Miracle-dz/UniFAR-FTUs huggingface dataset:
The Effect of a Distributed Virtual Reality Simulation Training Program on Dissection Mastoidectomy Performance.

OBJECTIVE To investigate the effect on final-product performance of a distributed, virtual reality (VR) simulation training program on cadaveric dissection performance and learning curves compared with standard VR simulation training during a temporal bone course. STUDY DESIGN Educational interventional cohort study. SETTING The national Danish temporal bone courses of 2016 and 2017. SUBJECTS Postgraduate year 2 to 5 residents in otorhinolaryngology. INTERVENTION Nine participants volunteered for additional VR simulation training (intervention) before the temporal bone course, with training blocks distributed (i.e., separated). The remaining 28 participants received standard VR simulation training during the temporal bone course (control). MAIN OUTCOME MEASURE VR simulation and cadaveric dissection final-product performances were analyzed by blinded raters using a 26-item modified Welling Scale. RESULTS Distributed VR simulation training before the temporal bone course (intervention) significantly increased dissection final-product performance by 25% compared with standard VR simulation training during the course (control) (mean scores 12.8 points versus 10.3 points, p < 0.01). Distributed and repeated VR simulation practice markedly decreased drilling time. Guidance by the simulator-integrated tutor-function significantly increased final-product performance by 2.3 points compared with nontutored procedures but at the cost of increased drilling time. CONCLUSION Skills acquired in a VR simulation environment translate to cadaveric dissection skills and repeated and distributed VR simulation can be used to further increase performance compared with standard VR simulation training during a temporal bone course. Further dissemination of inexpensive VR simulators would allow all future temporal bone course participants to train locally before attending future centralized courses.
Aging in Tunisia

Owing in part to its diversity of citizenship, Tunisia has a rich history of economic and social changes-including some of the same age-based demographic changes witnessed globally. Faced with an increasing older population and fewer young adults available to provide support, the government of Tunisia has implemented policies for the older population. These new governmental policies are intended to provide limited funds for older adults to supplement financial assistance provided by their families. Yet, even with a demographic transition occurring, recent published research on the aging Tunisian adult is limited at best. Policy change and research that improve the well-being of Tunisia's aging population must be based on adequate data. Thus, understanding the state of aging in Tunisia provides policymakers and researchers more complete information to use in decision making. Further studies should address more aspects of the Tunisian aging experience and add data that are more contemporary.
Rapid Expansion of a Highly Germline-Expressed Mariner Element Acquired by Horizontal Transfer in the Fire Ant Genome

Abstract Transposable elements (TEs) are present in almost all organisms and affect the host in various ways. TE activity can increase genomic variation and thereby affect host evolution. Currently active TEs are particularly interesting because they are likely generating new genomic diversity. These active TEs have been poorly studied outside of model organisms. In this study, we aimed to identify currently active TEs of a notorious invasive species, the red imported fire ant Solenopsis invicta. Using RNA profiling of male and female germline tissues, we found that the majority of TE-containing transcripts in the fire ant germline belong to the IS630-Tc1-Mariner superfamily. Subsequent genomic characterization of fire ant mariner content, molecular evolution analysis, and population comparisons revealed a highly expressed and highly polymorphic mariner element that is rapidly expanding in the fire ant genome. Additionally, using comparative genomics of multiple insect species we showed that this mariner has undergone several recent horizontal transfer events (<5.1 My). Our results document a rare case of a currently active TE originating from horizontal transfer.
The structural basis for cancer drug interactions with the catalytic and allosteric sites of SAMHD1

Significance Nucleoside analog drugs are widely used to treat a variety of cancers and viral infections. With an essential role in regulating the nucleotide pool in the cell by degrading cellular nucleotides, SAMHD1 has the potential to decrease the cellular concentration of frequently prescribed nucleoside analogs and thereby decrease their clinical efficacy in cancer therapy. To improve future nucleoside analog treatments, it is important to understand SAMHD1 interactions with these drugs. Our work thoroughly examines the extent to which nucleotide analogs interact with the catalytic and allosteric sites of SAMHD1. This work contributes to the assessment of SAMHD1 as a potential therapeutic target for cancer therapy and the future design of SAMHD1 modulators that might improve the efficacy of existing therapies. SAMHD1 is a deoxynucleoside triphosphate triphosphohydrolase (dNTPase) that depletes cellular dNTPs in noncycling cells to promote genome stability and to inhibit retroviral and herpes viral replication. In addition to being substrates, cellular nucleotides also allosterically regulate SAMHD1 activity. Recently, it was shown that high expression levels of SAMHD1 are also correlated with significantly worse patient responses to nucleotide analog drugs important for treating a variety of cancers, including acute myeloid leukemia (AML). In this study, we used biochemical, structural, and cellular methods to examine the interactions of various cancer drugs with SAMHD1. We found that both the catalytic and the allosteric sites of SAMHD1 are sensitive to sugar modifications of the nucleotide analogs, with the allosteric site being significantly more restrictive. We crystallized cladribine-TP, clofarabine-TP, fludarabine-TP, vidarabine-TP, cytarabine-TP, and gemcitabine-TP in the catalytic pocket of SAMHD1. We found that all of these drugs are substrates of SAMHD1 and that the efficacy of most of these drugs is affected by SAMHD1 activity. Of the nucleotide analogs tested, only cladribine-TP with a deoxyribose sugar efficiently induced the catalytically active SAMHD1 tetramer. Together, these results establish a detailed framework for understanding the substrate specificity and allosteric activation of SAMHD1 with regard to nucleotide analogs, which can be used to improve current cancer and antiviral therapies.
Novel extremophilic proteases from Pseudomonas aeruginosa M211 and their application in the hydrolysis of dried distiller's grain with solubles

Proteases are the most important group of industrial enzymes and they can be used in several fields including biorefineries for the valorization of industrial byproducts. In this study, we purified and characterized novel extremophilic proteases produced by a Pseudomonas aeruginosa strain isolated from Mauritia flexuosa palm swamps soil samples in Peruvian Amazon. In addition, we tested their ability to hydrolyze distillers dried grains with solubles (DDGS) protein. Three alkaline and thermophilic serine proteases named EI, EII, and EIII with molecular weight of 35, 40, and 55 kDa, respectively, were purified. EI and EIII were strongly inhibited by EDTA and Pefabloc being classified as serine‐metalloproteases, while EII was completely inhibited only by Pefabloc being classified as a serine protease. In addition, EI and EII exhibited highest enzymatic activity at pH 8, while EIII at pH 11 maintaining almost 100% of it at pH 12. All the enzymes demonstrated optimum activity at 60°C. Enzymatic activity of EI was strongly stimulated in presence of Mn2+ (6.9‐fold), EII was stimulated by Mn2+ (3.7‐fold), while EIII was slightly stimulated by Zn2+, Ca2+, and Mg2+. DDGS protein hydrolysis using purified Pseudomonas aeruginosa M211 proteases demonstrated that, based on glycine released, EIII presented the highest proteolytic activity toward DDGS. This enzyme enabled the release 63% of the total glycine content in wheat DDGS protein, 2.2‐fold higher that when using the commercial Pronase®. Overall, our results indicate that this novel extremopreoteases have a great potential to be applied in DDGS hydrolysis. © 2018 American Institute of Chemical Engineers Biotechnol. Prog. , 35: e2728, 2019
User-Assisted Information Extraction from Twitter During Emergencies

Disasters and emergencies bring uncertain situations. People involved in such situations look for quick answers to their rapid queries. Moreover, humanitarian organizations look for situational awareness information to launch relief operations. Existing studies show the usefulness of social media content during crisis situations. However, despite advances in information retrieval and text processing techniques, access to relevant information on Twitter is still a challenging task. In this paper, we propose a novel approach to provide timely access to the relevant information on Twitter. Specifically, we employee Word2vec embeddings to expand initial users queries and based on a relevance feedback mechanism we retrieve relevant messages on Twitter in real-time. Initial experiments and user studies performed using a real world disaster dataset show the significance of the proposed approach.
Liquorice flavonoid oil suppresses hyperglycaemia accompanied by skeletal muscle myocellular GLUT4 recruitment to the plasma membrane in KK-Ay mice

Abstract For over 4000 years, liquorice has been one of the most frequently employed botanicals as a traditional herbal medicine. Although previous reports have found that liquorice flavonoids possess various health beneficial effects, the underlying mechanism responsible for the anti-diabetic effect of liquorice flavonoids remains unclear. The present study demonstrates that liquorice flavonoid oil (LFO) improves type 2 diabetes mellitus through GLUT4 translocation to the plasma membrane by activating both the adenosine monophosphate-activated protein kinase (AMPK) pathway and Akt pathway in muscle of KK-Ay mice. Furthermore, LFO lowered postprandial hyperglycaemia in a human study. These results indicate that LFO may exert a therapeutic effect on metabolic disorders, such as diabetes and hyperglycaemia, by modulating glucose metabolism through AMPK- and insulin-dependent pathways in skeletal muscle. Graphical Abstract
Counting points on hyperelliptic curves in large characteristic : algorithms and complexity. (Comptage de points de courbes hyperelliptiques en grande caractéristique : algorithmes et complexité)

Counting points on algebraic curves has drawn a lot of attention due to its many applications from number theory and arithmetic geometry to cryptography and coding theory. In this thesis, we focus on counting points on hyperelliptic curves over finite fields of large characteristic $p$. In this setting, the most suitable algorithms are currently those of Schoof and Pila, because their complexities are polynomial in $\log q$. However, their dependency in the genus $g$ of the curve is exponential, and this is already painful even in genus 3. Our contributions mainly consist of establishing new complexity bounds with a smaller dependency in $g$ of the exponent of $\log p$. For hyperelliptic curves, previous work showed that it was quasi-quadratic, and we reduced it to a linear dependency. Restricting to more special families of hyperelliptic curves with explicit real multiplication (RM), we obtained a constant bound for this exponent.In genus 3, we proposed an algorithm based on those of Schoof and Gaudry-Harley-Schost whose complexity is prohibitive in general, but turns out to be reasonable when the input curves have explicit RM. In this more favorable case, we were able to count points on a hyperelliptic curve defined over a 64-bit prime field
The incidence of atrial fibrillation and the added value of thumb ECG for detecting new cases

Abstract Objectives. To evaluate the incidence of atrial fibrillation (AF) as well as the value of thumb electrocardiography (ECG) for identification of paroxysmal AF in a Swedish cohort of middle-aged men from the general population. Design. A population based random cohort of 798 men underwent screening at the age of 50 and re-examined at the age of 60 and 71 years. At the last examination, a thumb ECG recording was conducted for 2 weeks twice a day in 479 men from the original cohort. Registered hospital AF diagnoses were retrieved from the Swedish Patient Registry from 1993 to 2014. Results. During a 21-year follow-up, 77 men (9.6%) were diagnosed with AF; of these men, 49.4% (38 of 77) had permanent AF. Fifteen of 479 (3.1%) patients had paroxysmal AF. Of those, seven had been previously diagnosed with paroxysmal AF through Patient Registry. The incidence of AF increased from 2.2 per 1000 years at risk at the age of 50–54 years to 9.3 per 1000 years at risk at the age 65–70 years. The prevalence of AF at the age of 71 years was increased from 7.1% to 9.9% using thumb ECG. Conclusions. In addition to medical history, patient register and 12-lead -ECG, the use of thumb ECG increased the number of detected paroxysmal AF by 21%.
TEPIC 2—an extended framework for transcription factor binding prediction and integrative epigenomic analysis

Abstract Summary Prediction of transcription factor (TF) binding from epigenetics data and integrative analysis thereof are challenging. Here, we present TEPIC 2 a framework allowing for fast, accurate and versatile prediction, and analysis of TF binding from epigenetics data: it supports 30 species with binding motifs, computes TF gene and scores up to two orders of magnitude faster than before due to improved implementation, and offers easy-to-use machine learning pipelines for integrated analysis of TF binding predictions with gene expression data allowing the identification of important TFs. Availability and implementation TEPIC is implemented in C++, R, and Python. It is freely available at https://github.com/SchulzLab/TEPIC and can be used on Linux based systems. Supplementary information Supplementary data are available at Bioinformatics online.
Estimating conductive sapwood area in diffuse and ring porous trees with electronic resistance tomography

Accurately estimating sapwood area is essential for modelling whole-tree or stand-scale transpiration from point-flow sap-flux observations. In this study, we tested the validity of electrical resistance tomography (ERT) to locate the sapwood-heartwood (SW/HW) interface for two ring porous (Quercus nigra L. and Quercus virginiana Mill.) and one diffuse porous (Acer rubrum L.) species. Estimates derived from the ERT analyses were compared with the SW/HW interface measured following dye perfusion testing. The ERT results revealed spatial variation in electrical resistance, with higher resistivity in the inner part of the cross sections. Regression analyses showed that ERT was able to accurately account for 97% and 80% of the variation in sapwood area (calculated as R2) for Q. virginiana (n = 19) and Q. nigra (n = 7), respectively, and 56% of the variation in the diffuse porous species (n = 8). Root mean square error (RMSE) values for sapwood areas of the ring porous species were 11.12 cm2 (19%) and 25.98 cm2 (33%) for Q. virginiana and Q. nigra, respectively. Sapwood area estimates for diffuse wood carried greater error (RMSE = 33.52 cm2 (131%)). Model bias for all sapwood area estimates was negative, suggesting that ERT had a tendency to overestimate sapwood areas. Electrical resistance tomography proved to be a significant predictor of sapwood area in the three investigated species, although it was more reliable for ring porous wood. In addition to the results, a comprehensive code sequence for use with R statistical software is provided, so that other investigators may follow the same method.
Vibro-tactile evoked potentials for BCI Communication of People with Disorders of Consciousness and locked-in Syndrome

In this publication, data of a vibro-tactile P300 BCI are shown. The tool serves for two tasks: for assessment of consciousness in people with disorders of consciousness (DOC) and locked-in syndrome (LIS), and for communication to provide YES/NO answers. Results from one patient, classified in unresponsive wakefulness state and two LIS patients are compared to three healthy controls. The shape of the event related potentials and differences between healthy controls and patients are investigated. We discuss which evoked potentials result in successful communication and provide online results of communication tests for all participants.
Curli-Containing Enteric Biofilms Inside and Out: Matrix Composition, Immune Recognition, and Disease Implications

Biofilms of enteric bacteria are highly complex, with multiple components that interact to fortify the biofilm matrix. Within biofilms of enteric bacteria such as Escherichia coli and Salmonella species, the main component of the biofilm is amyloid curli. Other constituents include cellulose, extracellular DNA, O antigen, and various surface proteins, including BapA. SUMMARY Biofilms of enteric bacteria are highly complex, with multiple components that interact to fortify the biofilm matrix. Within biofilms of enteric bacteria such as Escherichia coli and Salmonella species, the main component of the biofilm is amyloid curli. Other constituents include cellulose, extracellular DNA, O antigen, and various surface proteins, including BapA. Only recently, the roles of these components in the formation of the enteric biofilm individually and in consortium have been evaluated. In addition to enhancing the stability and strength of the matrix, the components of the enteric biofilm influence bacterial virulence and transmission. Most notably, certain components of the matrix are recognized as pathogen-associated molecular patterns. Systemic recognition of enteric biofilms leads to the activation of several proinflammatory innate immune receptors, including the Toll-like receptor 2 (TLR2)/TLR1/CD14 heterocomplex, TLR9, and NLRP3. In the model of Salmonella enterica serovar Typhimurium, the immune response to curli is site specific. Although a proinflammatory response is generated upon systemic presentation of curli, oral administration of curli ameliorates the damaged intestinal epithelial barrier and reduces the severity of colitis. Furthermore, curli (and extracellular DNA) of enteric biofilms potentiate the autoimmune disease systemic lupus erythematosus (SLE) and promote the fibrillization of the pathogenic amyloid α-synuclein, which is implicated in Parkinson's disease. Homologues of curli-encoding genes are found in four additional bacterial phyla, suggesting that the biomedical implications involved with enteric biofilms are applicable to numerous bacterial species.
Minimal Cost Server Configuration for Meeting Time-Varying Resource Demands in Cloud Centers

We consider the minimal cost server configuration for meeting resource demands over multiple time slots. Specifically, there are some heterogeneous servers. Each server is specified by a cost, certain amounts of several resources, and an active interval, i.e., the time interval that the server is planed to work. There are different overall demands for each type of resource over different time slots. A feasible solution is a set of servers such that at any time slot, the resources provided by the selected servers are at least their corresponding demands. Notice that, a selected server can not provide resources for the time slots out of its active interval. The total cost of the solution is the summation of the costs of all selected servers. The goal is to find a feasible solution with minimal total cost. This problem is proved to be NP-hard due to a reduction from the multidimensional knapsack problem (MKP), which is a well-known NP-hard combinational optimization problem. To solve our problem, we present a randomized approximation algorithm called partial rounding algorithm (<inline-formula><tex-math notation="LaTeX">$\mathcal {PRA}$ </tex-math><alternatives><inline-graphic xlink:href="liu-ieq1-2836452.gif"/></alternatives></inline-formula>), which guarantees <inline-formula><tex-math notation="LaTeX">$O\left(\log \left(KT \right) \right)$</tex-math><alternatives> <inline-graphic xlink:href="liu-ieq2-2836452.gif"/></alternatives></inline-formula>-approximation, i.e., <inline-formula><tex-math notation="LaTeX">$\eta \;\log \left(KT \right)$</tex-math><alternatives> <inline-graphic xlink:href="liu-ieq3-2836452.gif"/></alternatives></inline-formula>-approximation, where <inline-formula><tex-math notation="LaTeX">$K$</tex-math><alternatives> <inline-graphic xlink:href="liu-ieq4-2836452.gif"/></alternatives></inline-formula> is the number of kinds of resources, <inline-formula><tex-math notation="LaTeX">$T$</tex-math><alternatives> <inline-graphic xlink:href="liu-ieq5-2836452.gif"/></alternatives></inline-formula> is the number of time slots, and <inline-formula><tex-math notation="LaTeX">$\eta$</tex-math><alternatives> <inline-graphic xlink:href="liu-ieq6-2836452.gif"/></alternatives></inline-formula> is a positive constant. Furthermore, to minimize <inline-formula><tex-math notation="LaTeX">$\eta$</tex-math><alternatives> <inline-graphic xlink:href="liu-ieq7-2836452.gif"/></alternatives></inline-formula> as much as possible, we propose a varied Chernoff bound and apply it in <inline-formula><tex-math notation="LaTeX">$\mathcal {PRA}$</tex-math> <alternatives><inline-graphic xlink:href="liu-ieq8-2836452.gif"/></alternatives></inline-formula>. We perform extensive experiments with random inputs and a specific application input. The results show that <inline-formula> <tex-math notation="LaTeX">$\mathcal {PRA}$</tex-math><alternatives><inline-graphic xlink:href="liu-ieq9-2836452.gif"/> </alternatives></inline-formula> with our varied Chernoff conclusion can find solutions closing to the optimal one.
MMCode: Enhancing Color Channels for Screen-Camera Communication with Semi-Supervised Clustering

With the pervasive availability of LCD displays and phone cameras, screen-camera communication has attracted grate attentions due to the characteristics of convenience, security, infrastructure-free, and contactless. The existing screen-camera communication systems using dynamic barcodes suffer from poor ability of color recognition. In this paper, we propose a machine learning based multi-color dynamic barcode system called MMCode to overcome such limit. We formulate the color recognition problem as a machine learning task, and propose a semi-supervised clustering algorithm to achieve finer-grained color recognition. The proposed mechanism inserts reference colors in the barcode design, and adopts a semi-supervised Gaussian Mixed Model (GMM) algorithm for frame decoding. We implement MMCode as an Android APP and test its performance under real screen-camera communication scenarios. Extensive experiments show that the proposed MMCode achieves significant enhancement on the capacity of dynamic barcodes compared to the state-of-the-arts.