Miracle-dz/UniFAR-FTUs huggingface dataset:
Iterative phase retrieval by combining modulus constraints and angle relationships

In coherent diffraction imaging, modulus is recorded and phase is lost. Phase retrieval is to recover the lost phase from the recorded modulus. Iterative Fourier algorithm (IFA) solves this problem by imposing modulus constraints to make the phase converge. Here we show a modulus angle joint phase retrieval method. When both amplitude and phase modulation are applied, the angle relationship, which denotes the Fourier phase difference, can be exactly derived from the measured intensities. Based on this angle relationship, a new form of IFA called angle iteration is developed, which exhibits a faster but unstable convergence compared with tradition IFA (modulus iteration). By modulus-angle combined iteration, the proposed method reaches a quick and stable convergence. With the same intensity measurements, it drops nearly 80% the phase retrieval errors by traditional IFA but costs the same CPU time. This work reveals the fact that changing the constraint format would improve the original iteration process.
Thermal behavior simulation of bulk acoustic wave resonator

In order to predict the thermal behavior of bulk acoustic wave resonator (BAWR) and evaluate the power handling capacity, a BAWR thermal behavior simulation method is proposed. The conductor surface loss in the BAWR electromagnetic model is extracted and used as the heat source for thermal simulation to obtain the temperature distribution of the resonator. Then the signal feeding edge, active area shape and power handling capacity are researched. The simulation results show that in order to moderate the self-heating effect of BAWR, the signal feeding should follow the principle of “feeding in from long edge, feeding out from long edge”; active area shape has little to do with selfheating effect; the power handling capacity of the designed BAWR can reach to 3 W.
Spin morphologies and heat dissipation in spherical assemblies of magnetic nanoparticles

Aggregates of magnetic nanoparticles (MNPs) exhibit unusual properties due to the interplay of small system size and long-range dipole-dipole interactions. Using the micromagnetic simulation software oommf, we study the spin morphologies and heat dissipation in micron-size spherical assemblies of MNPs. In particular, we examine the sensitivity of these properties to the dipolar strength, manipulated by the interparticle separation. As oommf is not designed for such a study, we have incorporated a novel scaling protocol for this purpose. We believe that it is essential for all studies where volume fractions are varied. Our main results are as follows: (i) Dense assemblies exhibit strong dipolar effects which yield local magnetic order in the core but not on the surface, where moments are randomly oriented. (ii) The probability distribution of ground-state energy exhibits a long high-energy tail for surface spins in contrast to small tails for the core spins. Consequently, there is a wide variation in the energy of surface spins but not the core spins. (iii) There is strong correlation between ground-state energy and heating properties on application of an oscillating magnetic field $h(t)={h}_{o}cos2\ensuremath{\pi}ft$: the particles in the core heat uniformly, while those on the surface exhibit a wide range from cold to intensely hot. (iv) Specific choices of ${h}_{o}$ and $f$ yield characteristic spatial heat distributions, e.g., hot surface and cold core, or vice versa. (iv) For all values of ${h}_{o}$ and $f$ that we consider, heating was maximum at a specific volume fraction. These results are especially relevant in the context of contemporary applications such as hyperthermia and chemotherapy, and also for novel materials such as smart polymer beads and superspin glasses.
The effects of gratitude interventions: a systematic review and meta-analysis

ABSTRACT Introduction Gratitude has several implications. Over time, a logical relationship has been established between gratitude and well-being. In addition, researchers aimed to establish associations between gratitude and other factors of positive feelings using scientific methods. We conducted a systematic review and meta-analysis of interventions to develop gratitude and its benefits to human beings. Objective This study aimed to evaluate and quantify the available scientific evidence on interventions to acquire knowledge on gratitude as a quantifiable causal factor of benefit to human beings. Methods A systematic literature search was conducted to identify studies that investigated the effects of gratitude interventions. MEDLINE, Embase, and Central Cochrane databases were searched in addition to gray (Google Scholar) and manual search. Two authors independently evaluated the titles and abstracts, and selected the studies that met the inclusion criteria. The searches were conducted between January and July 2022. Results Sixty-four randomized clinical trials were included. The meta-analysis demonstrated that patients who underwent gratitude interventions experienced greater feelings of gratitude, better mental health, and fewer symptoms of anxiety and depression. Moreover, they experienced other benefits such as a more positive mood and emotions. Conclusion The results demonstrate that acts of gratitude can be used as a therapeutic complement for treating anxiety and depression and can increase positive feelings and emotions in the general population. Prospero database registration: (www.crd.york.ac.uk/prospero) under the number CRD42021250799.
Editorial: Altered expression of proteins in cancer: function and potential therapeutic targets, volume II

COPYRIGHT © 2023 Pessoa, Valenti, Bellance, Chiarella, Abebe, Gerratana, Pérez-Plasencia and Kzhyshkowska. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms. TYPE Editorial PUBLISHED 18 July 2023 DOI 10.3389/fonc.2023. 1242855
Editorial: Subcellular compartmentalization of plant antioxidants and ROS generating systems, volume II

COPYRIGHT © 2023 Palma, Rodrı́guez-Ruiz, Foyer and Corpas. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms. TYPE Editorial PUBLISHED 18 July 2023 DOI 10.3389/fpls.2023. 1224289
Epcoritamab-bysp (Epkinly) – A phenomenal breakthrough in the treatment of diffuse large B-cell lymphoma

The most prevalent non-Hodgkin lymphoma, Diffuse Large B-Cell Lymphoma (DLBCL), affects 25,000 people annually and accounts for roughly 30% of cases of Non-Hodgkin Lymphoma. 1 Rituximab and chemotherapy are commonly used in the treatment of diffuse large B-cell lymphoma (DLBCL) to cure the patient; however, a signi ﬁ cant portion of patients, up to 40%, are bound to experience relapsed or refractory disease. In such cases, salvage chemotherapy followed by autologous stem cell transplantation is the standard approach, but less than half of the patients achieve long-term disease control. 2 Those who face refractory disease or experience relapse after transplantation have limited treatment options and generally have poor overall survival rates. 2,3 To address this unmet medical need, the Food and Drug Administration (FDA) has recently given Epcoritamab-bysp (Epkinly, Genmab US, Inc.) accelerated approval for the treatment of relapsed or refractory DLBCL, including cases where DLBCL arises from indolent lymphoma or high-grade B-cell lymphoma after two or more lines of systemic therapy. This approval signi ﬁ es an important advancement, providing a potential therapeutic option for patients who have exhausted standard treatments. 4
A nomogram based on clinical factors to predict calendar year readmission in patients with ulcerative colitis

Background: Readmission shortly after discharge is indicative of an increased disease severity for patients with ulcerative colitis (UC) and ineffectiveness to medical therapy, which may contribute to a dismal prognosis. Objectives: This study aimed to explore prognostic variables with a nomogram to predict unplanned UC-related readmission within 1 year after discharge. Design: A retrospective cohort study. Methods: Electronic medical records of all UC patients treated at our center between 1 January 2014 and 31 June 2021 were reviewed. A comprehensive analysis of various characteristics, such as demographics, comorbidities, medical history, follow-up appointments, admission endoscopy, histopathologic features, etc., was used to determine the primary end point, which was unplanned UC-related calendar year readmission. Results: We found that the unplanned UC-related readmission rate within 1 year was 20.8%. In multivariable cox analysis, the predictors of the Elixhauser comorbidity index [Hazard ratio (HR): 3.50, 95% confidence interval (CI): 1.93–6.37], regular follow-up (HR: 0.29, 95% CI: 0.16–0.53), any history of corticosteroid use (HR: 3.38, 95% CI: 1.83–6.27), seral level of C-reactive protein (HR: 1.01, 95% CI: 1.00–1.02), and the UC endoscopic index of severity (HR: 1.29, 95% CI: 1.05–1.57) independently predicted calendar year readmission after discharge. The established nomogram had a consistently high accuracy in predicting calendar year readmission in the training cohort, with a concordance index of 0.784, 0.825, and 0.837 at 13, 26, and 52 weeks, respectively, which was validated in both the internal and external validation cohorts. Therefore, UC patients were divided into clinically low-, high-, and extremely high-risk groups for readmission, based on the calculated score of 272.5 and 378. Conclusion: The established nomogram showed good discrimination and calibration powers in predicting calendar year readmission in high-risk UC patients, who may need intensive treatment and regular outpatient visits.
Transcriptomic profiling of mice brain under Bex3 regulation

BEX family genes are expressed in various tissues and play significant roles in neuronal development. A mouse model of Bex3 gene knock-out was generated in this study, using the CRISPR-Cas9 system. Transcriptomic analysis of the brain was performed to identify genes and pathways under Bex3 regulation. Essential biological functions under the control of Bex3 related to brain development were identified. Ninety-five genes were differentially expressed under Bex3−/− regulation, with 53 down and 42 up. Among down-regulated genes, LOC102633156 is a member of zf-C2H2, Xlr3a is an X-linked lymphocyte regulated gene, LOC101056144 is a hippocampal related gene, 2210418O10Rik and Fam205a3 are cortex related genes. Among the upregulated genes, Zfp967 is a zf protein, Tgtp2 is a T cell-specific regulator, Trpc2 is a neuron-related gene, and Evi2 is related to NF1. A total of 34 KEGG disease terms were identified under the Bex3−/− regulation. The most prominent is non-syndromic X-linked mental retardation, where Fgd1 is enriched. Similarly, IRF, MBD, SAND, zf-BED, and zf-C2H2 were significantly enriched transcription factors. A further study is required to confirm and explain each aspect that has been identified in this study.
Range‐wide evolutionary relationships and historical demography of brown bears (Ursus arctos) revealed by whole‐genome sequencing of isolated central Asian populations

Phylogeographic studies uncover hidden pathways of divergence and inform conservation. Brown bears (Ursus arctos) have one of the broadest distributions of all land mammals, ranging from Eurasia to North America, and are an important model for evolutionary studies. Although several whole genomes were available for individuals from North America, Europe and Asia, limited whole‐genome data were available from Central Asia, including the highly imperilled brown bears in the Gobi Desert. To fill this knowledge gap, we sequenced whole genomes from nine Asian brown bears from the Gobi Desert of Mongolia, Northern Mongolia and the Himalayas of Pakistan. We combined these data with published brown bear sequences from Europe, Asia and North America, as well as other bear species. Our goals were to determine the evolutionary relationships among brown bear populations worldwide, their genetic diversity and their historical demography. Our analyses revealed five major lineages of brown bears based on a filtered set of 684,081 single nucleotide polymorphisms. We found distinct evolutionary lineages of brown bears in the Gobi, Himalayas, northern Mongolia, Europe and North America. The lowest level of genetic diversity and the highest level of inbreeding were found in Pakistan, the Gobi Desert and Central Italy. Furthermore, the effective population size (Ne) for all brown bears decreased over the last 70,000 years. Our results confirm the genetic distinctiveness and ancient lineage of brown bear subspecies in the Gobi Desert of Mongolia and the Himalayas of Pakistan and highlight their importance for conservation.
Characterisation of extracellular vesicles isolated from hydatid cyst fluid and evaluation of immunomodulatory effects on human monocytes

Hydatidosis is a disease caused by the larval stage of Echinococcus granulosus, which involves several organs of intermediate hosts. Evidence suggests a communication between hydatid cyst (HC) and hosts via extracellular vesicles. However, a little is known about the communication between EVs derived from HC fluid (HCF) and host cells. In the current study, EVs were isolated using differential centrifugation from sheep HCF and characterized by western blot, electron microscope and size distribution analysis. The uptake of EVs by human monocyte cell line (THP‐1) was evaluated. The effects of EVs on the expression levels of pro‐ and anti‐inflammatory cytokines were investigated using quantitative real‐time PCR (RT‐PCR), 3 and 24 h after incubation. Moreover, the cytokine level of IL‐10 was evaluated in supernatant of THP‐1 cell line at 3 and 24 h. EVs were successfully isolated and showed spherical shape with size distribution at 130.6 nm. After 3 h, the expression levels of pro‐inflammatory cytokine genes (IL1Β, IL15 and IL8) were upregulated, while after 24 h, the expression levels of pro‐inflammatory cytokines were decreased and IL13 gene expression showed upregulation. A statistically significant increase was seen in the levels of IL‐10 after 24 h. The main mechanism of the communication between EVs derived from HCF and their host remains unclear; however, time‐dependent anti‐inflammatory effects in our study suggest that HC may modulate the immune responses via EVs.
Undescribed Phenolic Glycosides from Syzygium attopeuense and Their Inhibition of Nitric Oxide Production

Four undescribed phenolic glycosides including three stilbene derivatives (1 and 3) and sodium salt of 3 (2), and a chalcone glycoside (4), together with thirteen known compounds (5–17) were isolated from the leaves of Syzygium attopeuense (Gagnep.) Merr. & L.M. Perry. Their chemical structures were elucidated to be (Z)‐gaylussacin (1), 6′′‐O‐galloylgaylussacin sodium salt (2), 6′′‐O‐galloylgaylussacin (3), 4′‐O‐[β‐D‐glucopyranosyl‐(1→6)‐glucopyranosyl]oxy‐2′‐hydroxy‐6′‐methoxydihydrochalcone (4), gaylussacin (5), pinosilvin 3‐O‐β‐D‐glucopyranoside (6), myricetin‐3‐O‐(2′′‐O‐galloyl)‐α‐L‐rhamnopyranoside (7), myricetin‐3‐O‐(3′′‐O‐galloyl)‐α‐L‐rhamnopyranoside (8), myricetin‐3‐O‐α‐L‐rhamnopyranoside (9), quercitrin (10), myricetin‐3‐O‐β‐D‐glucopyranoside (11), myricetin‐3‐O‐β‐D‐galactopyranoside (12), quercetin 3‐O‐α‐L‐arabinopyranoside (13), myricetin‐3‐O‐2′′‐O‐galloyl)‐α‐L‐arabinopyranoside (14), (+)‐gallocatechin (15), (−)‐epigallocatechin (16), and 3,3’,4’‐trimethoxyellagic acid 4‐O‐β‐D‐glucopyranoside (17) by the analysis of HR‐ESI‐MS, 1D and 2D NMR spectra in comparison with the previously reported data. Compounds 1–3, 5, and 6 significant inhibition of NO production in LPS‐activated RAW264.7 cells, with IC50 values ranging from 18.37±1.38 to 35.12±2.53 μM, compared to a positive control (dexamethasone) with an IC50 value of 15.37±1.42 μM.
On the shape of invading population in anisotropic environments

We analyze the properties of population spreading in environments with spatial anisotropy within the frames of a lattice model of asymmetric (biased) random walkers. The expressions for the universal shape characteristics of the instantaneous configuration of population, such as asphericity A and prolateness S are found analytically and proved to be dependent only on the asymmetric transition probabilities in different directions. The model under consideration is shown to capture, in particular, the peculiarities of invasion in presence of an array of oriented tubes (fibers) in the environment.
The root of the mystery: the role of long non-coding RNAs in regulating transcription

Gene expression specificity is a core aspect of transcriptional regulation—genes are expressed in specific temporal and spatial patterns to promote distinct developmental and environmental responses. Transcriptomic analyses have elucidated many of these gene expression profiles but have mostly focused on genes that encode for proteins. Far less studied is the role of other transcriptional products, such as long intergenic noncoding RNAs (lincRNAs), in gene expression. In animal systems, lincRNAs have been shown to affect chromatin structure, mRNA splicing and stability, and translation (Statello et al. 2021). In plants, a couple studies have surveyed lincRNAs in the genome
NB-MAFIA: An N-List Based Maximal Frequent Itemset Algorithm

The authors propose an efficient algorithm, NB-MAFIA, for mining maximal frequent itemset using NList, which uses node list of prefix tree to represent itemsets. By using N-List, itemsets’ support can be efficiently computed because of the high compactness of N-List and the efficiency of the method to intersect two N-Lists. Meanwhile, the authors employ some search space pruning strategies and superset checking strategy to improve NB-MAFIA. To evaluate NB-MAFIA, the authors compare proposed algorithm with two state-of-the-art algorithms on a variety of real and synthesis datasets. Experimental results show that NB-MAFIA is efficient and outperform the baseline algorithms in most case. Especially, NB-MAFIA is more efficient on dense datasets.
Personalized medicine with germline pathogenic variants: Importance of population‐ and region‐wide evidence

Rare germline pathogenic variants in cancer‐predisposing genes have a high impact and potential for clinical utility. In the last 30 years, based on evidence of cancer risk associated with germline pathogenic variants, several measures have been suggested for personalized medicine, including the development of novel treatments, treatment stratification, risk reduction by surgical measures, chemoprevention, removal of environmental factors, and surveillance for early detection among specific high‐risk individuals. However, this evidence is mainly based on evaluations of European populations. Our large‐scale analyses of more than 100,000 individuals, including 14 disease cases and non‐cancer controls in the Japanese population, suggest some discrepancies in the associations between cancer‐predisposing genes and diseases, expansion of the targeted diseases of BRCA1 and BRCA2, and a potential novel risk‐reduction measure for gastric cancer. They are likely to be explained by population and region variations; therefore, more population‐wide and region‐wide research could provide improved personalized medicine as well as a better understanding of disease mechanisms. This review summarizes current personalized medicine and discusses the potential use of germline pathogenic variants.
The role of neurotransmitters in mediating the relationship between brain alterations and depressive symptoms in patients with inflammatory bowel disease

A growing body of evidence from neuroimaging studies suggests that inflammatory bowel disease (IBD) is associated with functional and structural alterations in the central nervous system and that it has a potential link to emotional symptoms, such as anxiety and depression. However, the neurochemical underpinnings of depression symptoms in IBD remain unclear. We hypothesized that changes in cortical gamma‐aminobutyric acid (GABA+) and glutamine (Glx) concentrations are related to cortical thickness and resting‐state functional connectivity in IBD as compared to healthy controls. To test this, we measured whole‐brain cortical thickness and functional connectivity within the medial prefrontal cortex (mPFC), as well as the concentrations of neurotransmitters in the same brain region. We used the edited magnetic resonance spectroscopy (MRS) with the MEGA‐PRESS sequence at a 3 T scanner to quantitate the neurotransmitter levels in the mPFC. Subjects with IBD (N = 37) and healthy control subjects (N = 32) were enrolled in the study. Compared with healthy controls, there were significantly decreased GABA+ and Glx concentrations in the mPFC of patients with IBD. The cortical thickness of patients with IBD was thin in two clusters that included the right medial orbitofrontal cortex and the right posterior cingulate cortex. A seed‐based functional connectivity analysis indicated that there was higher connectivity of the mPFC with the left precuneus cortex (PC) and the posterior cingulate cortex, and conversely, lower connectivity in the left frontal pole was observed. The functional connectivity between the mPFC and the left PC was negatively correlated with the IBD questionnaire score (r = −0.388, p = 0.018). GABA+ concentrations had a negative correlation with the Hamilton Depression Scale (HAMD) score (r = −0.497, p = 0.002). Glx concentration was negatively correlated with the HAMD score (r = −0.496, p = 0.002) and positively correlated with the Short‐Form McGill Pain Questionnaire score (r = 0.330, p = 0.046, uncorrected). There was a significant positive correlation between the ratio of Glx to GABA+ and the HAMD score (r = 0.428, p = 0.008). Mediation analysis revealed that GABA+ significantly mediated the main effect of the relationship between the structural and functional alterations and the severity of depression in patients with IBD. Our study provides initial evidence of neurochemistry that can be used to identify potential mechanisms underlying the modulatory effects of GABA+ on the development of depression in patients with IBD.
The cell cycle protein MAD2 facilitates endocytosis of the serotonin transporter in the neuronal soma

Monoamine transporters retrieve serotonin (SERT), dopamine (DAT), and norepinephrine (NET) from the synaptic cleft. Transporter internalization contributes to the regulation of their surface expression. Clathrin‐mediated endocytosis of plasma membrane proteins requires adaptor protein‐2 (AP2), which recruits cargo to the nascent clathrin cage. However, the intracellular portions of monoamine transporters are devoid of a conventional AP2‐binding site. Here, we identify a MAD2 (mitotic arrest deficient‐2) interaction motif in the C‐terminus of SERT, which binds the closed conformation of MAD2 and allows for the recruitment of two additional mitotic spindle assembly checkpoint (SAC) proteins, BubR1 and p31comet, and of AP2. We visualize MAD2, BubR1, and p31comet in dorsal raphe neurons, and depletion of MAD2 in primary serotonergic rat neurons decreases SERT endocytosis in the soma. Our findings do not only provide mechanistic insights into transporter internalization but also allow for rationalizing why SAC proteins are present in post‐mitotic neurons.