Miracle-dz/UniFAR-FTUs huggingface dataset:
Identification of genetic determinants of tomato brown rugose fruit virus that enable infection of plants harbouring the Tm‐22 resistance gene

Abstract Tomato cultivars containing the Tm‐22 resistance gene have been widely known to resist tobacco mosaic virus (TMV) and tomato mosaic virus. Tomato brown rugose fruit virus (ToBRFV), a new emerging tobamovirus, can infect tomato plants carrying the Tm‐22 gene. However, the virulence determinant of ToBRFV that overcomes the resistance conferred by the Tm‐22 gene remains unclear. In this study, we substituted the movement protein (MP) encoding sequences between ToBRFV and TMV infectious clones and conducted infectivity assays. The results showed that MP was the virulence determinant for ToBRFV to infect Tm‐22 transgenic Nicotiana benthamiana plants and Tm‐22 ‐carrying tomato plants. A TMV MP chimera with amino acid residues 60–186 of ToBRFV MP failed to induce hypersensitive cell death in the leaves of Tm‐22 transgenic N. benthamiana plants. Chimeric TMV containing residues 60–186 of ToBRFV MP could, but chimeric ToBRFV containing 61–187 residues of TMV MP failed to infect Tm‐22 transgenic N. benthamiana plants, indicating that 60–186 residues of MP were important for ToBRFV to overcome Tm‐22 gene‐mediated resistance. Further analysis showed that six amino acid residues, H67, N125, K129, A134, I147, and I168 of ToBRFV MP, were critical in overcoming Tm‐22 ‐mediated resistance in transgenic N. benthamiana plants and tomato plants. These results increase our understanding of the mechanism by which ToBRFV overcomes Tm‐22 ‐mediated resistance.
The role of exosomes from BALF in lung disease

Exosomes are released from a variety of immune cells and nonimmune cells, the phospholipid vesicle bilayer membrane structure actively secreted into tissues. Recently, exosomes were demonstrated to be effectively delivered proteins, cholesterol, lipids, and amounts of DNA, mRNA, and noncoding RNAs to a target cell or tissue from a host cell. These can be detected in blood, urine, exhaled breath condensates, bronchoalveolar lavage fluid (BALF), ascites, and cerebrospinal fluid. BALF is a clinical examination method for obtaining alveolar cells and biochemical components, reflecting changes in the lungs, so it is also called liquid biopsy. Exosomes from BALF become a new method for intercellular communication and well‐documented in various pulmonary diseases. In chronic obstructive pulmonary disease (COPD), BALF exosomes can predict the degree of COPD damage and serve as an effective monitoring indicator for airflow limitation and airway remodeling. It also mediates antigen presentation in the airways to the adaptive immune system as well as costimulatory effects. Furthermore, BALF exosomes from acute lung injury and infective diseases are closely related to various infections and lack of oxygen status. BALF exosomes play an important role in the diagnosis and prognosis of lung cancer. The effect of immunomodulatory role for BALF exosomes in adaptive and innate immune responses has been studied in sarcoidosis. The intercellular communication in the microenvironment of BALF exosomes in pulmonary fibrosis and lung remodeling have been studied. In this review, we summarize the novel findings of exosomes in BALF, executed function by protein, miRNA, DNA cytokine, and so on in several pulmonary diseases.
Large Hall and Nernst responses from thermally induced spin chirality in a spin-trimer ferromagnet

Significance The scalar spin chirality (SSC) produced by noncoplanar spins is a cornerstone of the foundation of skyrmionics and the physics of geometrically frustrated magnets; this quantity translates the topology of the magnetic structure to the language of directly measurable responses in transport properties. In this work, we not only report the gigantic Hall and Nernst effects emerging from thermally induced SSC in a conducting ferromagnet, but also find arguments for the relevance of the momentum space description of the generated Berry phase. Furthermore, we demonstrate that the idea of fluctuating SSC is not limited to magnets with conduction electrons strongly Hund’s-rule–coupled to local magnetic moments but is valid for a broader group of itinerant magnets with triangular-like lattice geometry. The long-range order of noncoplanar magnetic textures with scalar spin chirality (SSC) can couple to conduction electrons to produce an additional (termed geometrical or topological) Hall effect. One such example is the Hall effect in the skyrmion lattice state with quantized SSC. An alternative route to attain a finite SSC is via the spin canting caused by thermal fluctuations in the vicinity of the ferromagnetic ordering transition. Here, we report that for a highly conducting ferromagnet with a two-dimensional array of spin trimers, the thermally generated SSC can give rise to a gigantic geometrical Hall conductivity even larger than the intrinsic anomalous Hall conductivity of the ground state. We also demonstrate that the SSC induced by thermal fluctuations leads to a strong response in the Nernst effect. A comparison of the sign and magnitude of fluctuation–Nernst and Hall responses in fundamental units indicates the need for a momentum–space picture to model these thermally induced signals.
Capabilities and limitations of using DNA metabarcoding to study plant–pollinator interactions

Many pollinator populations are experiencing declines, emphasizing the need for a better understanding of the complex relationship between bees and flowering plants. Using DNA metabarcoding to describe plant–pollinator interactions eliminates many challenges associated with traditional methods and has the potential to reveal a more comprehensive understanding of foraging behaviour and pollinator life history. Here we use DNA metabarcoding of ITS2 and rbcL gene regions to identify plant species present in pollen loads of 404 bees from three habitats in eastern Oregon. Our specific objectives were to (i) determine whether plant species identified using DNA metabarcoding are consistent with plant species identified using observations, (ii) compare characterizations of diet breadth derived from foraging observations to those based on plant species assignments obtained using DNA metabarcoding, and (iii) compare plant species assignments produced by DNA metabarcoding using a “regional” reference database to those produced using a “local” database. At the three locations, 31%–86% of foraging observations were consistent with DNA metabarcoding data, 8%–50% of diet breadth characterizations based on observations differed from those based on DNA metabarcoding data, and 22%–25% of plant species detected using the regional database were not known to occur in the study area in question. Plant–pollinator networks produced from DNA metabarcoding data had higher sampling completeness and significantly lower specialization than networks based on observations. Here, we examine some strengths and limitations of using DNA metabarcoding to identify plant species present in bee pollen loads, make ecological inferences about foraging behaviour and provide guidance for future research.
Abrupt and altered cell-type specific DNA methylation profiles in blood during acute HIV infection persists despite prompt initiation of ART

HIV-1 disrupts the host epigenetic landscape with consequences for disease pathogenesis, viral persistence, and HIV-associated comorbidities. Here, we examined how soon after infection HIV-associated epigenetic changes may occur in blood and whether early initiation of antiretroviral therapy (ART) impacts epigenetic modifications. We profiled longitudinal genome-wide DNA methylation in monocytes and CD4+ T lymphocytes from 22 participants in the RV254/SEARCH010 acute HIV infection (AHI) cohort that diagnoses infection within weeks after estimated exposure and immediately initiates ART. We identified monocytes harbored 22,697 differentially methylated CpGs associated with AHI compared to 294 in CD4+ T lymphocytes. ART minimally restored less than 1% of these changes in monocytes and had no effect upon T cells. Monocyte DNA methylation patterns associated with viral load, CD4 count, CD4/CD8 ratio, and longitudinal clinical phenotypes. Our findings suggest HIV-1 rapidly embeds an epigenetic memory not mitigated by ART and support determining epigenetic signatures in precision HIV medicine. Trial Registration:NCT00782808 and NCT00796146.
SHP2 Potentiates the Oncogenic Activity of β-Catenin to Promote Triple-Negative Breast Cancer

Previous studies have reported dysregulated cytoplasmic and nuclear expression of the β-catenin protein in triple-negative breast cancer (TNBC) in the absence of Wnt signaling pathway dysregulation. However, the mechanism that sustains β-catenin protein dysregulation independent of Wnt signaling is not understood. In this study, we show that Src homology phosphotyrosyl phosphatase 2 (SHP2) is essential for β-catenin protein stability and for sustaining the cytoplasmic and nuclear pools in TNBC cells. The first evidence for this possibility came from immunofluorescence (IF) and immunoblotting (IB) studies that showed that inhibition of SHP2 induces E-cadherin expression and depletion of cytoplasmic and nuclear β-catenin, which in turn confers adherence junction mediated cell–cell adhesion. We further show that SHP2 promotes β-catenin protein stability by mediating the inactivation of GSK3β through its positive effect on Akt and ERK1/2 activation, which was confirmed by direct pharmacologic inhibition of the PI3K-Akt and the MEK-ERK signaling pathway. Finally, we show that SHP2-stabilized β-catenin contributes to TNBC cell growth, transformation, cancer stem cell (CSC) properties, and tumorigenesis and metastasis. Overall, the findings in this report show that SHP2 mediates β-catenin protein stability to promote TNBC. Implications: Data presented in this article demonstrates that SHP2 positively regulates β-catenin protein stability, which in turn promotes triple-negative breast cancer (TNBC) cell transformation, tumorigenesis, and metastasis.
The impact of socio-cultural values on autistic women: An interpretative phenomenological analysis

It is well recognised that culture plays an important role in how people experience the world. However, there is limited knowledge on the impact of socio-cultural norms and values on the lives of autistic women. This qualitative study used individual semi-structured interviews to explore how eight cis-gendered autistic women, without co-occurring intellectual disabilities, describe dominant socio-cultural beliefs, values and norms and their influence on their own sense of self. Findings elucidated three interdependent themes related to the ‘pervasive influence of cultural values’, ‘individualisation as an autistic woman’ and ‘social connectivity’. Autistic women described how they experienced their environments and made choices about their place within the dominant culture and the impact of these decisions on their identities and experience. The findings of this study have implications for the continued need to shift societal and clinical attitudes towards understanding and appreciating diversity among autistic women. Lay abstract Autistic women with average or above intellectual abilities are often overlooked clinically or identified at older ages compared to autistic males. Their experiences can provide insight into the socio-cultural factors that impact on how they develop and are seen by others. This study asked autistic women to describe the culture around them and explore how this has influenced their lived experiences. Individual semi-structured interviews were conducted with eight autistic women without a co-occurring diagnosis of intellectual disabilities. These were used for interpretative phenomenological analysis. Overall, we found three closely connected themes on the pervasive influence of cultural values on autistic women, how autistic women define themselves and the importance of connecting with society. These findings suggest that dominant cultural beliefs, values and norms effect how autistic women are recognised by others and develop their sense of self. Broadening how people think about autistic women in society and clinically may benefit how we identify and support autistic women.
Type of headache at onset and risk for complications in reversible cerebral vasoconstriction syndrome

In a recent Italian study, 30% of patients with reversible cerebral vasoconstriction syndrome (RCVS) presented without thunderclap headache (TCH), and tended to present more severe forms of RCVS than patients with TCH. We aimed to analyze the risk for complications of RCVS in patients with and without TCH at onset.
Anthocyanins from Pomegranate (Punica granatum L.) and Their Role in Antioxidant Capacities in Vitro

As phytochemicals, anthocyanins are not only responsible for the diverse colors in nature, but are associated with broad‐spectrum health‐promoting effects for human beings. Pomegranate is abundant in anthocyanins which possess high antioxidant capacities. However, the pomegranate anthocyanins profile and their contributions to antioxidant capacities are not fully depicted. The purpose of this article is to review anthocyanins from pomegranate as important antioxidants. Total anthocyanin content (TAC) and six major components vary greatly with intrinsic and extrinsic factors. In pomegranate, anthocyanins mainly acted as primary antioxidants, while their action as secondary antioxidants were not conclusive. The antioxidant potentials of anthocyanins were significantly affected by factors especially chemical structure and detection assays in vitro. The current knowledge may provide insights into potential applications for pomegranate anthocyanins based on their antioxidant activities.
Severe early‐onset fetal growth restriction: What do we tell the prospective parents?

Fetal growth restriction (FGR) is a common complication of pregnancy, associated with higher risk of perinatal mortality and adverse health and developmental outcomes for surviving infants. True FGR relates to a pathological restriction of fetal growth resulting from complex interactions between maternal, placental, fetal, and environmental factors. Early‐onset FGR (onset <32 weeks' gestation) is often first suspected at routine mid‐trimester sonographic assessment of fetal morphology, or identified as part of the placental syndrome, commonly maternal pre‐eclampsia. Prenatal investigations may identify the cause of FGR. Timing of delivery is guided by serial sonographic surveillance of fetal growth and well‐being and maternal condition, balancing the risk of stillbirth with the benefits of advancing gestation. This is particularly pertinent to severe early‐onset FGR, a leading iatrogenic cause of very preterm birth. Prognosis is largely determined by the severity of FGR and its causes, gestation at birth, and birthweight. Pregnancy termination may be considered. Antenatal care and delivery in a tertiary center, provided by a multi‐disciplinary team with expertise in managing high‐risk pregnancies, are imperative to optimizing outcomes.
Pathogenic bacteria in cheese, raw and pasteurised milk

Abstract Background Foodborne diseases, especially those transmitted by milk and its products, are worldwide problem. Milk is not only a complete food but also a unique medium for activating various bacteria such as Listeria monocytogenes, Staphylococcus aureus and Salmonella typhi. In recent years, numerous bacteria with multiple drug resistance patterns have appeared, and there have been many problems in infection control. Today, ranchers use antibiotics for control of the animal disease, and humans are constantly using animal products containing antibiotics. Objective The purpose of this study was to evaluate the contamination status of raw and pasteurised milk as well as local cheese and to find a rapid Multiplex PCR method for investigation of contamination. Determination of antibiotic resistant isolates is also desirable. Materials and Methods One hundred samples were collected from livestock and retail outlets using culture and molecular methods to identify S. aureus, L. monocytogenes and S. typhi. The antibiotic resistance pattern was determined for the isolates. Results In this study, culture results for 100 samples showed 10% S. aureus isolates while no cases of S. typhi and L. monocytogenes were detected. In real‐time qPCR, S. aureus was isolated in 60% (n = 60) of samples, S. typhi in 53% (n = 53) and L. monocytogenes in 2% (n = 2). The results of sensitivity and specificity of Multiplex PCR for the three studied bacteria indicated general specificity of 72% and sensitivity of 80%. Conclusion Based on the results of this study, it can be concluded that S. typhi, L. monocytogenes and S. aureus are more likely to be detected by real‐time qPCR because of the high sensitivity of this test to culture. Multiplex method was not reliable in this study and cannot be suggested for rapid diagnosis.
Port delivery system: a novel drug delivery platform to treat retinal diseases

ABSTRACT Introduction Retinal disease treatment delivery is mostly limited to intravitreal injections and slow-release injectable implants due to structural barriers in the eye, and carry associated adverse effects and relatively high treatment burden. The Port Delivery System with ranibizumab (PDS) is a novel drug delivery device that is surgically implanted into the vitreous cavity and allows for continuous release of the anti-vascular endothelial growth factor (anti-VEGF) ranibizumab, eliminating the need for frequent intravitreal injections while maintaining therapeutic intraocular drug levels to control disease activity. Investigations of PDS are summarized in this review. Areas covered The most recent reported findings from preliminary studies and phase I–III trials are reviewed. We discuss the ramifications of these studies and the future potential for PDS in the treatment of retinal diseases. Expert opinion PDS is a novel drug delivery platform for the treatment of retinal diseases. Currently, the data from the PDS has shown promising efficacy and ability to substantially mitigate treatment burden while effectively generating visual and anatomic outcomes similar to those in patients receiving the standard monthly ranibizumab for neovascular age-related macular degeneration. Further studies are ongoing to investigate this novel drug delivery system in other disease states.
Socioeconomic Position and Late-Onset Dementia: A Nationwide Register-Based Study

Objectives Previous research on the association between socioeconomic position (SEP) and dementia has not sufficiently accounted for the complex relationship between education and occupation. We investigated the independent and joint effects of educational attainment and occupation-based SEP on dementia. Methods We used register-based information about educational attainment, occupation-based SEP, and dementia from 1,210,720 individuals. Information about cognitive ability at conscription was available for a subsample of men. Results When mutually adjusted, lower educational attainment and occupation-based SEP were associated with higher dementia risk in a dose–response manner. Higher occupation-based SEP partly mitigated the higher dementia risk associated with lower educational attainment. After adjusting for cognitive ability in a subgroup of men, only unskilled work was associated with higher dementia risk. Discussion Occupation-based SEP is independently associated with dementia and may mitigate the higher dementia risk associated with short education. Future research should elucidate the mechanisms underlying social inequality in dementia.
The spatial footprint and patchiness of large‐scale disturbances on coral reefs

Ecosystems have always been shaped by disturbances, but many of these events are becoming larger, more severe and more frequent. The recovery capacity of depleted populations depends on the frequency of disturbances, the spatial distribution of mortality and the scale of dispersal. Here, we show that four mass coral bleaching events on the Great Barrier Reef (in 1998, 2002, 2016 and 2017) each had markedly larger disturbance footprints and were less patchy than a severe category 5 tropical cyclone (Cyclone Yasi, 2011). Severely bleached reefs in 2016 and 2017 were isolated from the nearest lightly affected reefs by up to 146 and 200 km, respectively. In contrast, reefs damaged by Cyclone Yasi were on average 20 km away from relatively undisturbed reefs, well within the estimated range of larval dispersal for most corals. Based on these results, we present a model of coral reef disturbance and recovery to examine (1) how the spatial clustering of disturbances modifies large‐scale recovery rates; and (2) how recovery rates are shaped by species' dispersal abilities. Our findings illustrate that the spatial footprint of the recent mass bleaching events poses an unprecedented threat to the resilience of coral species in human history, a threat that is even larger than the amount of mortality suggests.
Learning Curricula for Multilingual Neural Machine Translation Training

Low-resource Multilingual Neural Machine Translation (MNMT) is typically tasked with improving the translation performance on one or more language pairs with the aid of high-resource language pairs. In this paper and we propose two simple search based curricula – orderings of the multilingual training data – which help improve translation performance in conjunction with existing techniques such as fine-tuning. Additionally and we attempt to learn a curriculum for MNMT from scratch jointly with the training of the translation system using contextual multi-arm bandits. We show on the FLORES low-resource translation dataset that these learned curricula can provide better starting points for fine tuning and improve overall performance of the translation system.
On nature and causes of observed MT errors

This work describes analysis of nature and causes of MT errors observed by different evaluators under guidance of different quality criteria: adequacy and comprehension and and a not specified generic mixture of adequacy and fluency. We report results for three language pairs and two domains and eleven MT systems. Our findings indicate that and despite the fact that some of the identified phenomena depend on domain and/or language and the following set of phenomena can be considered as generally challenging for modern MT systems: rephrasing groups of words and translation of ambiguous source words and translating noun phrases and and mistranslations. Furthermore and we show that the quality criterion also has impact on error perception. Our findings indicate that comprehension and adequacy can be assessed simultaneously by different evaluators and so that comprehension and as an important quality criterion and can be included more often in human evaluations.
Investigating Active Learning in Interactive Neural Machine Translation

Interactive-predictive translation is a collaborative iterative process and where human translators produce translations with the help of machine translation (MT) systems interactively. Various sampling techniques in active learning (AL) exist to update the neural MT (NMT) model in the interactive-predictive scenario. In this paper and we explore term based (named entity count (NEC)) and quality based (quality estimation (QE) and sentence similarity (Sim)) sampling techniques – which are used to find the ideal candidates from the incoming data – for human supervision and MT model’s weight updation. We carried out experiments with three language pairs and viz. German-English and Spanish-English and Hindi-English. Our proposed sampling technique yields 1.82 and 0.77 and 0.81 BLEU points improvements for German-English and Spanish-English and Hindi-English and respectively and over random sampling based baseline. It also improves the present state-of-the-art by 0.35 and 0.12 BLEU points for German-English and Spanish-English and respectively. Human editing effort in terms of number-of-words-changed also improves by 5 and 4 points for German-English and Spanish-English and respectively and compared to the state-of-the-art.