Miracle-dz/UniFAR-FTUs huggingface dataset:
TGFβ/BMP activate the smooth muscle/bone differentiation programs in mesoangioblasts

Mesoangioblasts are vessel-derived stem cells that can be induced to differentiate into different cell types of the mesoderm such as muscle and bone. The gene expression profile of four clonal derived lines of mesoangioblasts was determined by DNA micro-array analysis: it was similar in the four lines but different from 10T1/2 embryonic fibroblasts, used as comparison. Many known genes expressed by mesoangioblasts belong to response pathways to developmental signalling molecules, such as Wnt or TGFβ/BMP. Interestingly, mesoangioblasts express receptors of the TGFβ/BMP family and several Smads and, accordingly, differentiate very efficiently into smooth muscle cells in response to TGFβ and into osteoblasts in response to BMP. In addition, insulin signalling promotes adipogenic differentiation, possibly through the activation of IGF-R. Several Wnts and Frizzled, Dishevelled and Tcfs are expressed, suggesting the existence of an autocrine loop for proliferation and indeed, forced expression of Frzb-1 inhibits cell division. Mesoangioblasts also express many neuro-ectodermal genes and yet undergo only abortive neurogenesis, even after forced expression of neurogenin 1 or 2, MASH or NeuroD. Finally, mesoangioblasts express several pro-inflammatory genes, cytokines and cytokine receptors, which may explain their ability to be recruited by tissue inflammation. Our data define a unique phenotype for mesoangioblasts, explain several of their biological features and set the basis for future functional studies on the role of these cells in tissue histogenesis and repair.
Speech in 5-year-olds born with unilateral cleft lip and palate: a Prospective Swedish Intercenter Study

Abstract Studies on the impact of cleft palate surgery on speech with stringent methodology are called for, since we still do not know the best timing or the best method for surgery. The purpose was to report on speech outcome for all Swedish-speaking 5-year-olds born with a non-syndromic unilateral cleft lip and palate (UCLP), in 2008–2010, treated at Sweden’s six cleft palate centres, and to compare speech outcomes between centres. Speech was assessed in 57 children with percent consonants correct adjusted for age (PCC-A), based on phonetic transcriptions from audio recordings by five independent judges. Also, hypernasality and perceived velopharyngeal function were assessed. The median PCC-A for all children was 93.9, and medians in the different groups varied from 89.9 to 96.8. In the total group, 9 children (16%) had more than mild hypernasality. Twenty-two children (38.5%) were perceived as having competent/sufficient velopharyngeal function, 25 (44%) as having marginally incompetent/insufficient velopharyngeal function, and 10 children (17.5%) as having incompetent/insufficient velopharyngeal function. Ten children were treated with secondary speech improving surgery and/or fistula surgery. No significant differences among the six groups, with eight to ten children in each group, were found. The results were similar to those in other studies on speech of children with UCLP, but poorer than results in normative data of Swedish-speaking 5-year-olds without UCLP. Indications of differences in frequency of surgical treatment and speech treatment between centres were observed.
Mapping of epitopes on Ul snRNP polypeptide A with synthetic peptides and autoimmune sera

The ability of synthetic peptides encompassing almost the entire sequence of snRNP U1A polypeptide to be recognized in ELISA by sera of autoimmune patients was investigated. Sera from 18 patients with mixed connective tissue disease (MCTD), 145 with systemic lupus erythematosus (SLE) and 120 with other rheumatic autoimmune diseases were tested with 13 overlapping peptides. Among them, peptide 257–282 and, to a lower extent, peptide 1–11 were recognized by MCTD, SLE and Sjogren's syndrome sera. In contrast, peptide 35–58 was recognized by 94% of MCTD and only 19% of SLE sera. It did not react with any of the other patient sera. The ELISA results were compared with the pattern of reactivity observed in immunoblotting. The results indicate that peptide 35–58 probably contains a major epitope recognized by MCTD autoantibodies. It is noteworthy that in snRNP particles, this region of U1A interacts with RNA and presents only limited homology with the corresponding sequence 32–50 of U2B”.
A Novel Role of Vimentin Filaments: Binding and Stabilization of Collagen mRNAs

ABSTRACT The stem-loop in the 5′ untranslated region (UTR) of collagen α1(I) and α2(I) mRNAs (5′SL) is the key element regulating their stability and translation. Stabilization of collagen mRNAs is the predominant mechanism for high collagen expression in fibrosis. LARP6 binds the 5′SL of α1(I) and α2(I) mRNAs with high affinity. Here, we report that vimentin filaments associate with collagen mRNAs in a 5′SL- and LARP6-dependent manner and stabilize collagen mRNAs. LARP6 interacts with vimentin filaments through its La domain and colocalizes with the filaments in vivo. Knockdown of LARP6 by small interfering RNA (siRNA) or mutation of the 5′SL abrogates the interaction of collagen mRNAs with vimentin filaments. Vimentin knockout fibroblasts produce reduced amounts of type I collagen due to decreased stability of collagen α1(I) and α2(I) mRNAs. Disruption of vimentin filaments using a drug or by expression of dominant-negative desmin reduces type I collagen expression, primarily due to decreased stability of collagen mRNAs. RNA fluorescence in situ hybridization (FISH) experiments show that collagen α1(I) and α2(I) mRNAs are associated with vimentin filaments in vivo. Thus, vimentin filaments may play a role in the development of tissue fibrosis by stabilizing collagen mRNAs. This finding will serve as a rationale for targeting vimentin in the development of novel antifibrotic therapies.
A multiscale analysis of DNA phase separation: from atomistic to mesoscale level

Abstract DNA condensation and phase separation is of utmost importance for DNA packing in vivo with important applications in medicine, biotechnology and polymer physics. The presence of hexagonally ordered DNA is observed in virus capsids, sperm heads and in dinoflagellates. Rigorous modelling of this process in all-atom MD simulations is presently difficult to achieve due to size and time scale limitations. We used a hierarchical approach for systematic multiscale coarse-grained (CG) simulations of DNA phase separation induced by the three-valent cobalt(III)-hexammine (CoHex3+). Solvent-mediated effective potentials for a CG model of DNA were extracted from all-atom MD simulations. Simulations of several hundred 100-bp-long CG DNA oligonucleotides in the presence of explicit CoHex3+ ions demonstrated aggregation to a liquid crystalline hexagonally ordered phase. Following further coarse-graining and extraction of effective potentials, we conducted modelling at mesoscale level. In agreement with electron microscopy observations, simulations of an 10.2-kb-long DNA molecule showed phase separation to either a toroid or a fibre with distinct hexagonal DNA packing. The mechanism of toroid formation is analysed in detail. The approach used here is based only on the underlying all-atom force field and uses no adjustable parameters and may be generalised to modelling chromatin up to chromosome size.
The effect of playground- and nature-based playtime interventions on physical activity and self-esteem in UK school children

School playtime provides opportunities for children to engage in physical activity (PA). Playground playtime interventions designed to increase PA have produced differing results. However, nature can also promote PA, through the provision of large open spaces for activity. The purpose of this study is to determine which playtime interventions are most effective at increasing moderate-to-vigorous physical activity (MVPA) and if this varies by school location. Fifty-two children from an urban and rural school participated in a playground sports (PS) and nature-based orienteering intervention during playtime for one week. MVPA was assessed the day before and on the final day of the interventions using accelerometers. Intervention type (p < 0.05) and school location (p < 0.001) significantly influenced MVPA; with PS increasing MVPA more than nature-based orienteering. Urban children seemed to respond to the interventions more positively; however, differences in baseline MVPA might influence these changes. There was a positive correlation for fitness and MVPA during PS (r = 0.32; p < 0.05), but not nature-based orienteering (p > 0.05). The provision of PS influences PA the most; however, a variety of interventions are required to engage less fit children in PA.
Threshold body mass index and sex-specific waist circumference for increased risk of heart failure with preserved ejection fraction

Background Body mass index †Deceased. (BMI) is a risk factor for heart failure with preserved ejection fraction (HFpEF). Design We investigated the threshold BMI and sex-specific waist circumference associated with increased HFpEF incidence in the SCReening Evaluation of the Evolution of New Heart Failure (SCREEN-HF) study, a cohort study of a community-based population at increased cardiovascular disease risk. Methods Inclusion criteria were age ≥60 years with one or more of self-reported hypertension, diabetes, heart disease, abnormal heart rhythm, cerebrovascular disease or renal impairment. Exclusion criteria were known heart failure, ejection fraction <50% or more than mild valve abnormality. Among 3847 SCREEN-HF participants, 73 were diagnosed with HFpEF at a median of 4.5 (interquartile range: 2.9–5.5) years after enrolment. Results HFpEF incidence rates were higher for BMI ≥27.5 kg/m2 than for BMI < 25 kg/m2, and for waist circumference >100 cm (men) or > 90 cm (women) than for waist circumference ≤94 cm (men) or ≤ 83 cm (women) in Poisson regression analysis. Semiparametric proportional hazards analyses confirmed these BMI and waist circumference thresholds, and exceeding these thresholds was associated with an attributable risk of HFpEF of 44–49%. Conclusions Both central obesity and overweight were associated with increased HFpEF incidence. Although a randomised trial of weight control would be necessary to establish a causal relationship between obesity/overweight and HFpEF incidence, these data suggest that maintenance of BMI and waist circumference below these thresholds in a community similar to that of the SCREEN-HF cohort may reduce the HFpEF incidence rate by as much as 50%.
pK(a) Calculations suggest storage of an excess proton in a hydrogen-bonded water network in bacteriorhodopsin.

Calculations of protonation states and pK(a) values for the ionizable groups in the resting state of bacteriorhodopsin have been carried out using the recently available 1.55 A resolution X-ray crystallographic structure. The calculations are in reasonable agreement with the available experimental data for groups on or near the ion transport chain (the retinal Schiff base; Asp85, 96, 115, 212, and Arg82). In contrast to earlier studies using lower-resolution structural data, this agreement is achieved without manipulations of the crystallographically determined heavy-atom positions or ad hoc adjustments of the intrinsic pK(a) of the Schiff base. Thus, the theoretical methods used provide increased reliability as the input structural data are improved. Only minor effects on the agreement with experiment are found with respect to methodological variations, such as single versus multi-conformational treatment of hydrogen atom placements, or retaining the crystallographically determined internal water molecules versus treating them as high-dielectric cavities. The long-standing question of the identity of the group that releases a proton to the extracellular side of the membrane during the L-to-M transition of the photocycle is addressed by including as pH-titratable sites not only Glu204 and Glu194, residues near the extracellular side that have been proposed as the release group, but also an H(5)O(2)(+) molecule in a nearby cavity. The latter represents the recently proposed storage of the release proton in an hydrogen-bonded water network. In all calculations where this possibility is included, the proton is stored in the H(5)O(2)(+) rather than on either of the glutamic acids, thus establishing the plausibility on theoretical grounds of the storage of the release proton in bacteriorhodopsin in a hydrogen-bonded water network. The methods used here may also be applicable to other proteins that may store a proton in this way, such as the photosynthetic reaction center and cytochrome c oxidase.
Microarray analysis reveals the changes of circular RNA expression and molecular mechanism in acute lung injury mouse model

Acute lung injury (ALI) is a severe disease with sudden onset, rapid progression, poor treatment response, and high mortality. An increasing number of studies had found that circular RNAs (circRNAs) has significant functions in various diseases, while the role of circRNAs in ALI is not yet clear. The purpose of this study was to find circRNAs related to ALI and their mechanism of action. Expression profiles of lung circRNAs and messenger RNAs (mRNAs) were analyzed by microarray in the ALI mice models and healthy controlled mice. Differentially expressed RNAs were identified, function and pathways were analyzed by bioinformatics analysis. Moreover, the results of the microarray were verified by real‐time PCR. We identified 2262 differentially expressed mRNAs and 581 circRNAs between ALI mice and control. Validation of candidate circRNAs by real‐time PCR indicates that the majority of circRNAs identified by microarray are reliable and worthy of further study. ALI induced circRNAs primarily function in the metabolic regulatory process. Moreover, differentially expressed circRNAs were mainly involved in signaling pathways of mitogen‐activated protein kinases, focal adhesion, FoxO, neurotrophin, and Wnt. In addition, a competitive endogenous RNA network was constructed to further interpret the molecular mechanism of ALI. This study observed significantly changed circRNAs profiles in LPS‐induced mouse model and revealed a potential role of circRNAs in ALI.
Using tRNA halves as novel biomarkers for the diagnosis of gastric cancer.

BACKGROUND tRNA halves (tiRNAs) are produced from mature tRNAs. They have important roles both with in normal cells and cancer cells. However, the diagnostic value of tiRNAs in cancers have not yet been elucidated. OBJECTIVE To explore the diagnostic value of tiRNA-5034-GluTTC-2 in gastric cancer. PATIENTS AND METHODS Quantitative reverse transcription-polymerase chain reaction was used to detect the expression levels of tiRNA-5034-GluTTC-2 in paired gastric cancer tissues and adjacent normal tissues, plasmas from patients with gastric cancer and healthy people, and gastric cancer cell lines. Then, the relationship between its levels and clinicopathological factors of patients with gastric cancer was analyzed. A receiver operating characteristic (ROC) curve was established to predict the diagnostic value. RESULTS tiRNA-5034-GluTTC-2 was first found to be down-regulated in gastric cancer tissues and plasmas. Its levels were significantly associated with tumor size. The area under the ROC curve (AUC) was 0.779 and 0.835 in tissue and plasma, respectively. The sensitivity, specificity and AUC were 84.7%, 92.8%, and 0.915 when tissues and plasmas were used in combination, respectively. The overall survival rate of patients with a lower expression of tiRNA-5034-GluTTC-2 was significantly lower than those with a higher expression. CONCLUSIONS These results indicated that tiRNA-5034-GluTTC-2 may be a novel biomarker for the diagnosis of gastric cancer.
Familial breast cancer. Part III: Genome instability and cancer risk.

PURPOSE The purpose of part III of this study was to direct our efforts towards more detailed genetic studies, which can be used in genetic counselling of patients with breast cancer and their relatives. PATIENTS AND METHODS We investigated 52 patients, 25 with chromosomal fragility and 17 with spontaneous chromosomal aberrations, all with familial breast cancer (study group). The control group consisted of 10 healthy women without a history of proliferative diseases or breast cancer in their families. The chromosomal fragility and spontaneous chromosomal aberrations were studied in peripheral blood lymphocytes cultured for 72 and 48 hours, respectively, at 37 degrees C, following a standard procedure. RESULTS In the patients with breast cancer the expression of chromosomal fragility was significantly higher (19.47%) compared to 11.61% in the control group (p<0.0001). In the patients with familial breast cancer the spontaneous chromosomal aberrations were significantly higher (6.72%) compared with those of the normal individuals (1.98%, p<0.0001). In the study group spontaneous breaks in a single lymphocyte were 0.15, while they were 0.05 in the control group (p<0.0001). CONCLUSION The values of chromosomal fragility and chromosomal aberrations have some practical and theoretical importance in genetic services. The different variants in genomic stability are related with individual breast cancer development risk. Our results support the idea that the fragile sites and chromosomal aberrations may act as predisposing factors in carcinogenesis.
Ecological risk assessment of boreal sediments affected by metal mining: Metal geochemistry, seasonality, and comparison of several risk assessment methods

The mining industry is a common source of environmental metal emissions, which cause long‐lasting effects in aquatic ecosystems. Metal risk assessment is challenging due to variations in metal distribution, speciation, and bioavailability. Therefore, seasonal effects must be better understood, especially in boreal regions in which seasonal changes are large. We sampled 4 Finnish lakes and sediments affected by mining for metals and geochemical characteristics in autumn and late winter, to evaluate seasonal changes in metal behavior, the importance of seasonality in risk assessment, and the sensitivity and suitability of different risk assessment methods. We compared metal concentrations in sediment, overlying water, and porewater against environmental quality guidelines (EQGs). We also evaluated the toxicity of metal mixtures using simultaneously extracted metals and an acid volatile sulfides (SEM‐AVS) approach together with water quality criteria (US Environmental Protection Agency equilibrium partitioning benchmarks). Finally, site‐specific risks for 3 metals (Cu, Ni, Zn) were assessed using 2 biotic ligand models (BLMs). The metal concentrations in the impacted lakes were elevated. During winter stratification, the hypolimnetic O2 saturation levels were low (<6%) and the pH was acidic (3.5–6.5); however, abundant O2 (>89%) and neutral pH (6.1–7.5) were found after the autumnal water overturn. Guidelines were the most conservative benchmark for showing an increased risk of toxicity in the all of the lakes. The situation remained stable between seasons. On the other hand, SEM‐AVS, equilibrium partition sediment benchmarks (ESBs), and BLMs provided a clearer distinction between lakes and revealed a seasonal variation in risk among some of the lakes, which evidenced a higher risk during late winter. If a sediment risk assessment is based on the situation in the autumn, the overall risk may be underestimated. It is advisable to carry out sampling and risk assessment during periods in which metals are assumed to be the most environmentally harmful. Integr Environ Assess Manag 2016;12:759–771. © 2015 SETAC
A comparison of wound healing following treatment with Lavandula x allardii honey or essential oil

The increased interest in complementary therapies has led to the investigation of products traditionally believed to have a beneficial effect in wound healing. Two such products are honey and lavender essential oil. In this study a rat excisional wound model was used to investigate the action of Lavandula x allardii honey and essential oil, and a standard therapeutic honey (Medihoney®). Four 8 mm wounds were created surgically on the dorsal surface of each rat and honey or essential oil applied to the wounds twice a day for 4 days. Wound healing was analysed by wound contraction and capillary volume at 5 and 12 days post‐surgery. Although no statistically significant difference in wound contraction was observed for the essential oil or honey treated wounds relative to the untreated control, both honeys were shown to reduce the capillary volume in the wound site at day 12 with no difference between the honeys (control 154 ± 14 µm3 vs L. x allardii honey 77 ± 18 µm3 and Medihoney 89 ± 39 µm3, p < 0.001; mean ± SD). This suggests that scar maturation in these animals was more advanced than in other groups. These data suggest that L. x allardii honey, but not essential oil, has a beneficial action in wound healing. Copyright © 2006 John Wiley & Sons, Ltd.
Amantadine in Parkinson's disease

A double-blind, placebo-controlled, crossover study with long-term follow-up of amantadine in Parkinson's disease was performed on 26 patients. Other antiparkinsonian medications were discontinued in all but three patients. Amantadine resulted in a statistically significant 12 percent overall improvement over placebo. Twenty of 26 patients, without breaking the code, selected amantadine for long-term usage. Ten patients continued treatment for 10 to 12 months, and an overall statistically significant improvement was noted at 2 weeks and at 1, 2, 3, and 10 to 12 months. Improvements in tremor and rigidity remained relatively constant, while there was some apparent loss of efficacy in timed tests and quality of timed tests. Amantadine appears effective in the long-term treatment of some patients with Parkinson's disease.