Miracle-dz/UniFAR-FTUs huggingface dataset:
The effect of rhizosphere microbes outweighs host plant genetics in reducing insect herbivory

Rhizosphere microbes affect plant performance, including plant resistance against insect herbivores; yet, a direct comparison of the relative influence of rhizosphere microbes versus plant genetics on herbivory levels and on metabolites related to defence is lacking. In the crucifer Boechera stricta, we tested the effects of rhizosphere microbes and plant population on herbivore resistance, the primary metabolome, and select secondary metabolites. Plant populations differed significantly in the concentrations of six glucosinolates (GLS), secondary metabolites known to provide herbivore resistance in the Brassicaceae. The population with lower GLS levels experienced ~60% higher levels of aphid (Myzus persicae) attack; no association was observed between GLS and damage by a second herbivore, flea beetles (Phyllotreta cruciferae). Rhizosphere microbiome (disrupted vs. intact native microbiome) had no effect on plant GLS concentrations. However, aphid number and flea beetle damage were respectively about three‐ and seven‐fold higher among plants grown in the disrupted versus intact native microbiome treatment. These differences may be attributable to shifts in primary metabolic pathways previously implicated in host defence against herbivores, including increases in pentose and glucoronate interconversion among plants grown with an intact microbiome. Furthermore, native microbiomes with distinct community composition (as estimated from 16s rRNA amplicon sequencing) differed two‐fold in their effect on host plant susceptibility to aphids. The findings suggest that rhizosphere microbes, including distinct native microbiomes, can play a greater role than population in defence against insect herbivores, and act through metabolic mechanisms independent of population.
The role and molecular mechanism of Trop2 induced epithelial‐mesenchymal transition through mediated β‐catenin in gastric cancer

The present study elucidates the potential role of Trop2 in tumor invasion and the promotion of epithelial‐mesenchymal transition (EMT) when binding β‐catenin in GC. The role of Trop2 in promoting EMT in GC cells was examined by a variety of experimental assays. Moreover, the underlying molecular mechanism of Trop2 in promoting EMT was studied by in vivo and in vitro assays. The Trop2 expression in relation to tumor metastasis status was detected by IHC in 248 cases of GC tissues and 86 cases of matched adjacent tissues. Trop2 promoted the metastasis and induces EMT in GC. Meanwhile, the elevated protein levels of Trop2 and mesenchymal markers were also found in the TGF‐β1‐induced EMT model in GC cells. Importantly, Trop2 physically bound and activated β‐catenin to promote EMT; moreover, Trop2 increased the accumulation of β‐catenin in the nucleus to accelerate metastasis in GC cells. Inhibition of Trop2 expression in GC cells prevented the migration and invasion of GC cells in vivo. Trop2+/vimentin+ expression was higher in GC tissues than that in matched adjacent tissues, and Trop2+/vimentin+ expression in GC was associated with the differentiation, TNM stage, and distant metastases. These sets of data reveal a novel regulatory network of Trop2 in EMT and GC metastasis, suggesting Trop2 as a useful marker for inducing EMT and metastasis of GC, which may help to lead a better understanding of the pathogenesis of the GC.
Effect of preoperative detrusor underactivity on long‐term surgical outcomes of photovaporization and holmium laser enucleation in men with benign prostatic hyperplasia: a lesson from 5‐year serial follow‐up data

To investigate the impact of preoperative detrusor underactivity (DU) on serial treatment outcomes over the course of 5 years after photovaporization (PV) or holmium laser enucleation (HoLEP) in patients with benign prostatic hyperplasia (BPH), to compare its impact after PV vs HoLEP, and to identify predictors of long‐term lower urinary tract symptoms (LUTS) improvement.
Elucidation of the functional roles of the Q and I motifs in the human chromatin-remodeling enzyme BRG1

The Snf2 proteins, comprising 53 different enzymes in humans, belong to the SF2 family. Many Snf2 enzymes possess chromatin-remodeling activity, requiring a functional ATPase domain consisting of conserved motifs named Q and I–VII. These motifs form two recA-like domains, creating an ATP-binding pocket. Little is known about the function of the conserved motifs in chromatin-remodeling enzymes. Here, we characterized the function of the Q and I (Walker I) motifs in hBRG1 (SMARCA4). The motifs are in close proximity to the bound ATP, suggesting a role in nucleotide binding and/or hydrolysis. Unexpectedly, when substituting the conserved residues Gln758 (Q motif) or Lys785 (I motif) of both motifs, all variants still bound ATP and exhibited basal ATPase activity similar to that of wildtype BRG1 (wtBRG1). However, all mutants lost the nucleosome-dependent stimulation of the ATPase domain. Their chromatin-remodeling rates were impaired accordingly, but nucleosome binding was retained and still comparable with that of wtBRG1. Interestingly, a cancer-relevant substitution, L754F (Q motif), displayed defects similar to the Gln758 variant(s), arguing for a comparable loss of function. Because we excluded a mutual interference of ATP and nucleosome binding, we postulate that both motifs stimulate the ATPase and chromatin-remodeling activities upon binding of BRG1 to nucleosomes, probably via allosteric mechanisms. Furthermore, mutations of both motifs similarly affect the enzymatic functionality of BRG1 in vitro and in living cells. Of note, in BRG1-deficient H1299 cells, exogenously expressed wtBRG1, but not BRG1 Q758A and BRG1 K785R, exhibited a tumor suppressor–like function.
Preoperative Metabolic Tumor Volume2.5 Associated with Early Systemic Metastasis in Resected Pancreatic Cancer: A Transcriptome-Wide Analysis

Background/Aims 18F-fluorodeoxyglucose-positron emission tomography (18F-FDG-PET) reflects biological aggressiveness and predicts prognoses in various tumors. Evaluating the oncologic significance of the preoperative metabolic phenotype might be necessary for planning the surgical strategy in resectable pancreatic cancers. Methods From January 2010 to December 2015, a total of 93 patients with pathologic T3 (pT3) pancreatic cancer were included in this study. Clinicopathological parameters and PET parameters were evaluated, and transcriptome-wide analysis was performed to identify the oncologic impact and molecular landscape of the metabolic phenotype of resectable pancreatic cancers. Results Preoperative metabolic tumor volume (MTV)2.5 was significantly higher in the pN1 group compared to the pN0 group (11.1±11.2 vs 6.5±7.8, p=0.031). Higher MTV2.5 values (MTV2.5 ≥4.5) were associated with multiple lymph node metastasis (p=0.003), and the lymph node ratio was also significantly higher in resected pT3 pancreatic cancer with MTV2.5 ≥4.5 compared to those with MTV2.5 <4.5 (0.12±0.13 vs 0.05±0.08, p=0.001). Disease-specific survival of patients with MTV2.5 <4.5 was better than that of patients with MTV2.5 ≥4.5 (mean, 28.8 months; 95% confidence interval [CI], 40.1 to 57.0 vs mean, 32.6 months; 95% CI, 25.5 to 39.7; p=0.026). Patients with MTV2.5 ≥4.5 who received postoperative adjuvant chemotherapy showed better survival outcomes than patients with MTV2.5 ≥4.5 who did not receive adjuvant treatment in resected pT3 pancreatic cancers (p<0.001). Transcriptome-wide analysis revealed that tumors with MTV2.5 ≥4.5 demonstrated significantly different expression of cancer-related genes reflecting aggressive tumor biology. Conclusions Resectable pancreatic cancer with high MTV2.5 is not only associated with lymph node metastasis but also early systemic metastasis. The molecular background of resectable pancreatic cancer with high MTV2.5 may be associated with aggressive biologic behavior, which might need to be considered when managing resectable pancreatic cancers. Further study is mandatory.
The Drosophila Ninein homologue Bsg25D cooperates with Ensconsin in myonuclear positioning

Skeletal muscle consists of multinucleated cells in which the myonuclei are evenly spaced throughout the cell. In Drosophila, this pattern is established in embryonic myotubes, where myonuclei move via microtubules (MTs) and the MT-associated protein Ensconsin (Ens)/MAP7, to achieve their distribution. Ens regulates multiple aspects of MT biology, but little is known about how Ens itself is regulated. We find that Ens physically interacts and colocalizes with Bsg25D, the Drosophila homologue of the centrosomal protein Ninein. Bsg25D loss enhances myonuclear positioning defects in embryos sensitized by partial Ens loss. Bsg25D overexpression causes severe positioning defects in immature myotubes and fully differentiated myofibers, where it forms ectopic MT organizing centers, disrupts perinuclear MT arrays, reduces muscle stiffness, and decreases larval crawling velocity. These studies define a novel relationship between Ens and Bsg25D. At endogenous levels, Bsg25D positively regulates Ens activity during myonuclear positioning, but excess Bsg25D disrupts Ens localization and MT organization, with disastrous consequences for myonuclear positioning and muscle function.
Quantifying the associations between diabetes mellitus, glycated haemoglobin and incidence of and mortality from cancer: analysis of longitudinal data from England and Scotland linked to Cancer Registry and mortality data

Background Studies which have sought to explore the associations between diabetes and cancer have produced heterogeneous results and there is a paucity of evidence related to glycated haemoglobin (HbA1c) and cancer risk. Methods Initial analyses utilised data from the Health Survey for England (HSE) and SHeS combined linked to mortality and Cancer Registry data (n=204,533, including 7,199 with diabetes) to explore the associations between diabetes, HbA1c and cancer incidence and mortality. Additional analyses used linked Whitehall I data (n= 19,019, including 237 with diabetes). Odds Ratios (ORs), Hazard Ratios and 95% Confidence Intervals (CI) were estimated adjusted for a range of confounding factors using logistic, multinomial and Cox regression. Results 18,310 deaths occurred within the HSE/SHeS follow-up period (4,997 from cancer). The adjusted OR for cancer among those with diabetes was 1.27, CI 1.12-1.43. Raised HbA1c was associated with an excess risk of dying/developing cancer; diabetes and HbA1c were associated with a number of site-specific cancers. When analyses were stratified by cardiovascular disease (CVD) baseline status, only those with diabetes who did not report CVD had a statistically significant excess in cancer mortality (adjusted OR: 1.27, 1.08-1.48). There were also sex differences in cancer incidence and mortality risk. 81% of Whitehall I participants died during follow-up (including 4,076 from cancer). These results did not replicate the initial analyses in finding no association between diabetes and cancer mortality -this is likely to relate to the age of the two cohorts and the differences in CVD mortality and incidence. Conclusion The association of diabetes and HbA1c with increased cancer incidence and mortality was not consistent across studies or population groups. Differences in risk by sex and CVD status suggest the need for health professionals to tailor services to take account of the individual circumstances of their diabetic patients.
Use of Bernard-Webster flap for lower lip reconstruction after excision of squamous cell carcinoma: analysis of functional results

Introduction: Defects in the lower lips after the excision of squamous cell carcinoma (SCC) are usually repaired using several surgical techniques. However, the functional reconstruction of full-thickness defects in the lower lip remains a challenge. Therefore, the objectives of this study were to describe surgical strategies for the reconstruction of full-thickness defects of the lower lip after surgical excision of the SCC and evaluate the functional results. Methods: This was a retrospective study of all patients with full-thickness defects in the lower lip after excisions of SCC that were greater than one third of the lip that were repaired using the Bernard-Webster flap between 2011 and 2014. The functional results (sphincteric, motor and sensory function) were evaluated according to previously used criteria. Results: Six lip defects were reconstructed without complications using Bernard-Webster flaps. During the postoperative period, the patients reported liquid incontinence (16.67%), intermittent salivary incontinence (16.67%), and difficulty fully opening the mouth (33.33%). The tests revealed sensory deficits in the labiomental areas (100%) and lower lip (33.33%). There was full recovery of all functional changes an average of 3 months after surgery. The observed late functional results were considered satisfactory. Conclusions: The Bernard-Webster flap was an excellent alternative to repairing the defects that affect more than one third of the lower lip since it allowed the use of similar local tissues, a single surgery could be performed, and the result was functionally efficient.
Failure of Staphylococcus aureus to Acquire Direct and Cross Tolerance after Habituation to Cinnamon Essential Oil

Utilization of sublethal concentrations of cinnamon essential oil (CEO) for food preservation has been proposed. However, exposure to stressful, sublethal growth conditions may induce bacterial tolerance to homologous or heterologous stressing agents. Hence, the ability of CEO to stimulate bacterial stress response was evaluated in the current work. Staphylococcus aureus was exposed to 1/4 and 1/2 of the minimum inhibitory concentration (MIC, 500 μL/L) of CEO for 18 h. It was found that overnight habituation to CEO failed to induce direct tolerance and cross-tolerance to lactic acid (pH 4.5), NaCl (10 g/100 mL) and high temperature (45 °C) in S. aureus. Likewise, S. aureus cells subjected to successive habituation with increasing amounts (1/16 MIC to 2× MIC) of CEO developed no direct tolerance. Taken together, CEO has no inductive effect on the acquisition of stress tolerance in S. aureus.
Factors Associated with Serum 25-Hydroxyvitamin D Concentration in Two Cohorts of Pregnant Women in Southern Ontario, Canada

Vitamin D deficiency in pregnancy is widely reported, but whether this applies in North America is unclear since no population-based surveys of vitamin D status in pregnancy exist in Canada or the United States. The objectives were to assess (i) the intake and sources of vitamin D, (ii) vitamin D status, and (iii) factors associated with serum 25-hydroxyvitamin D (25-OHD) concentration in two cohorts of pregnant women from Southern Ontario, Canada, studied over a span of 14 years. Maternal characteristics, physical measurements, fasting blood samples and nutrient intake were obtained at enrolment in 332 pregnant women from the Family Atherosclerosis Monitoring In early Life (FAMILY) study and 191 from the Be Healthy in Pregnancy (BHIP) study. Serum 25-OHD was measured by LC/MS-MS. The median (Q1, Q3) total vitamin D intake was 383 IU/day (327, 551) in the FAMILY study and 554 IU/day (437, 796) in the BHIP study. Supplemental vitamin D represented 64% of total intake in participants in FAMILY and 78% in BHIP. The mean (SD) serum 25-OHD was 76.5 (32.9) nmol/L in FAMILY and 79.7 (22.3) nmol/L in BHIP. Being of European descent and blood sampling in the summer season were significantly associated with a higher maternal serum 25-OHD concentration. In summary, health care practitioners should be aware that vitamin D status is sufficient in the majority of pregnant Canadian women of European ancestry, likely due to sun exposure.
Cognition and emotion: a plea for theory

ABSTRACT Research on cognition and emotion during the past 30 years has made reasonable progress in theory, methods and empirical research. New theories of the cognition–emotion relation have been proposed, emotion research has become more interdisciplinary, and improved methods of emotion measurement have been developed. On the empirical side, the main achievement of the past 30 years is seen to consist in the reduction of the set of serious contenders for a theory of emotions. Still, several important issues are not fully resolved, including the computational implementation of appraisal processes, the nature of emotions, and the link between emotions and actions. Also, quantitative theories of the cognition–emotion relation need to be refined and tested, and improved theories of the link between emotions and bodily and facial expressions need to be developed. To counter the dangers of theoretical fragmentation and knowledge loss, more efforts should be devoted to the analysis, reconstruction, comparison and integration of important theories and hypotheses in the field of emotion, as well as to the systematization of arguments in favor and against these theories and hypotheses.
Can Texture Analysis Be Used to Distinguish Benign From Malignant Adrenal Nodules on Unenhanced CT, Contrast-Enhanced CT, or In-Phase and Opposed-Phase MRI?

OBJECTIVE The purpose of this study is to determine whether second-order texture analysis can be used to distinguish lipid-poor adenomas from malignant adrenal nodules on unenhanced CT, contrast-enhanced CT (CECT), and chemical-shift MRI. MATERIALS AND METHODS In this retrospective study, 23 adrenal nodules (15 lipid-poor adenomas and eight adrenal malignancies) in 20 patients (nine female patients and 11 male patients; mean age, 59 years [range, 15-80 years]) were assessed. All patients underwent unenhanced CT, CECT, and chemical-shift MRI. Twenty-one second-order texture features from the gray-level cooccurrence matrix and gray-level run-length matrix were calculated in 3D. The mean values for 21 texture features and four imaging features (lesion size, unenhanced CT attenuation, CECT attenuation, and signal intensity index) were compared using a t test. The diagnostic performance of texture analysis versus imaging features was also compared using AUC values. Multivariate logistic regression models to predict malignancy were constructed for texture analysis and imaging features. RESULTS Lesion size, unenhanced CT attenuation, and the signal intensity index showed significant differences between benign and malignant adrenal nodules. No significant difference was seen for CECT attenuation. Eighteen of 21 CECT texture features and nine of 21 unenhanced CT texture features revealed significant differences between benign and malignant adrenal nodules. CECT texture features (mean AUC value, 0.80) performed better than CECT attenuation (mean AUC value, 0.60). Multivariate logistic regression models showed that CECT texture features, chemical-shift MRI texture features, and imaging features were predictive of malignancy. CONCLUSION Texture analysis has a potential role in distinguishing benign from malignant adrenal nodules on CECT and may decrease the need for additional imaging studies in the workup of incidentally discovered adrenal nodules.
Warmer and browner waters decrease fish biomass production

Climate change studies have long focused on effects of increasing temperatures, often without considering other simultaneously occurring environmental changes, such as browning of waters. Resolving how the combination of warming and browning of aquatic ecosystems affects fish biomass production is essential for future ecosystem functioning, fisheries, and food security. In this study, we analyzed individual‐ and population‐level fish data from 52 temperate and boreal lakes in Northern Europe, covering large gradients in water temperature and color (absorbance, 420 nm). We show that fish (Eurasian perch, Perca fluviatilis) biomass production decreased with both high water temperatures and brown water color, being lowest in warm and brown lakes. However, while both high temperature and brown water decreased fish biomass production, the mechanisms behind the decrease differed: temperature affected the fish biomass production mainly through a decrease in population standing stock biomass, and through shifts in size‐ and age‐distributions toward a higher proportion of young and small individuals in warm lakes; brown water color, on the other hand, mainly influenced fish biomass production through negative effects on individual body growth and length‐at‐age. In addition to these findings, we observed that the effects of temperature and brown water color on individual‐level processes varied over ontogeny. Body growth only responded positively to higher temperatures among young perch, and brown water color had a stronger negative effect on body growth of old than on young individuals. Thus, to better understand and predict future fish biomass production, it is necessary to integrate both individual‐ and population‐level responses and to acknowledge within‐species variation. Our results suggest that global climate change, leading to browner and warmer waters, may negatively affect fish biomass production, and this effect may be stronger than caused by increased temperature or water color alone.
Action-Stage Emphasized Spatiotemporal VLAD for Video Action Recognition

Despite outstanding performance in image recognition, convolutional neural networks (CNNs) do not yet achieve the same impressive results on action recognition in videos. This is partially due to the inability of CNN for modeling long-range temporal structures especially those involving individual action stages that are critical to human action recognition. In this paper, we propose a novel action-stage (ActionS) emphasized spatiotemporal vector of locally aggregated descriptors (ActionS-ST-VLAD) method to aggregate informative deep features across the entire video according to adaptive video feature segmentation and adaptive segment feature sampling (AVFS-ASFS). In our ActionS-ST-VLAD encoding approach, by using AVFS-ASFS, the keyframe features are chosen and the corresponding deep features are automatically split into segments with the features in each segment belonging to a temporally coherent ActionS. Then, based on the extracted keyframe feature in each segment, a flow-guided warping technique is introduced to detect and discard redundant feature maps, while the informative ones are aggregated by using our exploited similarity weight. Furthermore, we exploit an RGBF modality to capture motion salient regions in the RGB images corresponding to action activity. Extensive experiments are conducted on four public benchmarks—HMDB51, UCF101, Kinetics, and ActivityNet for evaluation. Results show that our method is able to effectively pool useful deep features spatiotemporally, leading to the state-of-the-art performance for video-based action recognition.
Robustness Conditions for MIIV-2SLS When the Latent Variable or Measurement Model is Structurally Misspecified

Most researchers acknowledge that virtually all structural equation models (SEMs) are approximations due to violating distributional assumptions and structural misspecifications. There is a large literature on the unmet distributional assumptions, but much less on structural misspecifications. In this paper, we examine the robustness to structural misspecification of the model implied instrumental variable, two-stage least square (MIIV-2SLS) estimator of SEMs. We introduce two types of robustness: robust-unchanged and robust-consistent. We develop new robustness analytic conditions for MIIV-2SLS and illustrate these with hypothetical models, simulated data, and an empirical example. Our conditions enable a researcher to know whether, for example, a structural misspecification in the latent variable model influences the MIIV-2SLS estimator for measurement model equations and vice versa. Similarly, we establish robustness conditions for correlated errors. The new robustness conditions provide guidance on the types of structural misspecifications that affect parameter estimates and they assist in diagnosing the source of detected problems with MIIVs.