Miracle-dz/UniFAR-FTUs huggingface dataset:
Validation of reference genes for gene expression studies in tartary buckwheat (Fagopyrum tataricum Gaertn.) using quantitative real-time PCR

Quantitative real-time reverse transcriptase polymerase chain reaction is a sensitive technique for quantifying gene expression levels. By implementing three distinct algorithms (geNorm, normFinder and BestKeeper), we have validated the stability of the expression of seven candidate reference genes in tartary buckwheat, including FtSAND, FtCACS, FtExpressed1, FtGAPDH, FtActin, FtEF-1a and FtH3. In this study, the results indicated that FtCACS and FtSAND were the best reference genes for ‘abiotic cotyledons’, FtExpressed1 and FtEF-1α were the best reference genes for aluminium treatment, FtCACS and FtExpressed1 performed the best for the immature seed stage, FtCACS was best for the abiotic treatment, and FtH3 appeared to be the most suitable reference gene for the abiotic treatment in hypocotyls and all samples in this study. In contrast, FtActin and FtGAPDH are unsuitable genes. Our findings offer additional stable reference genes for gene expression research on tartary buckwheat at the immature seed stage and under abiotic treatment.
Secondary pneumothorax in end-stage lung disease complicated by noninvasive ventilation and a persistent air leak

A 75-year-old man initially presented to the respiratory service in 2012 with severe chronic obstructive pulmonary disease (COPD) defined as Global Initiative for Chronic Obstructive Lung Disease stage 3. Forced expiratory volume in 1 s (FEV1) was 1.1 L (33% predicted) with FEV1/forced vital capacity 32%. He required long-term oxygen therapy at home at 4 L·min−1 and by 2015 nocturnal high-pressure noninvasive ventilation (NIV) was required due to progressive symptomatic hypercapnic respiratory failure including a carbon dioxide tension (PCO2) of 7.9 kPa and bicarbonate of 28.3 mmol·L−1. Pneumothorax is a well-recognised complication of end-stage COPD, but the management is often complex and may be complicated by other sequelae of advanced respiratory disease including the requirement for NIV http://ow.ly/vkoJ30mB4nZ
Impaired Interneuron Development in a Novel Model of Neonatal Brain Injury

Abstract Prematurity is associated with significantly increased risk of neurobehavioral pathologies, including autism and schizophrenia. A common feature of these psychiatric disorders is prefrontal cortex (PFC) inhibitory circuit disruption due to GABAergic interneuron alteration. Cortical interneurons are generated and migrate throughout late gestation and early infancy, making them highly susceptible to perinatal insults such as preterm birth. Term and preterm PFC pathology specimens were assessed using immunohistochemical markers for interneurons. Based on the changes seen, a new preterm encephalopathy mouse model was developed to produce similar PFC interneuron loss. Maternal immune activation (MIA; modeling chorioamnionitis, associated with 85% of extremely preterm births) was combined with chronic sublethal hypoxia (CSH; modeling preterm respiratory failure), with offspring of both sexes assessed anatomically, molecularly and neurobehaviorally. In the PFC examined from the human preterm samples compared to matched term samples at corrected age, a decrease in somatostatin (SST) and calbindin (CLB) interneurons was seen in upper cortical layers. This pattern of interneuron loss in upper cortical layers was mimicked in the mouse PFC following the combination of MIA and CSH, but not after either insult alone. This persistent interneuron loss is associated with postnatal microglial activation that occurs during CSH only after MIA. The combined insults lead to long-term neurobehavioral deficits which parallel human psychopathologies that may be seen after extremely preterm birth. This new preclinical model supports a paradigm in which specific cellular alterations seen in preterm encephalopathy can be linked with a risk of neuropsychiatric sequela. Specific interneuron subtypes may provide therapeutic targets to prevent or ameliorate these neurodevelopmental risks.
Association between vegetarian diets and cardiovascular risk factors in non-Hispanic white participants of the Adventist Health Study-2

Abstract The association between dietary patterns and CVD risk factors among non-Hispanic whites has not been fully studied. Data from 650 non-Hispanic white adults who participated in one of two clinical sub-studies (about 2 years after the baseline) of the Adventist Health Study-2 (AHS-2) were analysed. Four dietary patters were identified using a validated 204-item semi-quantitative FFQ completed at enrolment into AHS-2: vegans (8·3 %), lacto-ovo-vegetarians (44·3 %), pesco-vegetarians (10·6 %) and non-vegetarians (NV) (37·3 %). Dietary pattern-specific prevalence ratios (PR) of CVD risk factors were assessed adjusting for confounders with or without BMI as an additional covariable. The adjusted PR for hypertension, high total cholesterol and high LDL-cholesterol were lower in all three vegetarian groups. Among the lacto-ovo-vegetarians the PR were 0·57 (95 % CI 0·45, 0·73), 0·72 (95 % CI 0·59, 0·88) and 0·72 (95 % CI 0·58, 0·89), respectively, which remained significant after additionally adjusting for BMI. The vegans and the pesco-vegetarians had similar PR for hypertension at 0·46 (95 % CI 0·25, 0·83) and 0·62 (95 % CI 0·42, 0·91), respectively, but estimates were attenuated and marginally significant after adjustment for BMI. Compared with NV, the PR of obesity and abdominal adiposity, as well as other CVD risk factors, were significantly lower among the vegetarian groups. Similar results were found when limiting analyses to participants not being treated for CVD risk factors, with the vegans having the lowest mean BMI and waist circumference. Thus, compared with the diet of NV, vegetarian diets were associated with significantly lower levels of CVD risk factors among the non-Hispanic whites.
Dynamic control of hippocampal spatial coding resolution by local visual cues

The ability to flexibly navigate an environment relies on a hippocampal-dependent internal cognitive map. Explored space can be internally mapped at different spatial resolutions. However, whether hippocampal spatial coding resolution can be dynamically controlled within and between environments is unknown. In this work we recorded the firing of hippocampal principal cells in mice navigating virtual reality environments, which differed by the presence of local visual cues (virtual 3D objects). Objects improved spatial coding resolution globally with a higher proportion of place cells, smaller place fields, increased spatial selectivity and stability. Spatial coding resolution was notably enhanced locally near objects and could be rapidly tuned by their manipulations. In the presence of objects, place cells also displayed improved theta phase precession and theta timescale spike coordination. These results suggest that local visual cues can rapidly tune the resolution of the hippocampal mapping system within and between environments.
Reverse torque evaluation in indexed and nonindexed abutments of Morse Taper implants in a mechanical fatigue test

Background: This experimental study assessed reverse torque of indexed and nonindexed (NI) abutments in Morse Taper (MT) implants in a mechanical fatigue test. Materials and Methods: In this experimental study It was used 37 implants MT and over them installed Pilar Flex abutments (4.8 mm × 6 mm × 1.5 mm). The groups were as follows: Group A used 19 MT implants with a NI Pilar Flex abutment loaded with 32 N/cm and Group B used 18 MT implants with an indexed (IN) Pilar Flex abutment loaded with 20 N/cm. The abutments were tested according to ISO standard 14801/2007. The specimens were installed at 30° from the axial axis and underwent a 133 N load, 4 Hz frequency, and 1,000,000 cycles. Once the test was completed, the reverse torque was provided by an electronic torque meter. Data were submitted to statistical analysis using the t-test for independent samples and paired t-test. The significance level was considered P < 0.05. Results: Results obtained showed that the indexed Pilar Flex abutment had a percentage of torque loss from the initial torque of 49% and the NI Pilar Flex abutment lost 14%. Paired Student's t-tests revealed that for both NI (P < 0.001) and indexed (P < 0.001) abutments, the counter torque values were significantly lower than those applied at the initial torque. Conclusion: According on the methodology used, the NI Pilar Flex abutment was more effective regarding the reverse torque in single-unit implant prostheses versus the indexed Pilar Flex abutment. A greater loosening in the indexed Pilar Flex abutment retaining screw was noted in the reverse torque test, and the Pilar Flex abutment failed to show good outcomes related to the cold welding effect.
Expression analysis of four pseudo-response regulator (PRR) genes in Chrysanthemum morifolium under different photoperiods

Genes encoding pseudo-response regulator (PRR) proteins play significant roles in plant circadian clocks. In this study, four genes related to flowering time were isolated from Chrysanthemum morifolium. Phylogenetic analysis showed that they are highly homologous to the counterparts of PRRs of Helianthus annuus and named as CmPRR2, CmPRR7, CmPRR37, and CmPRR73. Conserved motifs prediction indicated that most of the closely related members in the phylogenetic tree share common protein sequence motifs, suggesting functional similarities among the PRR proteins within the same subtree. In order to explore functions of the genes, we selected two Chrysanthemum varieties for comparison; that is, a short-day sensitive Zijiao and a short-day insensitive Aoyunbaixue. Compared to Aoyunbaixue, Zijiao needs 13 more days to complete the flower bud differentiation. Evidence from spatio-temporal gene expression patterns demonstrated that the CmPRRs are highly expressed in flower and stem tissues, with a growing trend across the Chrysanthemum developmental process. In addition, we also characterized the CmPRRs expression patterns and found that CmPRRs can maintain their circadian oscillation features to some extent under different photoperiod treatment conditions. These lines of evidence indicated that the four CmPRRs undergo circadian oscillation and possibly play roles in regulating the flowering time of C. morifolium.
An Innovative Curriculum Using a Simulated Electronic Health Record to Teach Internal Medicine Residents About ICD–10-CM

Introduction This module introduces learners to the International Classification of Diseases, Tenth Revision, Clinical Modification (ICD–10-CM) coding system and its relevance to patient care, billing, and public health. Knowledge of this coding system is critical for residents about to enter independent practice. Methods This case was developed for internal medicine residents at all levels of training and was delivered in three 50-minute sessions. Associated materials include a test given before and after the module, the answer key to that test, the clinical case and associated learning objectives, a faculty guide, and an evaluation form. This module features a simulated patient encounter in an electronic health record, the details of which are given in the faculty guide. Results Eighty-eight percent of learners reported that they found this exercise useful, and there was a significant improvement in posttest scores after completion. Ninety-four percent of learners reported a commitment to using appropriate ICD–10-CM codes in their own practice after completion of the exercise. Discussion This effective module has been integrated into our ambulatory curriculum. Knowledge of ICD–10-CM coding allows physicians to document specifically and appropriately as they move forward in their practice.
Human In Vitro Vascularization, Adipocytes and Vascularized Adipose Tissue : Three relevant models for studies of vascularization, adipocytes and their interaction

Adipose tissue related diseases such as obesity and type 2 diabetes are worldwide epidemics. In order to develop in vitro adipose tissue cultures which mimic more faithfully the physiology in vivo, new well characterized and publicly accepted differentiation methods of human adipose stem cells are needed. The aims of this study were (i) to improve the existing natural adipose tissue extract (ATE)-based induction method and (ii) to study the effects of differentiation method on insulin responsiveness of the resulting adipocytes. Different induction media were applied on human adipose stromal cell (hASC) monocultures to study the differentiation capacity of the induction media and the functionality of the differentiated adipocytes. Cells were differentiated for 14 days to assess triglyceride accumulation per cell and adipocyte-specific gene expression (PPAR , adiponectin, AP2, leptin, Glut4, Prdm16, CIDEA, PGC1, RIP140, UCP and ADCY5). Insulin response was studied by measuring glucose uptake and inhibition of lipolysis after incubation with 100 or 500 nM insulin. The selected differentiation method included 3-day induction with adipose tissue extract, 6 days in serumfree medium supplemented with 1.15 M insulin and 9.06 M Troglitazone, followed by 4 days in a defined serumand insulin-free stimulation medium. This protocol induced prominent general adipocyte gene expression, including markers for both brown and white adipocytes, and triglyceride accumulation. Moreover, the cells were sensitive to insulin as observed from increased glucose uptake and inhibition of lipolysis. This differentiation protocol developed provides a promising approach for induction of hASC adipogenesis to obtain functional and mature human adipocytes.
Lambdacism, Rhotacism and Sigmatism in Preschool Children: Frequency and Distribution

BACKGROUND: Speech sound appears first in the child’s speech development and is the primary means of expression. Articulation disorders can hinder the comprehensibility of children’s speech. The speech, in turn, can limit the child’s inclusion in the social and educational environment. AIM: To establish frequency and distribution of lambdacism, rhotacism and sigmatism or their combination in preschool children and the frequency and distribution of these articulation disorders among boys and girls. MATERIAL AND METHODS: A retrospective analysis of data from preventive examination for early diagnosis of impairments of hearing, speech and sounds in preschool children has been carried out. In the selected sample, only the data for children diagnosed with lambdacism, rhotacism, sigmatism or their combination are analysed. The data is statistically examined, represented in tables and figures and analysed descriptively. RESULTS: In the analysed sample, the greater presence of lambdacism was observed before rhotacism and sigmatism. Most commonly, these three types of articulation disorder appear alone, as isolated cases, instead of a combination of two out of the three impairments. They are more common in boys than in girls. CONCLUSION: Timely diagnosis and rehabilitation of lambdacism, rhotacism and sigmatism or their combination in preschool children will enable easier and faster integration of the children in the social and educational environment without leaving lasting consequences.
Fungal diversity of mangrove-associated sponges from New Washington, Aklan, Philippines

ABSTRACT Sponge-associated fungi are the least explored marine fungal groups. It is only in recent years that fungal symbionts of marine sponges have received attention mainly due to the isolation of bioactive metabolites while not much attention was given to their specificity, biogeography and exact roles in marine sponges. The diversity of fungi associated with mangrove sponges (Axinella sp., Halichondria cf. panicea, Haliclona sp., Tedania sp.) collected from New Washington, Aklan, Philippines were investigated using morphological observation. A total of 110 species of sponge-associated fungi belonging to 22 genera of ascomycetes with 18 genera of asexual morphs whose sexual stage is unknown, 2 genera of basidiomycetes, 21 morphospecies of Mycelia sterilia, 1 unidentified yeast species and 11 unidentified hyphomycetes were isolated from four species of mangrove sponges. This is the first study that explored the diversity and ecology of sponge-associated fungi in mangrove habitats from the Philippines. The results of the study suggest host-preference by various fungal taxa and the development of fungi on these hosts appeared to be strongly influenced by the characteristics or nature of the immediate environment.
Activation of TAp73 and inhibition of TrxR by Verteporfin for improved cancer therapy in TP53 mutant pancreatic tumors

Aim: TAp73 is a tumor suppressor, which compensates for p53 loss and induces apoptosis in tumors in response to genotoxic stress or small-molecule treatments. Pancreatic ductal adenocarcinoma has a late onset of the disease, responds poorly to the existing therapies and has a very low survival rates. Result: Here, using drug-repurposing approach, we found that protoporphyrin IX (PpIX) and benzoporphyrin derivative (BPD) monoacid ring A activate TAp73 and induce apoptosis in pancreatic cancer cells. PpIX and BPD induce reactive oxygen species and inhibit thioredoxin reductase 1. Conclusion: Thus, PpIX and BPD target cancer cells’ vulnerabilities namely activate TAp73 tumor suppressor and inhibit oncogenic Trx1. Our findings may contribute to faster repurposing of PpIX and BPD to treat pancreatic tumors.
The prevalence of PTSD and major depression in the global population of adult war survivors: a meta-analytically informed estimate in absolute numbers

ABSTRACT Background: Elevated prevalences of post-traumatic stress disorder (PTSD) and major depression (MD) have been reported in populations exposed to war. However, no global estimates of war survivors suffering from PTSD and/or MD in absolute numbers have been reported. Objective: We made the first attempt to estimate in absolute numbers how many adult war survivors globally may suffer PTSD and/or MD, which should inform local and global mental health programmes. Method: Drawing on the Uppsala Conflict Database, we reviewed all countries that suffered at least one war within their own territory between 1989 and 2015 (time span chosen on availability of geo-referenced data and population estimates). We then conducted a meta-analysis of current randomized epidemiological surveys on prevalence of PTSD and/or MD among war survivors. Finally, we extrapolated our results from the meta-analysis on the global population of adult war survivors by means of using general population data from the United Nations. Results: We estimate that about 1.45 billion individuals worldwide have experienced war between 1989 and 2015 and were still alive in 2015, including one billion adults. On the basis of our meta-analysis, we estimate that about 354 million adult war survivors suffer from PTSD and/or MD. Of these, about 117 million suffer from comorbid PTSD and MD. Conclusions: Based on the slim available evidence base, the global number of adult war survivors suffering PTSD and/or MD is vast. Most war survivors live in low-to-middle income countries with limited means to handle the enormous mental health burden. Since representative high quality data is lacking from most of these countries, our results contain a large margin of uncertainty and should be interpreted with caution. HIGHLIGHTS • We estimate that 1.45 billion people worldwide have experienced war between 1989 and 2015. • We estimate that 354 million adult war survivors globally suffer from PTSD and/or MD. • We estimate that 117 million adult war survivors globally suffer from a comorbidity of PTSD+MD. • Most war survivors live in low-to-middle income countries with limited means to handle the associated mental health burden.
The analysis of a time-course transcriptome profile by systems biology approaches reveals key molecular processes in acute kidney injury

Background: Acute kidney injury is a common debilitating disease with no curative treatment. The recent development of big biological data is expected to expand our understanding of the disorder if appropriately analyzed to generate translational knowledge. We have here re-analyzed a time-course microarray data on mRNA expression of rat kidneys exposed to ischemia-reperfusion to identify key underlying biological processes. Materials and Methods: The dataset was quality controlled by principal component analysis and hierarchical clustering. Using limma R package, differentially expressed (DE) genes were detected which were then clustered according to their expression trajectories. The biological processes related to each cluster were harvested using gene ontology enrichment analysis. In addition, the interaction map of proteins encoded by the DE genes was constructed, and the functions related to network central genes were determined. Furthermore, signaling pathways related to the DE genes were harvested using pathway enrichment analysis. Results: We found 8139 DE genes that drive critical processes such as the control of blood circulation, reactive species metabolism, mitochondrial respiration, apoptosis, cell proliferation, as well as inflammatory and immunological reactions. The role of less recognized pathways such as olfactory signaling in acute kidney injury is also proposed that remains to be investigated in future studies. Conclusion: Using systems biology top-down approach, we have suggested novel potential genes and pathways to be intervened toward kidney regeneration.
The top 10 most-cited articles on the management of fractured instruments: a bibliometric analysis

Objectives The purpose of this research was to identify the top 10 most-cited articles on the management of fractured or broken instruments and to perform a bibliometric analysis thereof. Materials and Methods Published articles related to fractured instruments were screened from online databases, such as Web of Science, Scopus, PubMed, and ScienceDirect, and highly cited papers, with at least 50 citations since publication, were identified. The most-cited articles were selected and analysed with regard to publication title, authorship, the journal of publication, year, institution, country of origin, article type, and number of citations. Results The top 10 most-cited articles were from various journals. Most were published in the Journal of Endodontics, followed by the International Endodontic Journal, and Dental Traumatology. The leading countries were Australia, Israel, Switzerland, the USA, and Germany, and the leading institution was the University of Melbourne. The majority of articles among the top 10 articles were clinical research studies (n = 8), followed by a basic research article and a non-systematic review article. Conclusions This bibliometric analysis revealed interesting information about scientific progress in endodontics regarding fractured instruments. Overall, clinical research studies and basic research articles published in high-impact endodontic journals had the highest citation rates.