Miracle-dz/UniFAR-FTUs huggingface dataset:
Coordinated Regulation of UGT2B15 Expression by Long Noncoding RNA LINC00574 and hsa-miR-129-5p in HepaRG Cells

Recent studies have shown that microRNAs and long noncoding RNAs (lncRNAs) regulate the expression of drug metabolizing enzymes (DMEs) in human hepatic cells and that a set of DMEs, including UDP glucuronosyltransferase (UGT) 2B15, is down-regulated dramatically in liver cells by toxic acetaminophen (APAP) concentrations. In this study we analyzed mRNA, microRNA, and lncRNA expression profiles in APAP-treated HepaRG cells to explore noncoding RNA-dependent regulation of DME expression. The expression of UGT2B15 and lncRNA LINC00574 was decreased in APAP-treated HepaRG cells. UGT2B15 levels were diminished by LINC00574 suppression using antisense oligonucleotides or small interfering RNA. Furthermore, we found that hsa-miR-129-5p suppressed LINC00574 and decreased UGT2B15 expression via LINC00574 in HepaRG cells. In conclusion, our results indicate that LINC00574 acts as an important regulator of UGT2B15 expression in human hepatic cells, providing experimental evidence and new clues to understand the role of cross-talk between noncoding RNAs. SIGNIFICANCE STATEMENT We showed a molecular network that displays the cross-talk and consequences among mRNA, micro RNA, long noncoding RNA, and proteins in acetaminophen (APAP)-treated HepaRG cells. APAP treatment increased the level of hsa-miR-129-5p and decreased that of LINC00574, ultimately decreasing the production of UDP glucuronosyltransferase (UGT) 2B15. The proposed regulatory network suppresses UGT2B15 expression through interaction of hsa-miR-129-5p and LINC00574, which may be achieved potentially by recruiting RNA binding proteins.
Multicenter External Validation of the Liverpool Uveal Melanoma Prognosticator Online: An OOG Collaborative Study

Uveal melanoma (UM) is fatal in ~50% of patients as a result of disseminated disease. This study aims to externally validate the Liverpool Uveal Melanoma Prognosticator Online V3 (LUMPO3) to determine its reliability in predicting survival after treatment for choroidal melanoma when utilizing external data from other ocular oncology centers. Anonymized data of 1836 UM patients from seven international ocular oncology centers were analyzed with LUMPO3 to predict the 10-year survival for each patient in each external dataset. The analysts were masked to the patient outcomes. Model predictions were sent to an independent statistician to evaluate LUMPO3’s performance using discrimination and calibration methods. LUMPO3’s ability to discriminate between UM patients who died of metastatic UM and those who were still alive was fair-to-good, with C-statistics ranging from 0.64 to 0.85 at year 1. The pooled estimate for all external centers was 0.72 (95% confidence interval: 0.68 to 0.75). Agreement between observed and predicted survival probabilities was generally good given differences in case mix and survival rates between different centers. Despite the differences between the international cohorts of patients with primary UM, LUMPO3 is a valuable tool for predicting all-cause mortality in this disease when using data from external centers.
Hyper-Graph Regularized Constrained NMF for Selecting Differentially Expressed Genes and Tumor Classification

Non-negative Matrix Factorization (NMF) is a dimensionality reduction approach for learning a parts-based and linear representation of non-negative data. It has attracted more attention because of that. In practice, NMF not only neglects the manifold structure of data samples, but also overlooks the priori label information of different classes. In this paper, a novel matrix decomposition method called Hyper-graph regularized Constrained Non-negative Matrix Factorization (HCNMF) is proposed for selecting differentially expressed genes and tumor sample classification. The advantage of hyper-graph learning is to capture local spatial information in high dimensional data. This method incorporates a hyper-graph regularization constraint to consider the higher order data sample relationships. The application of hyper-graph theory can effectively find pathogenic genes in cancer datasets. Besides, the label information is further incorporated in the objective function to improve the discriminative ability of the decomposition matrix. Supervised learning with label information greatly improves the classification effect. We also provide the iterative update rules and convergence proofs for the optimization problems of HCNMF. Experiments under The Cancer Genome Atlas (TCGA) datasets confirm the superiority of HCNMF algorithm compared with other representative algorithms through a set of evaluations.
Epidemiological and comparative genomic analysis of Bacillus anthracis isolated from northern Vietnam

To understand the epidemiological and genetic background of anthrax cases occurring in Vietnam from 2011 to 2015, we surveilled and genetically analyzed Bacillus anthracis isolated in the north of the country. Epidemiological surveillance showed that most human cutaneous anthrax cases occurred in association with animal dissection. Whole-genome sequences were obtained from six B. anthracis strains from human patients with cutaneous anthrax in the endemic area. Comparative genomic analysis showed that the genetic homogeneity among Vietnamese B. anthracis strains was very high. All Vietnamese B. anthracis strains belonged to the canSNP lineage of A.Br. 011/009, which mostly consists of strains of the trans-Eurasian (TEA) group, including the most closely related strain, Carbosap. To clarify the genetic diversity of Vietnamese strains and strains belonging to A.Br. 011/009 and A.Br. 008/011 canSNP lineages, we applied a reference genome-based single-nucleotide polymorphism (SNP) and gene-by-gene genomic analysis (whole-genome MLST) strategy. The phylogeny from core genome SNPs revealed that the Vietnamese strains were positioned close to each other; moreover, several SNPs specific to Vietnamese B. anthracis were identified. Whole-genome MLST analysis revealed the differences in the number of SNPs between Vietnamese strains, which could enable discrimination at the strain level.
One‐hour universal protocol for mouse genotyping

Transgenic animals are widely used for research and for most of them, genotyping is unavoidable. Published protocols may be powerful but may also present disadvantages such as their cost or the requirement of additional steps/equipment. Moreover, if more than one strain must be genotyped, several protocols may need to be developed.
Microperimetric Biofeedback Training After Successful Inverted Flap Technique for Large Macular Hole

Background: Despite the high closure rate of large macular hole (LMH) after surgery, visual recovery is often worse than expected. Microperimetric biofeedback can improve visual function in macular pathologies. We evaluated the efficacy of biofeedback on macular function after successful inverted flap technique for LMH. Methods: In this prospective comparative study, 26 patients after LMH surgical closure were enrolled. The whole sample was equally divided into two groups. In Group 1 (trained), patients underwent a double cycle of microperimetric biofeedback, using structured light stimulus plus acoustic tone; in Group 2 (control), patients underwent scheduled visits. We analyzed visual acuity, retinal sensitivity at central 12° (macular sensitivity, MS) and 4° (central macular sensitivity, CMS), and fixation stability over twelve months. Results: Visual acuity improved mainly in the trained group, without any significant differences between the groups (p > 0.05). Only after training did MS significantly improve (p = 0.01). CMS more significantly improved in the trained (p < 0.001) than the control group (p < 0.01) (Group 1 vs. 2, p = 0.004). Only in the trained group did fixation significantly improve (3 months, p ≤ 0.03; 12 months, p ≤ 0.01). An equality test on matched data confirmed a greater significant improvement of CMS (p ≤ 0.02) at all follow-up and fixation (p ≤ 0.02) at last follow-up after training. Conclusions: Microperimetric biofeedback consolidates and increases the improvement of retinal sensitivity and fixation gained after successful inverted flap technique.
Chemically Crosslinked Sulfonated Polyphenylsulfone (CSPPSU) Membranes for PEM Fuel Cells

Sulfonated polyphenylsulfone (SPPSU) with a high ion exchange capacity (IEC) was synthesized using commercially available polyphenylsulfone (PPSU), and a large-area (16 × 18 cm2) crosslinked sulfonated polyphenylsulfone (CSPPSU) membrane was prepared. In addition, we developed an activation process in which the membrane was treated with alkaline and acidic solutions to remove sulfur dioxide (SO2), which forms as a byproduct during heat treatment. CSPPSU membranes obtained using this activation method had high thermal, mechanical and chemical stabilities. In I-ViR free studies for fuel cell evaluation, high performances similar to those using Nafion were obtained. In addition, from the hydrogen (H2) gas crossover characteristics, the durability is much better than that of a Nafion212 membrane. In the studies evaluating the long-term stabilities by using a constant current method, a stability of 4000 h was obtained for the first time. These results indicate that the CSPPSU membrane obtained by using our activation method is promising as a polymer electrolyte membrane.
Dual PI3K/mTOR Inhibitor NVP-BEZ235 Enhances Radiosensitivity of Head and Neck Squamous Cell Carcinoma (HNSCC) Cell Lines Due to Suppressed Double-Strand Break (DSB) Repair by Non-Homologous End Joining

The PI3K/Akt/mTOR pathway is frequently altered in human papillomavirus (HPV)-positive and negative squamous cell carcinoma of the head and neck (HNSCC) and overstimulation is associated with poor prognosis. PI3K drives Akt activation and constitutive signaling acts pro-proliferative, supports cell survival, DNA repair, and contributes to radioresistance. Since the small molecule NVP-BEZ235 (BEZ235) is a potent dual inhibitor of this pathway, we were interested whether BEZ235 could be an efficient radiosensitizer. The 50 nM BEZ235 was found to abrogate endogenous and irradiation-induced phosphorylation of Akt (Ser473). The anti-proliferative capacity of the drug resulted in an increase in G1-phase cells. Repair of radiation-induced DNA double-strand breaks (DSBs) was strongly suppressed. Reduction in DSB repair was only apparent in G1- but not in G2-phase cells, suggesting that BEZ235 primarily affects non-homologous end joining. This finding was confirmed using a DSB repair reporter gene assay and could be attributed to an impaired phosphorylation of DNA-PKcs (S2056). Cellular radiosensitivity increased strongly after BEZ235 addition in all HNSCC cell lines used, especially when irradiated in the G0 or G1 phase. Our data indicate that targeting the PI3K/Akt/mTOR pathway by BEZ235 with concurrent radiotherapy may be considered an effective strategy for the treatment of HNSCC, regardless of the HPV and Akt status.
miR‐181a negatively modulates synaptic plasticity in hippocampal cultures and its inhibition rescues memory deficits in a mouse model of Alzheimer’s disease

MicroRNAs play a pivotal role in rapid, dynamic, and spatiotemporal modulation of synaptic functions. Among them, recent emerging evidence highlights that microRNA‐181a (miR‐181a) is particularly abundant in hippocampal neurons and controls the expression of key plasticity‐related proteins at synapses. We have previously demonstrated that miR‐181a was upregulated in the hippocampus of a mouse model of Alzheimer's disease (AD) and correlated with reduced levels of plasticity‐related proteins. Here, we further investigated the underlying mechanisms by which miR‐181a negatively modulated synaptic plasticity and memory. In primary hippocampal cultures, we found that an activity‐dependent upregulation of the microRNA‐regulating protein, translin, correlated with reduction of miR‐181a upon chemical long‐term potentiation (cLTP), which induced upregulation of GluA2, a predicted target for miR‐181a, and other plasticity‐related proteins. Additionally, Aβ treatment inhibited cLTP‐dependent induction of translin and subsequent reduction of miR‐181a, and cotreatment with miR‐181a antagomir effectively reversed the effects elicited by Aβ but did not rescue translin levels, suggesting that the activity‐dependent upregulation of translin was upstream of miR‐181a. In mice, a learning episode markedly decreased miR‐181a in the hippocampus and raised the protein levels of GluA2. Lastly, we observed that inhibition of miR‐181a alleviated memory deficits and increased GluA2 and GluA1 levels, without restoring translin, in the 3xTg‐AD model. Taken together, our results indicate that miR‐181a is a major negative regulator of the cellular events that underlie synaptic plasticity and memory through AMPA receptors, and importantly, Aβ disrupts this process by suppressing translin and leads to synaptic dysfunction and memory impairments in AD.
Aspirin and fracture risk: a systematic review and exploratory meta-analysis of observational studies

Objectives This review provides insights into the potential for aspirin to preserve bone mineral density (BMD) and reduce fracture risk, building knowledge of the risk-benefit profile of aspirin. Methods We conducted a systematic review and exploratory meta-analysis of observational studies. Electronic searches of MEDLINE and Embase, and a manual search of bibliographies was undertaken for studies published to 28 March 2018. Studies were included if: participants were men or women aged ≥18 years; the exposure of interest was aspirin; and relative risks, ORs and 95% CIs for the risk of fracture or difference (percentage or absolute) in BMD (measured by dual energy X-ray absorptiometry) between aspirin users and non-users were presented. Risk of bias was assessed using the Joanna Briggs Institute Critical Appraisal Checklists for observational studies. Pooled ORs for any fracture and standardised mean differences (SMDs) for BMD outcomes were calculated using random-effects models. Results Twelve studies met the inclusion criteria and were included in the meta-analysis. Aspirin use was associated with a 17% lower odds for any fracture (OR 0.83, 95% CI 0.70 to 0.99; I2=71%; six studies; n=511 390). Aspirin was associated with a higher total hip BMD for women (SMD 0.03, 95% CI −0.02 to 0.07; I2=0%; three studies; n=9686) and men (SMD 0.06, 95% CI −0.02 to 0.13, I2=0%; two studies; n=4137) although these associations were not significant. Similar results were observed for lumbar spine BMD in women (SMD 0.03, 95% CI −0.03 to 0.09; I2=34%; four studies; n=11 330) and men (SMD 0.08; 95% CI −0.01 to 0.18; one study; n=432). Conclusions While the benefits of reduced fracture risk and higher BMD from aspirin use may be modest for individuals, if confirmed in prospective controlled trials, they may confer a large population benefit given the common use of aspirin in older people.
City limits to partisan polarization in the American public

Abstract How pervasive is partisan sorting and polarization over public policies in the American public? We examine whether the barriers of partisan sorting and polarization seen in national politics extend to important local policies that shape economic development. To describe the extent of partisan sorting and polarization over local development policies, we employ conjoint survey experiments in representative surveys of eight US metropolitan areas and a hierarchical modeling strategy for studying heterogeneity across respondents. We find that strong partisans are sorted by party in some of their policy opinions, but rarely polarized. The same voters who disagree about national issues have similar preferences about local development issues suggesting a greater scope for bipartisan problem solving at the local level.
Telecommunications Ownership and Control ( TOSCO ) . A new dataset on ownership of internet infrastructure in Africa , 2000-2016

The internet provides a space for sharing digital information and communication. This space is built on a physical infrastructure owned by a variety of state and private actors, foreign and domestic, that reflect a multitude of interests. This paper presents TOSCO, a new dataset on ownership and control of internet service providers that allows for comparative large-N analysis of the determinants and effects of varying ownership structures and identities in the transforming context of African countries from 2000 to 2016. We provide a detailed discussion of the conceptualization and operationalization of ownership as a variable. Descriptive statistics illustrate varying ownership of ISP since the internet became accessible to a larger population across the continent, and correlational statistics illuminate potential venues for research using our data.
Generating Optimal Gripper Orientation for Robotic Grasping of Unknown Objects using Neural Network

Grasping objects in robotics is often claimed to be solved since a lot of different approaches to this problem give fair results in particular applications. In service robotics, it still remains an open problem: robots still do not demonstrate human-like abilities to manipulate objects in an unknown environment. In this research, a method of improving state of the art grasping pose generation by more natural gripper orientation is proposed. Generating grasping orientation does not involve any computationally intensive optimization, but uses single propagation through a pre-trained deep neural network. The proposed method allows increasing usability of a manipulator in real-life tasks
Dependence

Dependence is often considered as a primarily negative state of being. It has gone from being described as a threat to individual self-reliance in early modern political theory in Western Europe to being a moral panic in political discourse across the world. Its negative connotation is particularly evident in the spheres of politics and economics, which this entry will focus on. Although anthropological theory has only recently made dependence a topic of explicit theoretical reflection, the idea has underpinned a wide variety of approaches throughout the discipline’s history. Given the tendency of anthropologists to stress the fundamental interdependence of human beings, they have emphasised that dependence is not always a bad thing and can even be desirable. They have also questioned whether or not we can neatly divide the world’s population into those in states of dependence versus independence. Lastly, they have considered the performative effects of ascribing dependence to some and independence to others. Ethnographically sifting through the different performative effects of ascriptions of dependence becomes particularly important today, as assumed states of dependence have become key tools in the management of populations across the world.
1 The Problem of Culturally Normal Belief *

By itself, the structure does not generate the problem. The problem arises when we ask how reasonable it is for the individual to hold the attitude that results from this absorption, and when we find opposing pressures among the plausible answers. Not every instance of the structure yields a problematic opposition, but some do. Consider for instance two passages from Harriet Beecher Stowe’s 19th-century American novel Uncle Tom’s Cabin. Both concern the slave owner Mr. Shelby’s decision to sell Tom and Harry, who are his slaves, in the face of economic pressures.
Learning of Utility Functions for the Behaviour Analysis in Maritime Surveillance Tasks

: For detecting suspicious activities in the maritime domain such as illegal, unreported and unregulated fishing, it is crucial to counter the increasing amount of available information regarding vessels at sea with sophisticated algorithms and user interfaces. Deep learning and other data driven approaches create good results, but for an operator to be able to intervene suspicious activities, the supporting algorithms must be explainable and transparent. One possibility is to use simulations based on utility functions and behaviour models derived from the field of human behaviour modelling like game theory. Here, an expensive and time-consuming way is to model these utility functions by experts. As this is not always feasible or the behaviour patterns might not be easily expressed by experts, this work follows a different approach by utilizing inverse reinforcement learning in order to estimate the utility functions for different ship types. For this study, data based on the automatic identification system (AIS) is used for comparing the behaviour of cargo vessels and fishing boats.
Are financial markets aligned with climate action? New evidence from the Paris Agreement

It is increasingly recognised that financial markets have a key role to play in meeting climate mitigation objectives. But are markets willing to direct more capital allocation towards such a low carbon pathway? This paper provides new evidence that financial markets value firms’ expansion into production of low carbon goods and services, but they remain cautious on divesting from the most polluting industries. We exploit the Paris Agreement as an exogenous political shock that signalled increased global commitment on climate action. Using an event study approach, we examine the daily stock prices of major publicly listed US companies. We distinguish green and brown firms using their green revenue share and their carbon intensity respectively. We find evidence that the cumulative returns of stocks for firms are re-priced during the five days following the Paris Agreement. Cumulative returns are up to 10% higher for green firms while the effect is less pronounced for brown firms and limited to firms active in the oil and gas extraction. Overall, our results suggest that capital markets are responding to opportunities but less to risks in the low carbon economy.
The Trust-Enabling Middleware: Introduction and Application

In this report, we present the Trust-Enabling Middleware (TEM) that is based on the messageand service-oriented organic middleware OCμ. The TEM enhances OCμ by features that enable the middleware as well as applications based on it to use trust data. These features include the possibility to save experiences made with interaction partners and to derive trust data with the help of trust metrics out of these saved experiences. Furthermore, we show an example application based on the Trust-Enabling Middleware that considers uncertainty in power networks, the Trusted Energy Grid, and especially illustrate its use of the Trust Metric Infrastructure provided by the TEM.
Towards a Case-Based Decision Support System for Recruiting Processes using T-Shapes

: Modeling the individual set of skills a person possesses is a difficult task. However, most people seek to find a job that suits them best, despite being unaware of which skills she inherits and what defines herself as a person. Recruiters are knowledgeable in terms of extracting these information by an informal phone call or when carrying out an assessment center. However, we suggest to set a step beforehand and provide a case-based decision support system by using T-Shapes as a model for matching personal skills with job requirements. We provide a first overview on how to structure and model the four knowledge containers of case-based reasoning and how we use these knowledge containers to obtain the most similar T-Shape (situation). This T-Shape can then be reused by the recruiter, providing her with all necessary information at a first glance.