Miracle-dz/UniFAR-FTUs huggingface dataset:
Effect of smoking status and programmed death-ligand 1 expression on the microenvironment and malignant transformation of oral leukoplakia: A retrospective cohort study

Tobacco smoking is associated with an increased risk of oral leukoplakia and head and neck cancer. Although it has recently been reported that the establishment of an immunosuppressive microenvironment in oral potentially malignant disorders may lead to malignant transformation, it is unclear whether the microenvironments of oral potentially malignant disorders differ according to smoking status. We examined differences in programmed death-ligand 1 (PD-L1) expression and subepithelial CD163+ TAM and CD8+ cell/lymphocyte counts in the microenvironment of oral leukoplakia of smoking and non-smoking patients and investigated their associations with malignant transformation. Pathology reports and original biopsy request forms from 1995–2015 were retrospectively reviewed. Lesions clinically characterized as white plaques/lesions of the oral mucosa and pathologically diagnosed as oral epithelial dysplasia were included. Immunohistochemistry was performed to evaluate PD-L1 expression and subepithelial CD163+/CD8+ cell counts. The significance of prognostic factors in predicting malignant transformation was determined using Cox regression analysis. Statistical significance was defined as P<0.05. In total, 200 patients with oral leukoplakia were selected. The mean age at diagnosis was higher in non-smoking patients (n = 141; 66.9 years) than in smoking patients (n = 59; 60.5 years). The 5-year cumulative malignant transformation rate was higher in non-smoking patients than in smoking patients (9.3% vs. 3.0%, respectively). Oral leukoplakia was associated with significantly higher PD-L1 expression and increased numbers of subepithelial CD163+ cells in the non-smoking group compared with the smoking group. Non-smoking-related oral leukoplakia with positive PD-L1 expression was associated with a 6.97-fold (95% confidence interval: 2.14–22.7) increased risk of malignant transformation. The microenvironment of oral leukoplakia differed according to smoking status. A combination of smoking status and PD-L1 expression may predict malignant transformation in oral leukoplakia patients. This study highlights the importance of understanding the interaction between smoking and the microenvironment in oral leukoplakia.
Dietary patterns and chronic kidney disease outcomes: A systematic review

Chronic kidney disease (CKD) is a serious public health problem and its prevalence is growing in many countries, often related to issues resulting from the lifestyle in growing economies and the population's life expectancy. Nutritional therapy is a beneficial but still neglected strategy for preventing CKD and delaying disease progression. The aim of this study was to assess the association of dietary patterns with CKD development and progression. Observational studies conducted in adult humans and the correlation between the adopted dietary pattern and prevalent and incident cases of CKD were assessed. A significant association was observed between unhealthy dietary patterns and an increased risk of developing or worsening CKD, as well as an adverse effect. Whereas healthy eating patterns characterized by the consumption of fruit, vegetables and dietary fibre showed nephroprotective outcomes.
Site‐specific features of active muscle stiffness and proximal aponeurosis strain in biceps femoris long head

Limited information is available on site‐specific features of muscle stiffness and aponeurosis strain of the biceps femoris long head (BFlh) during contractions. Therefore, understanding of the mechanics and etiology of hamstring strain injuries remains difficult. As a first step to gain further insight into them, the present study aimed to identify whether active muscle stiffness and proximal aponeurosis strain during contractions are varied along the long axis of the BFlh. The BFlh muscle shear wave speed (proxy for stiffness) was measured in the proximal, central, and distal sites during 20%, 50%, and 80% of maximal voluntary isometric contraction (MVC) of knee flexion exerted with the hip and knee joints flexed at 40° and 30°, respectively, using ultrasound shear wave elastography. Further, a segmental strain of the BFlh proximal aponeurosis was assessed in the proximal, central, and distal sites during isometric knee flexion, using B‐mode ultrasonography. The shear wave speed was significantly higher in the distal site than the proximal and central sites at 20% MVC (p ≤ .002, with a large effect size), whereas no significant difference was found between the three sites at 50% and 80% MVC. The BFlh proximal aponeurosis strain showed no significant difference between the proximal, central, and distal sites at any contraction intensity. These findings indicate that site‐specific differences in muscle stiffness and proximal aponeurosis strain are substantially small and that muscle stiffness and proximal aponeurosis strain of the BFlh at moderate‐to‐high contraction intensity is not exceptional in the site where a sprinting‐type hamstring strain typically occurs.
Sodium nitroprusside application improves morphological and physiological attributes of soybean (Glycine max L.) under salinity stress

Salinity is among the major abiotic stresses negatively affecting the growth and productivity of crop plants. Sodium nitroprusside (SNP) -an external nitric oxide (NO) donor- has been found effective to impart salinity tolerance to plants. Soybean (Glycine max L.) is widely cultivated around the world; however, salinity stress hampers its growth and productivity. Therefore, the current study evaluated the role of SNP in improving morphological, physiological and biochemical attributes of soybean under salinity stress. Data relating to biomass, chlorophyll and malondialdehyde (MDA) contents, activities of various antioxidant enzymes, ion content and ultrastructural analysis were collected. The SNP application ameliorated the negative effects of salinity stress to significant extent by regulating antioxidant mechanism. Root and shoot length, fresh and dry weight, chlorophyll contents, activities of various antioxidant enzymes, i.e., catalase (CAT), superoxide dismutase (SOD), peroxidase (POD) and ascorbate peroxidase (APX) were improved with SNP application under salinity stress compared to control treatment. Similarly, plants treated with SNP observed less damage to cell organelles of roots and leaves under salinity stress. The results revealed pivotal functions of SNP in salinity tolerance of soybean, including cell wall repair, sequestration of sodium ion in the vacuole and maintenance of normal chloroplasts with no swelling of thylakoids. Minor distortions of cell membrane and large number of starch grains indicates an increase in the photosynthetic activity. Therefore, SNP can be used as a regulator to improve the salinity tolerance of soybean in salt affected soils.
Genome-wide analysis of plant miRNA action clarifies levels of regulatory dynamics across developmental contexts

Development of complex organisms requires the delicate and dynamic spatiotemporal regulation of gene expression. Central to this are microRNAs (miRNAs). These mobile small RNAs offer specificity in conveying positional information and versatility in patterning the outcomes of gene expression. However, the parameters that shape miRNA output during development are still to be clarified. Here, we address this question on a genome-wide scale, using the maize shoot apex as a model. We show that patterns and levels of miRNA accumulation are largely determined at the transcriptional level, but are finessed post-transcriptionally in a tissue-dependent manner. The stem cell environments of the shoot apical meristem and vasculature appear particularly liable to this. Tissue-specific effects are also apparent at the level of target repression, with target cleavage products in the vasculature exceeding those of other tissues. Our results argue against a clearance mode of regulation purely at the level of transcript cleavage, leading us to propose that transcript cleavage provides a baseline level of target repression, onto which miRNA-driven translational repression can act to toggle the mode of target regulation between clearance and rheostat. Our data show how the inherent complexities of miRNA pathways allow the accumulation and activity of these small RNAs to be tailored in space and time to bring about the gene expression versatility needed during development.
Partial mycoheterotrophy is common among chlorophyllous plants with Paris-type arbuscular mycorrhiza.

BACKGROUND AND AIMS An arbuscular mycorrhiza is a mutualistic symbiosis with plants as carbon providers for fungi. However, achlorophyllous arbuscular mycorrhizal species are known to obtain carbon from fungi, i.e. they are mycoheterotrophic. These species all have the Paris type of arbuscular mycorrhiza. Recently, two chlorophyllous Paris-type species proved to be partially mycoheterotrophic. In this study, we explore the frequency of this condition and its association with Paris-type arbuscular mycorrhiza. METHODS We searched for evidence of mycoheterotrophy in all currently published 13C, 2H and 15N stable isotope abundance patterns suited for calculations of enrichment factors, i.e. isotopic differences between neighbouring Paris- and Arum-type species. We found suitable data for 135 plant species classified into the two arbuscular mycorrhizal morphotypes. KEY RESULTS About half of the chlorophyllous Paris-type species tested were significantly enriched in 13C and often also enriched in 2H and 15N, compared with co-occurring Arum-type species. Based on a two-source linear mixing model, the carbon gain from the fungal source ranged between 7 and 93 % with ferns > horsetails > seed plants. The seed plants represented 13 families, many without a previous record of mycoheterotrophy. The 13C-enriched chlorophyllous Paris-type species were exclusively herbaceous perennials, with a majority of them thriving on shady forest ground. CONCLUSIONS Significant carbon acquisition from fungi appears quite common and widespread among Paris-type species, this arbuscular mycorrhizal morphotype probably being a pre-condition for developing varying degrees of mycoheterotrophy.
Etanercept prevents TNF-α mediated mandibular bone loss in FcγRIIb-/- lupus model

Patients with systemic lupus erythematosus are at increased risk for alveolar bone loss due to periodontitis possibly as a result of a pathogenic immune response to oral bacteria and inflammation. The aim of the present study was to investigate whether an anti-TNF-α antagonist could prevent mandibular bone loss in the FcγRIIb-/- mouse model of lupus. Mice lacking FcγRIIb had decreased cancellous and cortical bone volume at 6 months of age. Etanercept increased cancellous but not cortical bone volume in WT and increased both cancellous bone volume and cortical thickness in FcγRIIb-deficient mice. FcγRIIb deficiency decreased mRNA levels for osteoblast marker genes, Osx, Col1a1 and Alp without any change in osteoclast marker genes. Etanercept increased Osx, Alp, and Ocn in both WT and FcγRIIb-/- mice. Osteoclast marker genes including TNF-α, Trap and RANKL/OPG ratio was decreased in WT. Serum markers of proinflammatory cytokines, TNF-α, IFNγ, IL-6, and IL-17A, were increased in FcγRIIb-/- mice and etanercept antagonized these effects in FcγRIIb-/- mice. Etanercept increased serum PTH levels in the FcγRIIb-/- mouse model of lupus. Our results suggest that deletion of FcγRIIb induces osteopenia by increasing the level of proinflammatory cytokines. Etanercept is effective in preventing mandibular bone loss in FcγRIIb-/- mice, suggesting that anti-TNF-α therapy may be able to ameliorate mandibular bone loss in SLE patients with periodontitis.
Tempo and mode in karyotype evolution revealed by a probabilistic model incorporating both chromosome number and morphology

Karyotype, including the chromosome and arm numbers, is a fundamental genetic characteristic of all organisms and has long been used as a species-diagnostic character. Additionally, karyotype evolution plays an important role in divergent adaptation and speciation. Centric fusion and fission change chromosome numbers, whereas the intra-chromosomal movement of the centromere, such as pericentric inversion, changes arm numbers. A probabilistic model simultaneously incorporating both chromosome and arm numbers has not been established. Here, we built a probabilistic model of karyotype evolution based on the “karyograph”, which treats karyotype evolution as a walk on the two-dimensional space representing the chromosome and arm numbers. This model enables analysis of the stationary distribution with a stable karyotype for any given parameter. After evaluating their performance using simulated data, we applied our model to two large taxonomic groups of fish, Eurypterygii and series Otophysi, to perform maximum likelihood estimation of the transition rates and reconstruct the evolutionary history of karyotypes. The two taxa significantly differed in the evolution of arm number. The inclusion of speciation and extinction rates demonstrated possibly high extinction rates in species with karyotypes other than the most typical karyotype in both groups. Finally, we made a model including polyploidization rates and applied it to a small plant group. Thus, the use of this probabilistic model can contribute to a better understanding of tempo and mode in karyotype evolution and its possible role in speciation and extinction.
Association between the renin–angiotensin system and chronic lung allograft dysfunction

Chronic lung allograft dysfunction (CLAD) is the major cause of death after lung transplantation. Angiotensin II (AngII), the main effector of the renin–angiotensin system, elicits fibrosis in both kidney and lung. We identified six AngII-regulated proteins (Ras homolog family member B (RHOB), bone marrow stromal cell antigen 1 (BST1), lysophospholipase 1 (LYPA1), glutamine synthetase (GLNA), thrombospondin 1 (TSP1) and laminin subunit β2 (LAMB2)) that were increased in urine of patients with kidney allograft fibrosis. We hypothesised that the renin–angiotensin system is active in CLAD and that AngII-regulated proteins are increased in bronchoalveolar lavage fluid (BAL) of CLAD patients. We performed immunostaining of AngII receptors (AGTR1 and AGTR2), TSP1 and GLNA in 10 CLAD lungs and five controls. Using mass spectrometry, we quantified peptides corresponding to AngII-regulated proteins in BAL of 40 lung transplant recipients (stable, acute lung allograft dysfunction (ALAD) and CLAD). Machine learning algorithms were developed to predict CLAD based on BAL peptide concentrations. Immunostaining demonstrated significantly more AGTR1+ cells in CLAD versus control lungs (p=0.02). TSP1 and GLNA immunostaining positively correlated with the degree of lung fibrosis (R2=0.42 and 0.57, respectively). In BAL, we noted a trend towards higher concentrations of AngII-regulated peptides in patients with CLAD at the time of bronchoscopy, and significantly higher concentrations of BST1, GLNA and RHOB peptides in patients that developed CLAD at follow-up (p<0.05). The support vector machine classifier discriminated CLAD from stable and ALAD patients at the time of bronchoscopy (area under the curve (AUC) 0.86) and accurately predicted subsequent CLAD development (AUC 0.97). Proteins involved in the renin–angiotensin system are increased in CLAD lungs and BAL. AngII-regulated peptides measured in BAL may accurately identify patients with CLAD and predict subsequent CLAD development. Components of the renin–angiotensin system are increased in chronic lung allograft dysfunction (CLAD) fibrosis. Angiotensin II-regulated proteins in bronchoalveolar lavage identify concurrent and predict future CLAD in lung transplant recipients. https://bit.ly/3eRYez7
Randomized pilot study of a special education advocacy program for Latinx/minority parents of children with autism spectrum disorder

This study reports on a randomized controlled pilot intervention study examining the effectiveness and feasibility of a low-intensity (i.e. three sessions), low-cost, parent advocacy intervention. The intervention study employed community-partnered research methods and targeted a low-income community of mostly Latinx, immigrant-origin parents of children with autism spectrum disorder. The study was designed to test a parent-to-parent advocacy mentorship program in order to increase parent’s special education advocacy knowledge and empowerment. The educational intervention was delivered in Spanish to Spanish-speaking parents. Results indicated significantly increased in parent’s knowledge in the immediate intervention group, but this knowledge did not lead to greater sense of parent’s empowerment. Increases in knowledge about special education rights of their children are the first step toward advocating for services for their children. While parents from low-income, racial/ethnic minority backgrounds, particularly Latinx parents, can significantly increase their advocacy skills with a low-intensity, low-cost program, they may need more support in changing their self-perceptions of empowerment and advocacy. Lay abstract Persistent racial and ethnic disparities in obtaining an autism spectrum disorder diagnosis and services have been documented for Latinx children and other racial/ethnic minorities. This study reports on an educational intervention examining the effectiveness and feasibility of a low-intensity (i.e. three sessions), low-cost, parent advocacy for Latinx and other minority parents of children with autism. Results indicated significantly increased parental knowledge and in the immediate intervention group, but this knowledge did not lead to greater empowerment. While parents from low-income, racial/ethnic minority backgrounds, particularly Latinx parents, can significantly increase their advocacy skills with a low-intensity, low-cost program, they may need more support in changing their self-perceptions of empowerment and advocacy.
Exploring Patients’ Perceptions on ICU Diaries: A Systematic Review and Qualitative Data Synthesis

Supplemental Digital Content is available in the text. OBJECTIVES: This study aims to summarize the current qualitative evidence on patients’ experiences of reading the ICU diaries. DATA SOURCES: We searched the online databases PubMed, Ovid, EMBASE, and EBSCO host from inception to July 2020. STUDY SELECTION: All studies that presented any qualitative findings regarding patients’ experiences of reading an ICU diary were included. DATA EXTRACTION: Study design, location, publication year, data collection method, and mode, all qualitative themes identified and reported, and participant quotations, when appropriate. We also extracted data regarding the diary structure, when available. A thematic synthesis approach was used to analyze and synthesize qualitative data. DATA SYNTHESIS: Seventeen studies were analyzed. Most patients reported positive experiences with the ICU diary, such as understanding what they survived during critical illness, better understanding the process of recovery, gaining coherence of nightmares and delusional memories, realizing the importance of the presence of family and loved ones during ICU stay, and humanizing healthcare professionals that helped them survive critical illness. Patients also reported which components of the diary were important for their recovery, such as the presence of photographs and reading the diary with a healthcare professional, allowing the improvement of the concept of the ICU diary. Conclusion: This qualitative synthesis shows that patients recommend having an ICU diary, enlightening benefits such as better coping with the slow recovery from critical illness, strengthening family ties, and humanizing the ICU staff. It also identifies characteristics of the diary valued by the patients, in order to standardize the ICU diary according to their perspectives, and allowing future comparability between randomized controlled trials.
Subjective health complaints in early adolescence reflect stress: A study among adolescents in Western Sweden

Aims: Mental health problems are common among Swedish adolescents and are sometimes referred to as ‘stress-related’. The overall aim of this study is to do an analysis of subjective health complaints (SHCs) and perceived general stress among adolescents in Sweden, both their prevalence and association, by gender, migration background, family structure and socioeconomic conditions. Methods: Data from the baseline (comprising 2283 adolescents aged 13) of the STudy of Adolescence Resilience and Stress (STARS) study in Västra Götaland in Sweden were used. SHCs were measured by the Psychosomatic Problems Scale (PSP-scale) and self-reported stress was measured by Cohen’s Perceived Stress Scale (PSS-10). Socioeconomic conditions were measured with the Family Affluence Scale (FAS) and the MacArthur Scale of Subjective Social Status (SSS). Statistical analyses included Student’s t-tests and ANOVAs of means, linear and logistic regression analyses and Pearson’s correlations. Results: Social inequalities in both SHCs and self-reported stress were found; levels were higher among girls, adolescents living with one parent or in families with less favourable socioeconomic conditions. Self-reported stress and SHCs were found to be strongly correlated (r=0.70). Correlations with self-reported stress were stronger for psychological complaints (r=0.71) than for somatic complaints (r=0.52). Correlations did not vary with socioeconomic conditions of the family. Conclusions: SHCs do reflect general stress among adolescents, and it is appropriate to address the complaints as ‘stress-related’. Measures to improve adolescents’ mental health by reducing levels of SHCs should pay special attention to stressors in adolescents’ daily lives and strengthening adolescent’s coping resources and strategies.
Lean-Docking: Exploiting Ligands' Predicted Docking Scores to Accelerate Molecular Docking

In structure-based virtual screening (SBVS), a binding site on a protein structure is used to search for ligands with favorable nonbonded interactions. Because it is computationally difficult, docking is time-consuming and any docking user will eventually encounter a chemical library that is too big to dock. This problem might arise because there is not enough computing power or because preparing and storing so many three-dimensional (3D) ligands requires too much space. In this study, however, we show that quality regressors can be trained to predict docking scores from molecular fingerprints. Although typical docking has a screening rate of less than one ligand per second on one CPU core, our regressors can predict about 5800 docking scores per second. This approach allows us to focus docking on the portion of a database that is predicted to have docking scores below a user-chosen threshold. Herein, usage examples are shown, where only 25% of a ligand database is docked, without any significant virtual screening performance loss. We call this method "lean-docking". To validate lean-docking, a massive docking campaign using several state-of-the-art docking software packages was undertaken on an unbiased data set, with only wet-lab tested active and inactive molecules. Although regressors allow the screening of a larger chemical space, even at a constant docking power, it is also clear that significant progress in the virtual screening power of docking scores is desirable.