Miracle-dz/UniFAR-FTUs huggingface dataset:
Deep Nested Hierarchical Dirichlet Processes

The focus of this paper is on deep Bayesian non-parametric models and, more specifically, on admixture models of this kind. In admixture or mixed membership models [5], each data item is modeled as a mixture over components, and such models have significantly richer representational power compared to mixture models and also wide applicability. The Hierarchical Dirichlet Process (HDP) [5] extends the notion of finite admixture models, famously captured by Latent Dirichlet Allocation (LDA) [4], to infinite mixture components. The HDP does this by coupling Dirichlet Processes (DP) [2], such that a draw from a DP serves as the base distribution for another DP. In this paper, we explore how such layers of admixtures can be nested arbitrarily deeply. While the Bayesian framework serves as a natural protection against overfitting, we would like to provide as much flexibility to a model within this framework. Layers of admixtures, instead of mixtures, provides such flexibility. The Author-Topic Model [9] explores such a two level model in the finite setting, where documents are mixtures over ‘topics’ and topics are mixtures over ‘authors’. We explore such models in the infinite setting, which are also arbitrarily deep where the representation consists of layers of entities, and each entity is a mixture over entities at the previous layer.
X-ray analysis of the galaxy group UGC 03957 beyond R200 with Suzaku

Context. In the last few years, the outskirts of galaxy clusters have been studied in detail and the analyses have brought up interesting results such as indications of possible gas clumping and the breakdown of hydrostatic, thermal, and ionization equilibrium. These phenomena affect the entropy profiles of clusters, which often show deviations from the self-similar prediction around R 200 . However, significant uncertainties remain for groups of galaxies. In particular the question, of whether entropy profiles are similar to those of galaxy clusters. Aims. We investigated the gas properties of the galaxy group UGC 03957 up to 1.4 R 200 ≈ 1.4 Mpc in four azimuthal directions with the Suzaku satellite. We checked for azimuthal symmetry and obtained temperature, entropy, density, and gas mass profiles. Previous studies point to deviations from equilibrium states at the outskirts of groups and clusters and so we studied the hydrodynamical status of the gas at these large radii. Methods. We performed a spectral analysis of five Suzaku observations of UGC 03957 with ~138 ks good exposure time in total and five Chandra snapshot observations for point source detection. We investigated systematic effects such as point spread function and uncertainties in the different background components, and performed a deprojection of the density and temperature profile. Results. We found a temperature drop of a factor of ~3 from the center to the outskirts that is consistent with previous results for galaxy clusters. The metal abundance profile shows a flat behavior towards large radii, which is a hint for galactic winds as the primary ICM enrichment process. The entropy profile is consistent with numerical simulations after applying a gas mass fraction correction. Feedback processes and AGN activity might be one explanation for entropy modification, imprinting out to larger radii in galaxy groups than in galaxy clusters. Previous analyses for clusters and groups often showed an entropy flattening or even a drop around ~ R 200 , which can be an indication of clumping or non-equilibrium states in the outskirts. Such entropy behavior is absent in UGC 03957. The gas mass fraction is well below the cosmic mean but rises above this value beyond R 200 , which could be a hint for deviations from hydrostatic equilibrium at these large radii. By measuring the abundance of the α -elements Si and S at intermediate radii we determined the relative number of different supernovae types and found that the abundance pattern can be described by a relative contribution of 80%−100% of core-collapse supernovae. This result is in agreement with previous measurements for galaxy groups.
Characteristics of environmental RNAi in potato psyllid, Bactericera cockerelli (Sulc) (Hemiptera: Psylloidea: Triozidae)

RNA interference (RNAi) has potential to become a major tool for integrated management of insect pests of agricultural crops based on sequence-specificity and low doses of rapidly biodegradable dsRNA. Deploying ‘environmental RNAi’ for control of insect vectors of plant pathogens is of increasing interest for combatting emerging plant diseases. Hemipteran insect vectors, including psyllids, are vascular feeders, making their development difficult to control specifically by targeting with pesticidal chemistries. Psyllids transmit “Candidatus Liberibacter solanacearum” the causal organism of potato zebra chip and tomato vein greening diseases, transmitted, respectively, by the potato or tomato psyllid (PoP). Until now, the optimal effective concentration(s) of double-stranded RNA (dsRNA) required for significant gene knockdown and RNAi persistence in PoP have not been determined. The objective of this study was to optimize RNAi in young PoP adults and 3rd instars for screening by oral delivery of dsRNAs. The minimal effective dsRNA concentrations required for robust knockdown and persistence were evaluated by delivering seven concentrations spanning 0.1 ng/μL to 500 ng/μL over post ingestion-access periods (IAP) ranging from 48 h to 12 days. The PoP gene candidates evaluated as targets were vacuolar ATPase subunit A, clathrin heavy chain, and non-fermenting protein 7, which were evaluated for knockdown by qPCR amplification. The minimum and/or the second most effective dsRNA concentration resulting in effective levels of gene knockdown was 100 ng/μL for all three targets. Higher concentrations did not yield further knockdown, indicating potential RISC saturation at the higher doses. Gene silencing post-IAP of 100 ng/μL dsRNA persisted for 3–5 days in adults and nymphs, with the PoP 3rd instar, followed by teneral and mature adults, respectively, exhibiting the most robust RNAi-response.
Calcium/calmodulin-mediated microbial symbiotic interactions in plants

Cytoplasmic calcium (Ca2+) transients and nuclear Ca2+ oscillations act as hubs during root nodulation and arbuscular mycorrhizal symbioses. Plants perceive bacterial Nod factors or fungal signals to induce the Ca2+ oscillation in the nucleus of root hair cells, and subsequently activate calmodulin (CaM) and Ca2+/CaM-dependent protein kinase (CCaMK). Ca2+ and CaM-bound CCaMK phosphorylate transcription factors then initiate down-stream signaling events. In addition, distinct Ca2+ signatures are activated at different symbiotic stages: microbial colonization and infection; nodule formation; and mycorrhizal development. Ca2+ acts as a key signal that regulates a complex interplay of downstream responses in many biological processes. This short review focuses on advances in Ca2+ signaling-regulated symbiotic events. It is meant to be an introduction to readers in and outside the field of bacterial and fungal symbioses. We summarize the molecular mechanisms underlying Ca2+/CaM-mediated signaling in fine-tuning both local and systemic symbiotic events.
Case report: Simultaneous occurrence of primary pulmonary lymphoma and opportunistic infections in a patient with chronic myeloid leukemia

Background The occurrence of primary pulmonary lymphoma (PPL) as a secondary malignancy in patients diagnosed with chronic myeloid leukemia (CML) is extremely rare. As the clinical manifestations are atypical, most patients with PPL tend to be misdiagnosed with pneumonia. When the radiographic features of PPL and pulmonary infection overlap, clinicians can be confused about the diagnosis. Here, we report the first case of coexistence of PPL and opportunistic infections in a patient with CML in chronic phase (CML-CP). Case presentation A 55-year-old woman presented with three weeks of hemorrhage of the oral mucosa at the Department of Hematology. After undergoing various examinations, she was diagnosed with CML-CP and was started on imatinib (400 mg/daily). Due to sudden respiratory distress, the patient was admitted to the respiratory intensive care unit 11 months later. Chest computed tomography (CT) revealed ground-glass opacities, patchy shadows, and multiple nodules in both lungs and enlarged mediastinal lymph nodes. The combination of biapenem and voriconazole antibiotic treatments was effective. The patient’s respiratory distress was relieved, but there was intermittent coughing. In the following time, the patient developed a fever, and the imaging findings indicated progression of the disease in both lungs. Bronchoalveolar lavage (BAL) identified pathogens of multiple opportunistic infections. The coexistence of lymphomatoid granulomatosis (LYG) was not confirmed in this patient until a second CT-guided biopsy was performed. Ultimately, the patient underwent chemotherapy in time and is currently alive today. Conclusions When the patient’s recurrent respiratory symptoms and imaging findings do not coincide, secondary tumors should be considered in addition to infection as a diagnosis. In these cases, multiple pathological tissue biopsies should be performed.
Bibliometric analysis of research on Alzheimer’s disease and non-coding RNAs: Opportunities and challenges

Background Non-coding RNAs (ncRNA) are a kind of RNA that does not encode protein, which play an important role in Alzheimer’s disease (AD). However, there is a lack of bibliometric analysis and visualization analysis of the research related to AD and ncRNAs. Materials and methods Literature related to AD and ncRNAs in the last decade were searched through the Web of Science Core Collection (WOSCC). The relevant information from all the searched articles was collected. The bibliometric visualization website, CiteSpace, and VOSviewer were used for visualization analysis of countries/regions, institutions, authors, and keywords. Results In total, 1,613 kinds of literature were published in the field. Literature in this field were published in 494 journals. The Journal of Alzheimer’s Disease was the most popular journal. China, Louisiana State University System, and Lukiw WJ were the countries/regions, institutions, and authors with the highest scientific productivity, respectively. The research hotspots in this field focused on the role and mechanism of ncRNAs, especially microRNAs, in AD. The level of research was mainly based on basic research, focusing on animal and cellular levels, and related to proteomics. “Circular RNAs,” “regulation of neuroinflammation,” and “tau protein” were the future research directions. Conclusion Taken together, the field of AD and ncRNAs is developing well. The research hotspots and frontiers in this field can provide a reference for researchers to choose their research direction.
Systematic analysis of the effects of genetic variants on chromatin accessibility to decipher functional variants in non-coding regions

Genome-wide association study (GWAS) has identified thousands of single nucleotide polymorphisms (SNPs) associated with complex diseases and traits. However, deciphering the functions of these SNPs still faces challenges. Recent studies have shown that SNPs could alter chromatin accessibility and result in differences in tumor susceptibility between individuals. Therefore, systematically analyzing the effects of SNPs on chromatin accessibility could help decipher the functions of SNPs, especially those in non-coding regions. Using data from The Cancer Genome Atlas (TCGA), chromatin accessibility quantitative trait locus (caQTL) analysis was conducted to estimate the associations between genetic variants and chromatin accessibility. We analyzed caQTLs in 23 human cancer types and identified 9,478 caQTLs in breast carcinoma (BRCA). In BRCA, these caQTLs tend to alter the binding affinity of transcription factors, and open chromatin regions regulated by these caQTLs are enriched in regulatory elements. By integrating with eQTL data, we identified 141 caQTLs showing a strong signal for colocalization with eQTLs. We also identified 173 caQTLs in genome-wide association studies (GWAS) loci and inferred several possible target genes of these caQTLs. By performing survival analysis, we found that ~10% caQTLs potentially influence the prognosis of patients. To facilitate access to relevant data, we developed a user-friendly data portal, BCaQTL (http://gong_lab.hzau.edu.cn/caqtl_database), for data searching and downloading. Our work may facilitate fine-map regulatory mechanisms underlying risk loci of cancer and discover the biomarkers or therapeutic targets for cancer prognosis. The BCaQTL database will be an important resource for genetic and epigenetic studies.
Molecular and physiologic mechanisms of advanced ripening by trunk girdling at early veraison of ‘Summer Black’ grape

Although the effects of girdling on grape berry development have been widely studied, the underlying mechanisms are poorly understood, especially at the molecular level. This study investigated the effect of trunk girdling on grape (Vitis L.) berry maturation. Girdling was performed on 5-year-old ‘Summer Black’ grapevines at early veraison, and transcriptional and physiologic analyses were performed. Trunk girdling promoted sugar accumulation and color development in berries and accelerated berry ripening by 25 days. Genes related to sucrose cleavage and polysaccharide degradation were upregulated at the transcriptional level, which was associated with increased monosaccharide accumulation and berry softening. Anthocyanin biosynthesis and accumulation were also enhanced by trunk girdling through the upregulation of anthocyanin biosynthesis genes including phenylalanine ammonia-lyase and UDP-glucose:flavonoid 3-O-glucosyltransferase (UFGT). The increased expression of two VvUFGT genes was accompanied by the upregulation of VvMYBA2 under girdling. The upregulation of genes involved in ethylene biosynthesis and hormone (abscisic acid and brassinosteroid) responses and downregulation of genes involved in indoleacetic acid biosynthesis and response may have also promoted berry ripening in the girdling group. A total of 120 differentially expressed transcription factor genes from 29 gene families including MYB, ERF, and MYB-related were identified in the girdling group, which may participate in the regulation of berry development and ripening. These results provide molecular-level insight into the positive effects of trunk girdling on berry development in grapes.
Spectral analysis of field emission flicker (1/f) noise

Spectral Analysis of Field Emission Flicker (II J) Noise Mark Alan Gesley, Ph.D. Oregon Graduate Center, 1985 Supervising professor: Lynwood W. Swanson Spectral analysis of field emission noise induced by emitter surface equilibrium density fluctuations is developed. The noise spectrum factors as S( w) = Soo(w) + SB( w) for a canonical ensemble, which characterizes adsorbate covered emitters. Soo( w) and SB( w) correspond to unbounded diffusion and the boundary effect respectively. Chemical diffusivity Dc is defined by Fick's first law. Its equilibrium limit, termed hydrodynamic Dh' is derived from S( w) and related to the adsorbate fluctuations. These diffusivities are compared using irreversible thermodynamic and Kubo relations. Their equality is ensured by evaluation of the excess entropy production only when the density gradient is small and no phase change occurs. Two dimensional adsorbate phase transitions are identified by correlating incipient nonlinearity in the Arrhenius plot of diffusivity with the onset of a temperature dependent total noise power, which is proportional to adsorbate isothermal compressibility. Examples using KIW, XefW, and HIW are given. Thermal field emission noise is characterized by a grand canonical ensemble (GCE). Here the diffusive fluctuation mechanism includes adatom creation and defect vacancy formation resulting from surface free energy minimization. Adatom dynamics are governed by a stochastic diffusion equation. A multidimensional version of Carson's theorem is formulated, which leads to S( w) ~ C( x =0, w) Nc-1(w), where (hkl) geometry affects C( x =0, w)
De novo transcriptome based insights into secondary metabolite biosynthesis in Malaxis acuminata (Jeevak)–A therapeutically important orchid

Malaxis acuminata D. Don [=Crepidium acuminatum (D. Don) Szlach. ] is an endangered medicinal orchid of the Ashtvarga group of plants in Ayurveda (Indian system of traditional medicine). Using a combination of aromatic cytokinin [meta-Topolin (mT)], plant biostimulant (chitosan), auxin [indole-3-butyric acid (IBA)], and a phenolic elicitor [phloroglucinol (PG)], plants of M. acuminata were regenerated in vitro for mass multiplication. The present research reveals the first-ever transcriptome of M. acuminata. A total of 43,111 transcripts encoding 23,951 unigenes were assembled de novo from a total of 815.02 million reads obtained from leaf and pseudobulb of in vitro raised M. acuminata. Expression analysis of genes associated with β-sitosterol and eugenol biosynthesis in leaf and pseudobulb provided vital clues for differential accumulation of metabolites in M. acuminata. Ultra-performance liquid chromatography (UPLC) confirmed higher amounts of β-sitosterol and eugenol content in the leaf as compared to the pseudobulb. Differential expression of transcripts related to starch and sucrose metabolism, plant hormone signal transduction, diterpenoid biosynthesis, phenylalanine metabolism, stilbenoid, diarylheptanoid, and gingerol biosynthesis suggested the operation of differential metabolic pathways in leaf and pseudobulb. The present research provides valuable information on the biosynthesis of secondary metabolites in M. acuminata, which could be used for advanced metabolite bioprospection using cell suspension culture and bioreactor-based approaches. Data also suggested that leaf tissues rather than pseudobulb can be used as an alternate source of bioactive metabolites thereby shifting the need for harvesting the pseudobulb. This will further facilitate the conservation and sustainable utilization of this highly valued medicinal orchid.
Outcomes of sonographically-suspected fetal intra-abdominal cysts: Surgical intervention, conservative management and spontaneous regression

Objective The prenatal diagnosis of fetal intra-abdominal cysts is challenging. This study aimed to evaluate the diagnostic ability of prenatal ultrasound for fetal intra-abdominal cysts and to develop a predictive method for pre- and postnatal outcomes. Methods We retrospectively reviewed fetuses with ultrasound-detected intra-abdominal cysts between January 2013 and January 2020. The maternal–fetal clinical characteristics and ultrasound parameters were integrated into a model of pre- or postnatal outcomes. Results The study enrolled 190 eligible fetuses, including 94 cases of spontaneous regression, 33 cases of conservative management and 63 cases of surgical intervention. For the 63 cases of surgical intervention, prenatal ultrasound was found to identify fetal intra-abdominal cysts with 80.00% sensitivity (95% CI: 67.03%–89.57%), 37.50% specificity (95% CI: 8.52%–75.51%), 89.80% positive predictive value (95% CI: 83.51%–93.86%), 21.43% negative predictive value (95% CI: 8.80%–43.53%) and 74.60% accuracy (95% CI: 62.06%–84.73%). The predictive model of prenatal spontaneous regression was as follows: y = −3.291 + 0.083 × gestational age + 1.252 × initial diameter, with an area under the curve (AUC) of 0.819 (95% CI: 0.739–0.899) and an optimal cut-off value of 0.74. The large cyst diameter before delivery was an independent predictor of postnatal surgical intervention (p < 0.001), with an AUC of 0.710 (95% CI: 0.625–0.794) and an optimal cut-off value of 3.35 cm. Conclusion Although ultrasound has a limited ability in the accurate diagnosis of fetal abdominal cysts, a simple method of measuring the diameter can predict fetal outcomes and identify the cases that may require surgical intervention or spontaneous regression.
First insights in perception of feet and lower-body stimuli for proximity and collision feedback in 3D user interfaces

The visual and auditory quality of computer-mediated stimuli for virtual and extended reality (VR/XR) is rapidly improving. Still, it remains challenging to provide a fully embodied sensation and awareness of objects surrounding, approaching, or touching us in a 3D environment, though it can greatly aid task performance in a 3D user interface. For example, feedback can provide warning signals for potential collisions (e.g., bumping into an obstacle while navigating) or pinpointing areas where one’s attention should be directed to (e.g., points of interest or danger). These events inform our motor behaviour and are often associated with perception mechanisms associated with our so-called peripersonal and extrapersonal space models that relate our body to object distance, direction, and contact point/impact. We will discuss these references spaces to explain the role of different cues in our motor action responses that underlie 3D interaction tasks. However, providing proximity and collision cues can be challenging. Various full-body vibration systems have been developed that stimulate body parts other than the hands, but can have limitations in their applicability and feasibility due to their cost and effort to operate, as well as hygienic considerations associated with e.g., Covid-19. Informed by results of a prior study using low-frequencies for collision feedback, in this paper we look at an unobtrusive way to provide spatial, proximal and collision cues. Specifically, we assess the potential of foot sole stimulation to provide cues about object direction and relative distance, as well as collision direction and force of impact. Results indicate that in particular vibration-based stimuli could be useful within the frame of peripersonal and extrapersonal space perception that support 3DUI tasks. Current results favor the feedback combination of continuous vibrotactor cues for proximity, and bass-shaker cues for body collision. Results show that users could rather easily judge the different cues at a reasonably high granularity. This granularity may be sufficient to support common navigation tasks in a 3DUI.
Editorial: What, how, and where to eat is more than an individual choice: New ways to achieve healthy eating

COPYRIGHT © 2022 Ginani, Saccol and Zandonadi. 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. Editorial: What, how, and where to eat is more than an individual choice: New ways to achieve healthy eating