected by flow cytometry using the SE12B6A4 antibody recognizing SIRPα. Furthermore, FiCAR engagement leads to robust activation of NFκβ and NFAT signaling, as demonstrated by the expression of the fluorescent reporter genes. Interestingly, the Jurkat reporter system also revealed tonic signaling by a HER-2 targeting FiCAR. FiCAR-equipped Jurkat T cells were cytotoxic in cocultures with target cells and target cell engagement lead to an upregulation of CD107a on the Jurkat reporter T cell surface. Phosphoproteomic analyses confirmed signal transduction via the intracellular CD28/CD3ζ sequences upon the interaction of the FiCAR1 with its antigen. In addition, downstream signaling of CD3ζ/ZAP70- SLP-76-PLCγ, PI3K–AKT–NFκB pathways and activation of NFAT and AP-1 were observed. Conclusion: We conclude that the FiCAR backbone can be shortened and lengthened at will by engineering it with one to three SIRPα derived Ig-like domains, and the FiCARs are functional when equipped with different single chain variable fragment target binding domains. The Jurkat reporter system expedites the analysis of novel CARs as to their expression, signaling function, evaluation of tonic signaling issues and cytotoxic activity.
ETNK2 Low-Expression Predicts Poor Prognosis in Renal Cell Carcinoma with Immunosuppressive Tumor Microenvironment

Background The ethanolamine kinase 2 (ETNK2) gene is implicated in carcinogenesis, but its expression and involvement in kidney renal clear cell carcinoma (KIRC) remain unknown. Methods Initially, we conducted a pan-cancer study in which we searched the Gene Expression Profiling Interactive Analysis, the UALCAN, and the Human Protein Atlas databases to determine the expression level of the ETNK2 gene in KIRC. The Kaplan–Meier curve was then used to calculate the overall survival (OS) of KIRC patients. We then used the differentially expressed genes (DEGs) and enrichment analysis to explain the mechanism of the ETNK2 gene. Finally, the immune cell infiltration analysis was performed. Results Although the ETNK2 gene expression was lower in KIRC tissues, the findings illustrated a link between the ETNK2 gene expression and a shorter OS time for KIRC patients. DEGs and enrichment analysis revealed that the ETNK2 gene in KIRC involved multiple metabolic pathways. Finally, the ETNK2 gene expression has been linked to several immune cell infiltrations. Conclusions According to the findings, the ETNK2 gene plays a crucial role in tumor growth. It can potentially serve as a negative prognostic biological marker for KIRC by modifying immune infiltrating cells.
Numerical investigation of nonlinear oscillations of gas bubbles in liquids

Forced oscillations of a spherical gas bubble in an incompressible, viscous liquid (water) are calculated numerically. The information gathered is mainly displayed in the form of frequency response curves of the steady‐state solutions showing the harmonics, subharmonics, and ultraharmonics. Bubbles oscillating ultraharmonically at frequencies below the main resonance may emit half the driving frequency. This fact gives rise to a new explanation for the occurrence of the first subharmonic in the spectrum of the cavitation noise in ultrasonic cavitation.Subject Classification: [43]30.70, [43]30.75.
In search of an ideal template for therapeutic genome editing: A review of current developments for structure optimization

Gene therapy is a fast developing field of medicine with hundreds of ongoing early-stage clinical trials and numerous preclinical studies. Genome editing (GE) now is an increasingly important technology for achieving stable therapeutic effect in gene correction, with hematopoietic cells representing a key target cell population for developing novel treatments for a number of hereditary diseases, infections and cancer. By introducing a double strand break (DSB) in the defined locus of genomic DNA, GE tools allow to knockout the desired gene or to knock-in the therapeutic gene if provided with an appropriate repair template. Currently, the efficiency of methods for GE-mediated knock-in is limited. Significant efforts were focused on improving the parameters and interaction of GE nuclease proteins. However, emerging data suggests that optimal characteristics of repair templates may play an important role in the knock-in mechanisms. While viral vectors with notable example of AAVs as a donor template carrier remain the mainstay in many preclinical trials, non-viral templates, including plasmid and linear dsDNA, long ssDNA templates, single and double-stranded ODNs, represent a promising alternative. Furthermore, tuning of editing conditions for the chosen template as well as its structure, length, sequence optimization, homology arm (HA) modifications may have paramount importance for achieving highly efficient knock-in with favorable safety profile. This review outlines the current developments in optimization of templates for the GE mediated therapeutic gene correction.
Dual functions of PsmiR172b-PsTOE3 module in dormancy release and flowering in tree peony (Paeonia suffruticosa)

Abstract MicroRNAs (miRNAs) are non-coding RNAs that interact with target genes and are involved in many physiological processes in plants. miR172-AP2 mainly plays a role in the regulation of flowering time and floral organ differentiation. Bud dormancy release is necessary for forcing culture of tree peony in winter, but the mechanism of dormancy regulation is unclear. In this study, we found that a miR172 family member, PsmiR172b, was downregulated during chilling-induced bud dormancy release in tree peony, exhibiting a trend opposite to that of PsTOE3. RNA ligase-mediated (RLM) 5′-RACE (rapid amplification of cDNA ends) confirmed that miR172b targeted PsTOE3, and the cleavage site was between bases 12 (T) and 13 (C) within the complementary site to miR172b. The functions of miR172b and PsTOE3 were detected by virus-induced gene silencing (VIGS) and their overexpression in tree peony buds. PsmiR172b negatively regulated bud dormancy release, but PsTOE3 promoted bud dormancy release, and the genes associated with bud dormancy release, including PsEBB1, PsEBB3, PsCYCD, and PsBG6, were upregulated. Further analysis indicated that PsTOE3 directly regulated PsEBB1 by binding to its promoter, and the specific binding site was a C-repeat (ACCGAC). Ectopic expression in Arabidopsis revealed that the PsmiR172b-PsTOE3 module displayed conservative function in regulating flowering. In conclusion, our results provided a novel insight into the functions of PsmiR172-PsTOE3 and possible molecular mechanism underlying bud dormancy release in tree peony.