Miracle-dz/UniFAR-FTUs huggingface dataset:
Identification of TAF1, SAT1, and ARHGEF9 as DNA methylation biomarkers for hepatocellular carcinoma

Hepatocellular carcinoma (HCC) is a major cause of cancer‐related deaths worldwide. More than 90% of primary HCC is HCC. Hepatitis C virus (HCV) infection and alcohol consumption have been widely accepted as two major risk factors for developing HCC. Herein, we aimed to identify DNA methylation genes related to both HCV infection and alcohol consumption. In this study, we identified methylation genes that were associated with the risk of HCV infection and alcohol consumption, respectively, by a large‐scale bioinformatic analysis. Through PPI network analysis, we revealed the associations between the two types of genes and found six hub genes—TAF1, SAT1, Phospholipase C‐beta 2, FGD1, ARHGAP4, and ARHGEF9—that may be associated with both HCV infection and alcohol consumption. Gene Ontology enrichment analysis was used to analyze the function which these genes in the network enriched. Among them, TAF1, SAT1, and ARHGEF9 were methylated genes that have been found to be related to tumor progression in HCC patients. Through independent data sets, we verified the methylation pattern of these six genes in HCC samples that had both HCV infection and alcohol consumption risks. Furthermore, we found that three of the six methylated genes were also associated with the prognosis of HCC patients. To summarize, we identified six hub genes that were associated with both HCV infection and alcohol consumption in the progress of HCC. The six methylation genes that might play an important role in both HCV infection and alcohol consumption would be potential therapy targets for HCC.
IsomiRs and tRNA‐derived fragments are associated with metastasis and patient survival in uveal melanoma

Uveal melanoma (UVM) is the most common primary intraocular malignancy in adults. With over 50% of patients developing metastatic disease, there is an unmet need for improved diagnostic and therapeutic options. Efforts to understand the molecular biology of the disease have revealed several markers that correlate with patient prognosis, including the copy number of chromosome 3, genetic alterations in the BAP1, EIF1AX and SF3B1 genes, and other transcriptional features. Here, we expand upon previous reports by comprehensively characterizing the short RNA‐ome in 80 primary UVM tumor samples. In particular, we describe a previously unseen complex network involving numerous regulatory molecules that comprise microRNA (miRNAs), novel UVM‐specific miRNA loci, miRNA isoforms (isomiRs), and tRNA‐derived fragments (tRFs). Importantly, we show that the abundance profiles of isomiRs and tRFs associate with various molecular phenotypes, metastatic disease, and patient survival. Our findings suggest deep involvement of isomiRs and tRFs in the disease etiology of UVM. We posit that further study and characterization of these novel molecules will improve understanding of the mechanisms underlying UVM, and lead to the development of new diagnostic and therapeutic approaches.
Evidence-Based Evaluation of the Ethics of Sham Surgery for Parkinson’s Disease

The stated purpose of sham or placebo surgery is to enable the implementation of surgical placebo-controlled trials (SPTs) for evaluating the safety and efficacy of surgical interventions. Exposing the participants to the burdens and harms of sham surgery has been justified on the grounds of the absolute necessity for controlling large placebo effects and observer bias, assumed to be associated with surgical procedures. In the present review, we argue that evidence obtained from SPTs of cellular therapies for the treatment of Parkinson’s disease (PD) has failed to demonstrate either large and consistent placebo effects or decisive methodological advantages for relying on sham surgical controls. We outline several alternative assessment strategies and designs available to establish the efficacy of cellular therapies. It is concluded that the evidence evaluated in the present analysis indicated that use of sham surgery in the context of developing novel surgical procedures for PD is not necessary, and therefore, unethical under a utilitarian model.
A comparison of four risk models for the prediction of cardiovascular complications in patients with a history of atrial fibrillation undergoing non‐cardiac surgery

It is unclear how best to predict peri‐operative cardiovascular risk in patients with atrial fibrillation undergoing non‐cardiac surgery. This study examined the accuracy of the revised cardiac risk index and three atrial fibrillation thrombo‐embolic risk models for predicting 30‐day cardiovascular events after non‐cardiac surgery in patients with a pre‐operative history of atrial fibrillation. We conducted a prospective cohort study in 28 centres from 2007 to 2013 of 40,004 patients ≥ 45 years of age undergoing inpatient non‐cardiac surgery who were followed until 30 days after surgery for cardiovascular events (defined as myocardial injury, heart failure, stroke, resuscitated cardiac arrest or cardiovascular death). The 2088 patients with a pre‐operative history of atrial fibrillation were at higher risk of peri‐operative cardiovascular events compared with the 34,830 patients without a history of atrial fibrillation (29% vs. 13%, respectively, adjusted odds ratio 1.30 (95%CI 1.17–1.45). Compared with the revised cardiac risk index (c‐index 0.60), all atrial fibrillation thrombo‐embolic risk scores were significantly better at predicting peri‐operative cardiovascular events: CHADS2 (c‐index 0.62); CHA2DS2‐VASc (c‐index 0.63); and R2CHADS2 (c‐index 0.65), respectively. Although the three thrombo‐embolic risk prediction models were significantly better than the revised cardiac risk index for prediction of peri‐operative cardiovascular events, none of the four models exhibited strong discrimination metrics. There remains a need to develop a better peri‐operative risk prediction model.
Impaired reward-related learning signals in remitted unmedicated patients with recurrent depression

Impairments in reward-related learning often persist following remission from major depression. Geugies et al. compare temporal difference error-related BOLD activity during Pavlovian conditioning in unmedicated patients in remission from recurrent depression versus controls. Abnormalities in reward-related learning signals in the ventral tegmental area are associated with anhedonia in remitted patients.
Borderline Personality and Bipolar Disorders Cannot Be Differentiated Electrophysiologically

Objectives. Certain studies have claimed that borderline personality disorder (BPD) could be evaluated as a subtype of bipolar disorder (BD), whereas others have argued that BPD should be regarded as an independent disorder because of its distinct clinical features. The aim of this study was to investigate if there was a difference between these 2 disorders biologically based on EEG recordings. Methods. A total of 111 subjects (11 healthy, 25 BPD, 75 BD) who had resting EEG recordings were included. The EEGs were analyzed to compute absolute power values. Results. One-way analysis of variance results revealed statistically significant differences among the 3 groups on 55 out of 229 EEG variables. However, post hoc analysis indicated that all of the significant changes were between healthy and patient groups and no significant differences were found between 2 clinical groups. Conclusion. The findings suggested that these 2 clinical entities are biologically similar; however, further research should be performed to explain the basis clinical differences between the 2 disorders.
Engineering high‐gravity fermentations for ethanol production at elevated temperature with Saccharomyces cerevisiae

Thermal damage, high osmolarity, and ethanol toxicity in the yeast Saccharomyces cerevisiae limit titer and productivity in fermentation to produce ethanol. We show that long‐term adaptive laboratory evolution at 39.5°C generates thermotolerant yeast strains, which increased ethanol yield and productivity by 10% and 70%, in 2% glucose fermentations. From these strains, which also tolerate elevated‐osmolarity, we selected a stable one, namely a strain lacking chromosomal duplications. This strain (TTY23) showed reduced mitochondrial metabolism and high proton efflux, and therefore lower ethanol tolerance. This maladaptation was bolstered by reestablishing proton homeostasis through increasing fermentation pH from 5 to 6 and/or adding potassium to the media. This change allowed the TTY23 strain to produce 1.3–1.6 times more ethanol than the parental strain in fermentations at 40°C with glucose concentrations ~300 g/L. Furthermore, ethanol titers and productivities up to 93.1 and 3.87 g·L −1·hr −1 were obtained from fermentations with 200 g/L glucose in potassium‐containing media at 40°C. Albeit the complexity of cellular responses to heat, ethanol, and high osmolarity, in this study we overcome such limitations by an inverse metabolic engineering approach.
Croatian Wines from Native Grape Varieties Have Higher Distinct Phenolic (Nutraceutic) Profiles than Wines from Non‐Native Varieties with the Same Geographic Origin

Croatian wines made from native (Plavac mali and Teran) and non‐native grape varieties (Cabernet Sauvignon and Merlot), all grown in Croatian coastal regions, were investigated. Analyses included measurements of antioxidant activities, total phenolic contents and concentrations of non‐colored phenolic compounds, chosen based on their known nutraceutical properties. Plavac mali wines were distinguished by higher antioxidant activity, total phenolic content and catechin concentrations but lower flavonol concentrations. Teran wines had higher hydroxytyrosol, myricetin and resveratrol concentrations. Merlot and Cabernet Sauvignon wines had higher flavonol concentrations (except myricetin). Canonical analysis was successful in discriminating Plavac mali from Teran wines, and both varieties were separated from non‐native varieties. The results indicate distinct genetic potentials of studied varieties and enable wine authentication based on the investigated bioactive compounds.
Proceedings of the Workshop on Statistical Machine Translation

The focus of our workshop was to use parallel corpora for machine translation. Recent experimentation has shown that the performance of SMT systems varies greatly with the source and target language. In this workshop we encouraged researchers to investigate ways to improve the performance of SMT systems for diverse languages, including morphologically more complex languages and languages with partial free word order. Prior to the workshop, in addition to soliciting relevant papers for review and possible presentation, we conducted a shared task that brought together machine translation systems for an evaluation on previously unseen data. This year's task resembled the one from last year's in many ways, but also included a manual evaluation of MT system output and focused on translation from English into other languages, whereas most other evaluations focus on translation into English. The results of the shared task were announced at the workshop, and these proceedings also include an overview paper for the shared task that summarizes the results, as well as provides information about the data used and any procedures that were followed in conducting or scoring the task. In addition, there are short papers from each participating team that describe their underlying system in some detail.
Artificial elevation of glutathione contents in salicylic acid-deficient tobacco (Nicotiana tabacum cv. Xanthi NahG) reduces susceptibility to the powdery mildew pathogen Euoidium longipes.

The effects of elevated glutathione levels on defense responses to powdery mildew (Euoidium longipes) were investigated in a salicylic acid-deficient tobacco (Nicotiana tabacum cv. Xanthi NahG) and wild type cv. Xanthi plants, where salicylic acid (SA) contents are normal. Aqueous solutions of reduced glutathione (GSH) and its synthetic precursor R-2-oxothiazolidine-4-carboxylic acid (OTC) were injected into leaves of tobacco plants three hours before powdery mildew inoculation. SA-deficient NahG tobacco was hyper-susceptible to E. longipes as judged by significantly more severe powdery mildew symptoms and enhanced pathogen accumulation. Strikingly, elevation of GSH levels in SA-deficient NahG tobacco restored susceptibility to E. longipes to the extent seen in wild type plants (i.e. enhanced basal resistance). However, expression of an SA-mediated pathogenesis related gene (NtPR-1a) did not increase significantly in GSH or OTC-pretreated and powdery mildew-inoculated NahG tobacco, suggesting that the induction of this PR gene may not be directly involved in the defense responses induced by GSH. Our results demonstrate that artificial elevation of glutathione contents can significantly reduce susceptibility to powdery mildew in an SA- deficient tobacco. This article is protected by copyright. All rights reserved.
An explanation for origin unwinding in eukaryotes

Twin CMG complexes are assembled head-to-head around duplex DNA at eukaryotic origins of replication. Mcm10 activates CMGs to form helicases that encircle single-strand (ss) DNA and initiate bidirectional forks. How the CMGs melt duplex DNA while encircling it is unknown. Here we show that S. cerevisiae CMG tracks with force while encircling double-stranded (ds) DNA and that in the presence of Mcm10 the CMG melts long blocks of dsDNA while it encircles dsDNA. We demonstrate that CMG tracks mainly on the 3’−5’ strand during duplex translocation, predicting that head-to-head CMGs at an origin exert force on opposite strands. Accordingly, we show that CMGs that encircle double strand DNA in a head-to-head orientation melt the duplex in an Mcm10-dependent reaction.
On the importance of sorting in "neural gas" training of vector quantizers

The paper considers the role of the sorting process in the well-known "neural gas" model for vector quantization. Theoretical derivations and experimental evidence show that complete sorting is not required for effective training, since limiting the sorted list to even a few top units performs effectively. This property has a significant impact on the implementation of the overall neural model at the local level.
Evaluating Cultural Competence in an Occupational Therapy Pediatric Course

Abstract This study examined the impact on student cultural competence of using specific guided activities in a pediatric occupational therapy course. A combined two-group pre-posttest design was used with a convenience sample of 41 entry-level occupational therapy doctoral students. Using a measure of cultural competence change, results indicated significant increase in scores from pre to post course testing suggesting cultural competence structured activities in course work were associated with an increase in student cultural competence. Implications for occupational therapy education are discussed.
Insecurity about getting old: age-contingent self-worth, attentional bias, and well-being

Abstract Objectives: Older adulthood has often been recognized as a time of increased well-being and positive cognitive biases. However, older adults can also experience many social and identity challenges. We sought to investigate which older adults might be most vulnerable to these difficulties. We propose that to the extent an older adult has age-related contingent self-esteem they will be at risk for lower well-being and negative attentional biases. Methods: Across three studies, we measured older adults’ self-reported aging self-worth contingencies, as well as various measures of well-being including subjective stress. We then had participants complete a cued-dot probe task, where each trial either began with an aging threat or not. Results: In an initial pilot study, we found that older adults reporting specific cognitive decline contingencies held an attentional bias toward rejection, primarily when cued with the word senile. In Study 1, we found general aging contingencies to be associated with lower well-being and a rejection bias when cued with old. In Study 2, we found that a stronger rejection bias, particularly when cued with old, was associated with greater stress. Conclusions: These findings demonstrate that older adults who are insecure about aging may have lower well-being and negatively biased social cognitive patterns. Negatively biased attentional patterns may play a key role in maintaining feelings of insecurity. Importantly, our research sheds light on those older adults who may not experience a positivity effect.
Instruments for Collective Design in a Professional Context: Digital Format or New Processes ?

This article reports on different collective practices and their instruments observed in the context of professional design activities. Based on interviews and in situ observations of customs in six architecture, engineering, and design agencies, it shows the diversity of typologies of collective activity, identifies the main factors of collaboration, and concludes on the needs for the instrumentation of professional practice. Is it a matter of building higher and higher performance digital formats for a shared modeling of the project or to lean instead towards the creation of new processes of group management and remote work by several people? From the results of this observation of collective practices in design, this article allows one to highlight the real needs of the agencies and to help their teamwork. These needs consist of: 1) facilitating reflection, 2) managing changing dynamics, 3) allowing the reflective exploration by several persons between space and time, and finally 4) guaranteeing a common progressive and exploratory strategy between actors whose expertise and commitment differ within the same process. Keywords-collaborative design; professional practice; observations; tools and processes.
Association between simple renal cyst and kidney damage in a Chinese cohort study

Abstract Background: The presence of simple renal cyst (SRC) has been associated to renal dysfunction, but the results were inconsistent. Accordingly, we conducted a longitudinal cohort study to explore the association between SRC and kidney damage. Methods: A total of 4274 adults (aged 45.4 ± 13.6 years) without chronic kidney disease at baseline were enrolled in 2008. SRC was assessed by ultrasonography. Logistic regression analysis were applied to explore the relationships between SRC and indicators of kidney damage (proteinuria and renal insufficiency), and also with relatively rapid decline in renal function (defined as the lowest quartile of △eGFR). Results: During 5 years of follow-up, participants in the SRC group had higher incidence of proteinuria (5.2% versus 2.4%, p = 0.004) and renal insufficiency (3.8% versus 0.97%, p < 0.001) compared with control group. SRC was correlated with proteinuria (OR 2.24; 95% CI 1.34–3.75) and renal insufficiency (OR 4.0; 95% CI 2.11–7.58) in univariable analysis, despite that the correlation was not significant after adjusted for traditional kidney disease risk factors. Furthermore, after adjusted for potential confounders, maximum diameter of the cyst (≥2.2 cm) was significantly associated with rapid decline in renal function (OR 2.19; 95% CI 1.24–3.87). Conclusions: Participants with SRC may be associated with higher incidence of proteinuria and renal insufficiency. This relationship may be obscured by age and other traditional risk factors. Higher diameter of the cysts contributed to more rapid decline in renal function of SRC participants.
Correcting encoder interpolation error on the Green Bank Telescope using an iterative model based identification algorithm

Abstract. Various forms of measurement errors limit telescope tracking performance in practice. A new method for identifying the correcting coefficients for encoder interpolation error is developed. The algorithm corrects the encoder measurement by identifying a harmonic model of the system and using that model to compute the necessary correction parameters. The approach improves upon others by explicitly modeling the unknown dynamics of the structure and controller and by not requiring a separate system identification to be performed. Experience gained from pin-pointing the source of encoder error on the Green Bank Radio Telescope (GBT) is presented. Several tell-tale indicators of encoder error are discussed. Experimental data from the telescope, tested with two different encoders, are presented. Demonstration of the identification methodology on the GBT as well as details of its implementation are discussed. A root mean square tracking error reduction from 0.68 arc seconds to 0.21 arc sec was achieved by changing encoders and was further reduced to 0.10 arc sec with the calibration algorithm. In particular, the ubiquity of this error source is shown and how, by careful correction, it is possible to go beyond the advertised accuracy of an encoder.
A Study of LDMOS BV Improvement by Gate Architecture Optimization

In this paper, various gate architectures of stepped gate oxide LDMOS are studied and multiple experiments are performed using two-dimensional TCAD simulation. It reveals that by using multi-gate structure with optimal underlying oxide thickness and field plate length, breakdown voltage (BV) can be greatly improved without sacrifice of specific on resistance (Rsp). The mechanism is that the optimal multi-gate structure has more uniform electric field distribution at the surface of device drift area.
In-band Interference Suppression Method of OFDM Signal Based on Double Sparsity K-SVD Algorithm Joint Dictionary Learning

To solve the in-band interference suppression problem in complex electromagnetic environment, a novel method of interference suppression for the orthog-gonal frequency division multiplexing (OFDM) signal based on the double sparsity K-singular value decomposition (K-SVD) joint dictionary learning is proposed. Firstly, the double sparsity K-SVD algorithm is used to respectively train the atomic dictionary of OFDM signal and the in-band interference. Then, the joint dictionary is constructed by using the weak correlation of OFDM signal and in-band interference. Finally, the in-band interference is reconstructed by using the orthogonal matching pursuit (OMP) algorithm and the interference component is removed from the receiving OFDM signal. The simulation results show that the interference suppression method could largely keep useful information and the double sparsity K-SVD algorithm could also reduce the computational complexity.
An Efficient Way to Detect Credit Card Fraud Using Machine Learning Methodologies

Attempted use of combinations of machine learning techniques to detect credit card fraud is presented in this paper. Credit card fraud is increasing day by day every year on a large scale, which results in great loss to organizations, this paper proposes a model to predict whether the credit card presented is fraudulent or not determined by more than 150 attributes per visitor, which have been trained before hand with a dataset. As the data used for the purposes of this paper was highly imbalanced, different sampling techniques have been used to balance the training data. The experiment shows good performance along with accuracy in fraud detection.