Miracle-dz/UniFAR-FTUs huggingface dataset:
Bacterial type III effector–induced plant C8 volatiles elicit antibacterial immunity in heterospecific neighbouring plants via airborne signalling

Abstract Upon sensing attack by pathogens and insect herbivores, plants release complex mixtures of volatile compounds. Here, we show that the infection of lima bean (Phaseolus lunatus L.) plants with the non‐host bacterial pathogen Pseudomonas syringae pv. tomato led to the production of microbe‐induced plant volatiles (MIPVs). Surprisingly, the bacterial type III secretion system, which injects effector proteins directly into the plant cytosol to subvert host functions, was found to prime both intra‐ and inter‐specific defense responses in neighbouring wild tobacco (Nicotiana benthamiana) plants. Screening of each of 16 effectors using the Pseudomonas fluorescens effector‐to‐host analyser revealed that an effector, HopP1, was responsible for immune activation in receiver tobacco plants. Further study demonstrated that 1‐octen‐3‐ol, 3‐octanone and 3‐octanol are novel MIPVs emitted by the lima bean plant in a HopP1‐dependent manner. Exposure to synthetic 1‐octen‐3‐ol activated immunity in tobacco plants against a virulent pathogen Pseudomonas syringae pv. tabaci. Our results show for the first time that a bacterial type III effector can trigger the emission of C8 plant volatiles that mediate defense priming via plant–plant interactions. These results provide novel insights into the role of airborne chemicals in bacterial pathogen‐induced inter‐specific plant–plant interactions.
Efficiency of extraction of antioxidant compounds in by-product from red guava processing

Studies that investigate efficient methods for extraction of antioxidant compounds in by-products of fruits can contribute to their appreciation in human food. This study aimed comparing two methods for phenolic extraction - single extraction (single solvent) and sequential (different solvents) in by-product from Paluma guava processing, evaluating the influence of the extracts on the stabilization of radicals by DPPH and ORAC assays. Sequential extraction showed higher efficiency in obtaining phenolic (2.60 > 0.56 mg GAE g -1 ), allowing the extraction of free phenolic, conjugated and fat-soluble, as well as determining the highest antioxidant capacity in these extracts. Acetone was characterized to be the responsible solvent for higher extraction of phenolic in the sequential extraction, being necessary 0.90 mg mL -1 of extract to reduce 50% the action of DPPH• radicals. Thus, sequential extraction of phenolic is a potential method for better use of antioxidant compounds in the guava processing by-product.
International female rugby union players’ anthropometric and physical performance characteristics: A five-year longitudinal analysis by individual positional groups

ABSTRACT Longitudinal changes in anthropometric and physical performance characteristics of International female rugby union players were evaluated across 5-seasons, according to field position. Sixty-eight international female rugby union players from a top 2 ranked international team, undertook anthropometric and physical performance measurements across five seasons. Anthropometric and physical performance changes occurred, with skinfolds decreasing between 2015 and 2017 and body mass increasing between 2017 and 2019. Single-leg isometric squat (SL ISO), 0–10 m momentum (0–10 Mom) and 20–30 m momentum (20–30Mom) were higher in 2018 and 2019 than all years. Front-row players were characterised by greater SL ISO and 1-RM bench press than inside and outside backs, with higher skinfolds and lower endurance levels than all positions. Between 2017 and 2019, front-row players had larger decreases and increases in endurance and one repetition maximum (1-RM) bench press, respectively, compared to all other positions. Forwards had the highest 0–10Mom and 20–30Mom, and scrum-half the lowest, while outside backs had faster 0–10, 30–40, and 40 m (TT40 m) times, and greater peak velocity (Vmax) compared to forward positions. These longitudinal findings show that physical performance has increased, with anthropometric and performance characteristics becoming more distinctive between positions, among elite female rugby union players.
Association between early childhood lower respiratory tract infections and subsequent asthma

Abstract Objective We examined the relationship between recurrent lower respiratory tract infections (LRTI) in young children and subsequent childhood asthma outcomes. Methods Retrospective cohort study using 2009–2017 Colorado All Payer Claims Database to assess 0- to 2-year-old children with visits due to LRTI and acute gastroenteritis (AGE). The primary exposure was number of LRTI visits prior to 2 years of age. Children with AGE served as the no LRTI comparator group. The primary outcome was incident asthma, defined by ICD-9 (490.XX) or ICD-10 (J45.9XX) codes, in the same children between 3 and 9 years of age. Multivariable accelerated failure time (AFT) models were used to estimate the effect of LRTI visits on median time to asthma diagnosis. Sensitivity analyses were performed using more conservative asthma diagnostic criteria and with hospitalized children only. Results Of 38,441 eligible subjects, 32,729 had ≥1 LRTI and 5,712 had AGE (no LRTI) between 0 and 2 years of age. Children with ≥3 LRTI visits had an 80% decrease in median time to asthma diagnosis relative to those with AGE visits only (time ratio [TR] 0.2; 95% CI 0.16, 0.24). Children with ≥3 LRTI hospitalizations had a 98% reduction in median time to asthma diagnosis relative to those with AGE hospitalizations only (TR 0.02; 95% CI 0.01, 0.07). History of atopy, wheezing, and family history of asthma documented prior to 2 years of age were also associated with earlier asthma diagnosis. Conclusions Recurrent LRTIs, especially LRTI hospitalizations, before 2 years of age are associated with earlier diagnosis of pediatric asthma.
Effect of renal impairment on the pharmacokinetics and safety of dorzagliatin, a novel dual‐acting glucokinase activator

Dorzagliatin is a novel allosteric glucokinase activator targeting both pancreatic and hepatic glucokinase currently under clinical investigation for treatment of type 2 diabetes (T2D). This study aimed to investigate the effect of renal impairment (RI) on dorzagliatin’s pharmacokinetics (PKs) and safety, and to guide appropriate clinical dosing in patients with diabetic kidney disease, including end‐stage renal disease (ESRD). Based on the results from physiologically‐based pharmacokinetic modeling, the predicted outcome of RI on dorzagliatin PK property would be minimum that the plasma exposure area under concentration (AUC) of dorzagliatin in patients with ESRD would increase at about 30% with minimal change in peak concentration (Cmax) comparing to those in healthy volunteers (HVs). To definitively confirm the prediction, a two‐part RI study was designed and conducted based on regulatory guidance starting with the patients with ESRD matched with HVs. Results of the RI study showed minimum difference between patients with ESRD and HVs with respect to dorzagliatin exposure with geometric mean ratio of ESRD to HV at 0.81 for Cmax and 1.11 for AUC. The elimination half‐life, volume of distribution, and systemic clearance for dorzagliatin were similar between the two groups. Dorzagliatin was well‐tolerated in patients with ESRD during the study. Therefore, RI showed no significant impact on dorzagliatin PK, suggesting that dorzagliatin can be readily used in patients with T2D at all stages of RI without need for dose adjustment.
Capacity building in screening and treatment of diabetic retinopathy in Asia-Pacific region

The focus of capacity building for screening and treatment of diabetic retinopathy (DR) is on health professionals who are nonophthalmologists. Both physicians and nonphysicians are recruited for screening DR. Although there is no standardization of the course syllabus for the capacity building, it is generally accepted to keep their sensitivity >80%, specificity >95%, and clinical failure rate <5% for the nonophthalmologists, if possible. A systematic literature search was performed using the PubMed database and the following search terms: diabetic retinopathy, diabetic retinopathy screening, Asia, diabetic retinopathy treatment, age-related macular degeneration, capacity building, deep learning, artificial intelligence (AI), nurse-led clinic, and intravitreal injection (IVI). AI may be a tool for improving their capacity. Capacity building on IVIs of antivascular endothelial growth factors for DR is focused on nurses. There is evidence that, after a supervision of an average of 100 initial injections, the trained nurses can do the injections effectively and safely, the rate of endophthalmitis ranges from 0.03 to 0.07%, comparable to ophthalmologists. However, laws and regulations, which are different among countries, are challenges and barriers for nonophthalmologists, particularly for nonphysicians, for both screening and treatment of DR. Even if nonphysicians or physicians who are nonophthalmologists are legally approved for these tasks, sustainability of the capacity is another important challenge, this may be achieved if the capacity building can be part of their career development. Patient acceptability is another important barrier for initiating care provided by nonophthalmologists, particularly in Asia. There are also collaborations between national eye institutes of high-income countries, nongovernment organizations, and local eye institutes to improve both the quality and quantity of ophthalmologists and retinal specialists in low-income countries in Asia. This approach may require more labor, cost, and time consuming than training nonophthalmologists.
Value of magnetic resonance combined with dual-source spectral computed tomography in improving the clinical diagnosis and treatment efficiency of lumbar disk herniation.

OBJECTIVE This study aims to investigate the value of magnetic resonance combined with dual-source spectral computed tomography in improving the clinical diagnosis and treatment efficiency of lumbar disk herniation. METHODS Two hundred patients with lumbar disk herniation were enrolled. Magnetic resonance and dual-source spectral computed tomography were used to perform the diagnosis. The treatment efficiency and effectiveness of different diagnostic methods were determined. RESULTS Eighty cases of lumbar disk herniation, 40 cases of prolapse, 33 cases of bulge, 27 cases of sequestration, and 20 cases of nodules were diagnosed based on pathologic evaluation. magnetic resonance detected lumbar disk herniation in 172 cases, with a detection rate of 86.00%. Dual-source spectral computed tomography detected 171 cases, with a detection rate of 85.50%. Magnetic resonance combined with dual-source spectral computed tomography detected 195 cases, with a detection rate of 97.50%. There was no significant difference between magnetic resonance and dual-source spectral computed tomography (p>0.05), but compared with the combined detection, there was a significant difference (p<0.05). One hundred and two cases of calcification, 83 cases of spinal cord deformity, 70 cases of intervertebral disk degeneration, 121 cases of intervertebral disk gas, 85 cases of dural sac compression, and 78 cases of nerve root compression were surgically demonstrated. The detection rate of diagnostic signs based on imaging by magnetic resonance or dual-source spectral computed tomography alone was lower than that of combined detection (p<0.05). CONCLUSION Magnetic resonance combined with dual-source spectral computed tomography can improve the diagnosis and treatment efficiency and effectiveness of lumbar disk herniation.
The Effects of Socioeconomic Status on Parent and Child Moderate-to-Vigorous Physical Activity and Body Mass Index

ABSTRACT Purpose: Physical inactivity and overweight status has been linked to low socioeconomic status (SES) in youth. Parents are known to influence both their child’s weight and physical activity (PA). The relationship between parent and child PA is of interest to many researchers; however, previous research typically relies on self-reported measures. The purpose of this study was to examine the relationship between parent and child moderate-to-vigorous PA (MVPA) and body mass index (BMI) in a sample of children (4–11 years old) using wrist-worn accelerometers and to explore mediating processes by which SES influences child MVPA and BMI through their parents MVPA and BMI. Methods: Parent and child dyads (n = 174) wore an ActiGraph GT3X+ accelerometer on their non-dominant wrist for 7 days. Mediation analyses were conducted to understand the indirect relationships between SES and child MVPA and BMI. Results: Weekend parent and child MVPA was significantly related (p < .01). Parent and child BMIs were also significantly related (p < .001). There was a significant negative direct effect of SES on child BMI (p < .05). Additionally, we observed a significant negative indirect effect of SES on child BMI via their parents BMI (B = −.04, SE .02, 95% CI = −.07 to −.01). Conclusions: Whilst parent and child MVPA were significantly related during the weekend, there were no associations between SES and MVPA. Future interventions aiming to improve health outcomes in children should consider the influence SES can have as well as parental activity on children’s weekend MVPA.
Behavior of hyperreflective spots noted on optical coherence tomography following intravitreal therapy in diabetic macular edema: A systematic review and meta-analysis

Purpose: Hyperreflective spots (HRS) are considered as spectral domain optical coherence tomography biomarkers in predicting response to intravitreal therapy (IVT) in diabetic macular edema (DME). We aimed to determine if there was a quantitative reduction in HRS following IVT in DME, if the response to antivascular endothelial growth factor (anti-VEGF) drugs was different from steroids, and if HRS-response was associated with improvement in visual acuity (VA) or reduction in central macular thickness (CMT). Methods: PubMed/MEDLINE, Scopus, ProQuest, CINAHL, Wiley online, and Web of Science were searched (between January 1, 2011 and July 1, 2020). Publication bias and heterogeneity were assessed. Meta-analysis was done using the random-effects model. Results: Totally, 1168 eyes from 19 studies were eligible for inclusion. IVT was associated with a reduction in quantitative HRS (z = -6.3, P < 0.0001). Studies, however, showed heterogeneity (I2 = 93.2%). There was no difference between anti-VEGF and steroid therapies (P = 0.23). The evidence on predicting VA and CMT outcomes were limited by the number of analyzable studies, owing to the wide variation in individual study designs, and lack of randomized controlled trials. Conclusion: We could conclude that there is a definite reduction in quantitative HRS following either form of IVT. We highlight the lacunae in the existing literature on HRS in DME and propose goals for future studies to harness the advantage of this promising biomarker.
The Recent Rise of Suicide Mortality in the United States.

Suicide is a major public health concern in the United States. Between 2000 and 2018, US suicide rates increased by 35%, contributing to the stagnation and subsequent decrease in US life expectancy. During 2019, suicide declined modestly, mostly owing to slight reductions in suicides among Whites. Suicide rates, however, continued to increase or remained stable among all other racial/ethnic groups, and little is known about recent suicide trends among other vulnerable groups. This article (a) summarizes US suicide mortality trends over the twentieth and early twenty-first centuries, (b) reviews potential group-level causes of increased suicide risk among subpopulations characterized by markers of vulnerability to suicide, and (c) advocates for combining recent advances in population-based suicide prevention with a socially conscious perspective that captures the social, economic, and political contexts in which suicide risk unfolds over the life course of vulnerable individuals. Expected final online publication date for the Annual Review of Public Health, Volume 43 is April 2022. Please see http://www.annualreviews. org/page/journal/pubdates for revised estimates.
Capturing tumour heterogeneity in pre- and post-chemotherapy colorectal cancer ascites-derived cells using single-cell RNA-sequencing

Abstract Malignant ascites is an abnormal accumulation of fluid within the peritoneal cavity, caused by metastasis of several types of cancers, including colorectal cancer (CRC). Cancer cells in ascites reflect poor prognosis and serve as a good specimen to study tumour heterogeneity, as they represent a collection of multiple metastatic sites in the peritoneum. In the present study, we have employed single-cell RNA-sequencing (scRNA-seq) to explore and characterise ascites-derived cells from a CRC patient. The samples were prepared using mechanical and enzymatic dissociations, and obtained before and after a chemotherapy treatment. Unbiased clustering of 19,653 cells from four samples reveals 14 subclusters with unique transcriptomic patterns in four major cell types: epithelial cells, myeloid cells, fibroblasts, and lymphocytes. Interestingly, the percentages of cells recovered from different cell types appeared to be influenced by the preparation protocols, with more than 90% reduction in the number of myeloid cells recovered by enzymatic preparation. Analysis of epithelial cell subpopulations unveiled only three out of eleven subpopulations with clear contraction after the treatment, suggesting that the majority of the heterogeneous ascites-derived cells were resistant to the treatment, potentially reflecting the poor treatment outcome observed in the patient. Overall, our study showcases highly heterogeneous cancer subpopulations at single-cell resolution, which respond differently to a particular chemotherapy treatment. All in all, this work highlights the potential benefit of single-cell analyses in planning appropriate treatments and real-time monitoring of therapeutic response in cancer patients through routinely discarded ascites samples.
Germanium Chalcogenide Thermoelectrics: Electronic Structure Modulation and Low Lattice Thermal Conductivity

Thermoelectric materials can convert untapped heat to electricity and are expected to have an important role in future energy utilization. IV–VI metal chalcogenides are the most promising candidates for mid-temperature thermoelectric power generation. Among them, PbTe and their alloys have been proven to be the superior thermoelectric materials. Unfortunately, the toxicity of lead (Pb) prevents the application of lead chalcogenides and demands the search for lead-free high-performance solids. This perspective discusses the recent progress of thermoelectric property studies on germanium chalcogenides (GeTe, GeSe, and GeS) for mid-temperature power generation. Here, we have discussed the crystal structure, chemical bonding, and phonon dispersion of germanium chalcogenides to understand the underlying lattice dynamics and low lattice thermal conductivity from a chemistry perspective. We have also discussed the uniqueness of the electronic structure of GeTe and GeSe, which plays an important role in tailoring.
Pseudokinases repurpose flexibility signatures associated with the protein kinase fold for noncatalytic roles

The bilobal protein kinase‐like fold in pseudokinases lack one or more catalytic residues, conserved in canonical protein kinases, and are considered enzymatically deficient. Tertiary structures of pseudokinases reveal that their loops topologically equivalent to activation segments of kinases adopt contracted configurations, which is typically extended in active conformation of kinases. Herein, anisotropic network model based normal mode analysis (NMA) was conducted on 51 active conformation structures of protein kinases and 26 crystal structures of pseudokinases. Our observations indicate that although backbone fluctuation profiles are similar for individual kinase‐pseudokinase families, low intensity mean square fluctuations in pseudo‐activation segment and other sub‐structures impart rigidity to pseudokinases. Analyses of collective motions from functional modes reveal that pseudokinases, compared to active kinases, undergo distinct conformational transitions using the same structural fold. All‐atom NMA of protein kinase‐pseudokinase pairs from each family, sharing high amino acid sequence identities, yielded distinct community clusters, partitioned by residues exhibiting highly correlated fluctuations. It appears that atomic fluctuations from equivalent activation segments guide community membership and network topologies for respective kinase and pseudokinase. Our findings indicate that such adaptations in backbone and side‐chain fluctuations render pseudokinases competent for catalysis‐independent roles.
Sleep, Dreams, and Nightmares During the COVID-19 Pandemic

The COVID-19 pandemic has affected the sleep and dreams of many individuals. Some have experienced improvements, while others have had more complaints. The changes to daily life such as working from home and spending more time indoors in confinement may have disturbed the circadian rhythms of some individuals. There were many reports of a shift towards a later bedtime during the pandemic, with several studies showing that in general, females experienced worse sleep than males, including more nighttime awakenings and nightmares. Increased dream and nightmare frequency during the pandemic has been shown in multiple studies. It has been postulated that because dreams are often guided by the dominant emotional state, that dreams and nightmares related to pandemic themes are a result of specific stressors related to COVID-19. Those experiencing unwanted sleep disturbances and nightmares could stand to benefit from mindfulness and relaxation practices that can ease stress and anxiety before bedtime. Striving to maintain a regular sleep schedule and enhance exposure to daylight–particularly during the first half of the day–may also be helpful.
Convex Multi-View Clustering Via Robust Low Rank Approximation With Application to Multi-Omic Data

Recent advances in high throughput technologies have made large amounts of biomedical omics data accessible to the scientific community. Single omic data clustering has proved its impact in the biomedical and biological research fields. Multi-omic data clustering and multi-omic data integration techniques have shown improved clustering performance and biological insight. Cancer subtype clustering is an important task in the medical field to be able to identify a suitable treatment procedure and prognosis for cancer patients. State of the art multi-view clustering methods are based on non-convex objectives which only guarantee non-global solutions that are high in computational complexity. Only a few convex multi-view methods are present. However, their models do not take into account the intrinsic manifold structure of the data. In this paper, we introduce a convex graph regularized multi-view clustering method that is robust to outliers. We compare our algorithm to state of the art convex and non-convex multi-view and single view clustering methods, and show its superiority in clustering cancer subtypes on publicly available cancer genomic datasets from the TCGA repository. We also show our method's better ability to potentially discover cancer subtypes compared to other state of the art multi-view methods.